Starting phenix.real_space_refine on Mon May 26 00:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8h_39046/05_2025/8y8h_39046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8h_39046/05_2025/8y8h_39046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8h_39046/05_2025/8y8h_39046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8h_39046/05_2025/8y8h_39046.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8h_39046/05_2025/8y8h_39046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8h_39046/05_2025/8y8h_39046.cif" } resolution = 3.65 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= 0.028 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 165 5.16 5 C 17399 2.51 5 N 4496 2.21 5 O 5299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27359 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 9060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9060 Classifications: {'peptide': 1187} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1130} Chain breaks: 3 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 9084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9084 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 8, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 143 Chain: "A" Number of atoms: 9061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9061 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1116} Chain breaks: 4 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.43, per 1000 atoms: 0.56 Number of scatterers: 27359 At special positions: 0 Unit cell: (139.4, 150.88, 216.48, 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 165 16.00 O 5299 8.00 N 4496 7.00 C 17399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, 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 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 565 " distance=2.02 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 495 " - pdb=" SG CYS C 565 " 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 B1301 " - " ASN B 725 " " NAG B1302 " - " ASN B 793 " " NAG B1303 " - " 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 793 " Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 3.7 seconds 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6682 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 70 sheets defined 24.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.530A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.601A pdb=" N ILE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.899A pdb=" N LEU C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 removed outlier: 4.052A pdb=" N ARG C 361 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.688A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 4.081A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.810A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 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 699 through 704 removed outlier: 3.630A pdb=" N ASN C 703 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 704 " --> pdb=" O VAL C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 699 through 704' Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 822 through 833 removed outlier: 3.851A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 860 removed outlier: 4.469A pdb=" N ASP C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 851 " --> pdb=" O ASN C 847 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 858 " --> pdb=" O GLN C 854 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 859 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 873 removed outlier: 3.872A pdb=" N ASN C 872 " --> pdb=" O SER C 869 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 873 " --> pdb=" O ASN C 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 873' Processing helix chain 'C' and resid 878 through 882 removed outlier: 3.701A pdb=" N ASN C 881 " --> pdb=" O ASP C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.876A pdb=" N LEU C 906 " --> pdb=" O PRO C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 923 removed outlier: 3.635A pdb=" N GLU C 920 " --> pdb=" O VAL C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 removed outlier: 3.605A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 940 " --> pdb=" O CYS C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.587A pdb=" N TYR C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 975 Processing helix chain 'C' and resid 978 through 989 removed outlier: 4.002A pdb=" N VAL C 983 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 989 " --> pdb=" O TYR C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.843A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1008 Processing helix chain 'C' and resid 1009 through 1018 removed outlier: 4.325A pdb=" N ILE C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLN C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C1017 " --> pdb=" O LEU C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.686A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1060 through 1064 removed outlier: 4.087A pdb=" N ARG C1064 " --> pdb=" O ILE C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1109 removed outlier: 3.569A pdb=" N ALA C1084 " --> pdb=" O GLY C1080 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C1107 " --> pdb=" O ALA C1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.543A pdb=" N THR B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.677A 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: 3.778A pdb=" N ILE B 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.665A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 removed outlier: 3.622A pdb=" N SER B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 removed outlier: 4.137A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.578A pdb=" N VAL B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 483' Processing helix chain 'B' and resid 553 through 556 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 696 through 704 removed outlier: 3.626A pdb=" N VAL B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN B 702 " --> pdb=" O SER B 698 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.550A pdb=" N VAL B 818 " --> pdb=" O CYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 828 removed outlier: 3.776A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 828' Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 832 through 861 removed outlier: 3.608A pdb=" N CYS B 836 " --> pdb=" O TYR B 832 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 840 " --> pdb=" O CYS B 836 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 849 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 857 " --> pdb=" O THR B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 872 No H-bonds generated for 'chain 'B' and resid 870 through 872' Processing helix chain 'B' and resid 878 through 882 removed outlier: 3.827A pdb=" N ASN B 881 " --> pdb=" O ASP B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 911 removed outlier: 4.061A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.520A pdb=" N PHE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.703A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.900A pdb=" N SER B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 957 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 removed outlier: 4.504A pdb=" N GLN B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1000 Processing helix chain 'B' and resid 1000 through 1019 removed outlier: 3.772A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1046 removed outlier: 3.565A pdb=" N ILE B1029 " --> pdb=" O ALA B1025 " (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: 3.544A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.700A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.958A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.699A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 4.043A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.773A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.692A pdb=" N ILE A 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.603A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.876A pdb=" N ARG A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 443 through 448' Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.641A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 482' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.833A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.505A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 861 removed outlier: 3.724A pdb=" N ASN A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.917A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 911 removed outlier: 4.233A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 4.017A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.695A pdb=" N ASN A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.564A pdb=" N ALA A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 990 removed outlier: 3.571A pdb=" N VAL A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 removed outlier: 4.149A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.518A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.686A pdb=" N LYS A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.672A 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 1059 through 1065 removed outlier: 3.616A pdb=" N LEU A1065 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1113 removed outlier: 3.863A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' 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 65 through 67 Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 214 removed outlier: 3.965A pdb=" N TYR C 212 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 104 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 202 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 102 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.989A pdb=" N ILE C 137 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.610A pdb=" N VAL C 280 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 306 through 310 removed outlier: 4.011A pdb=" N GLY C 308 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY C 675 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.248A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 346 through 349 removed outlier: 6.546A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 389 " --> pdb=" O ASN C 591 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 591 " --> pdb=" O ASP C 389 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 588 " --> pdb=" O TYR C 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 346 through 349 removed outlier: 6.546A pdb=" N PHE C 383 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 597 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 389 " --> pdb=" O ASN C 591 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 591 " --> pdb=" O ASP C 389 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AB4, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AB5, first strand: chain 'C' and resid 620 through 621 removed outlier: 3.634A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 667 " --> pdb=" O PHE C 658 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 690 through 691 removed outlier: 3.658A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 743 through 745 removed outlier: 3.513A pdb=" N ARG C 763 " --> pdb=" O ASP C 745 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 789 through 791 Processing sheet with id=AB9, first strand: chain 'C' and resid 794 through 795 removed outlier: 3.660A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.592A pdb=" N GLU C 801 " --> pdb=" O PHE C1143 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C1143 " --> pdb=" O GLU C 801 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.408A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1162 through 1163 removed outlier: 4.033A pdb=" N CYS C1163 " --> pdb=" O THR C1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 1170 through 1172 Processing sheet with id=AC5, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AC6, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.532A pdb=" N LEU B 61 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 268 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.111A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.616A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 201 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 104 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 105 " --> pdb=" O TRP B 257 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 257 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 109 through 112 removed outlier: 4.350A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 186 through 187 removed outlier: 3.915A pdb=" N THR B 149 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 138 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 127 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS B 234 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 305 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: 3.701A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 382 through 383 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 467 through 468 removed outlier: 3.578A 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 Processing sheet with id=AE2, first strand: chain 'B' and resid 619 through 624 removed outlier: 3.598A pdb=" N VAL B 620 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 631 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 714 through 715 removed outlier: 3.728A pdb=" N GLY B 718 " --> pdb=" O SER B 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 736 through 737 removed outlier: 4.410A pdb=" N LEU B 736 " --> pdb=" O ILE B 744 " (cutoff:3.500A) 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 795 through 797 removed outlier: 3.979A pdb=" N THR B 795 " --> pdb=" O LYS B1149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 800 through 803 removed outlier: 3.780A pdb=" N GLU B 801 " --> pdb=" O PHE B1143 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B1143 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1142 " --> pdb=" O GLN B1135 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.470A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 866 through 868 removed outlier: 7.421A pdb=" N LEU B 867 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 1162 through 1163 removed outlier: 3.524A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 1170 through 1172 Processing sheet with id=AF3, first strand: chain 'B' and resid 1175 through 1180 Processing sheet with id=AF4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AF5, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.556A pdb=" N GLY A 65 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 67 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.588A pdb=" N PHE A 200 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.835A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 126 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 137 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 140 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 187 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 150 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 110 through 112 Processing sheet with id=AF9, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.506A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 316 through 319 removed outlier: 7.420A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 627 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.273A pdb=" N THR A 435 " --> pdb=" O VAL A 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'A' and resid 345 through 349 removed outlier: 4.275A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 347 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 388 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 367 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 345 through 349 removed outlier: 4.275A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 347 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 388 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.673A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'A' and resid 460 through 463 Processing sheet with id=AG7, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.629A pdb=" N SER A 468 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.581A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.771A pdb=" N TYR A 667 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 712 through 713 removed outlier: 4.022A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 724 through 731 removed outlier: 3.533A pdb=" N PHE A 764 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 726 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR A 766 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N SER A 728 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 787 through 803 removed outlier: 6.289A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1149 " --> pdb=" O THR A 795 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 797 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A1147 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 803 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 787 through 803 removed outlier: 6.289A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1149 " --> pdb=" O THR A 795 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 797 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A1147 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 803 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 811 through 812 Processing sheet with id=AH6, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.572A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'A' and resid 1169 through 1172 removed outlier: 3.983A pdb=" N GLY A1169 " --> pdb=" O MET A1205 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 1986 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: 11.85 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8795 1.35 - 1.47: 7092 1.47 - 1.59: 11926 1.59 - 1.71: 0 1.71 - 1.83: 191 Bond restraints: 28004 Sorted by residual: 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 2.05e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " 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 B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 27999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 37847 2.01 - 4.02: 315 4.02 - 6.03: 10 6.03 - 8.03: 2 8.03 - 10.04: 1 Bond angle restraints: 38175 Sorted by residual: angle pdb=" CA VAL C 314 " pdb=" C VAL C 314 " pdb=" N ALA C 315 " ideal model delta sigma weight residual 116.60 120.08 -3.48 1.45e+00 4.76e-01 5.75e+00 angle pdb=" C PHE C 767 " pdb=" N GLU C 768 " pdb=" CA GLU C 768 " ideal model delta sigma weight residual 121.80 127.53 -5.73 2.44e+00 1.68e-01 5.51e+00 angle pdb=" N PRO A1067 " pdb=" CA PRO A1067 " pdb=" C PRO A1067 " ideal model delta sigma weight residual 110.70 113.56 -2.86 1.22e+00 6.72e-01 5.48e+00 angle pdb=" N GLY B 741 " pdb=" CA GLY B 741 " pdb=" C GLY B 741 " ideal model delta sigma weight residual 113.18 118.27 -5.09 2.37e+00 1.78e-01 4.61e+00 angle pdb=" N PRO B1067 " pdb=" CA PRO B1067 " pdb=" C PRO B1067 " ideal model delta sigma weight residual 110.70 113.25 -2.55 1.22e+00 6.72e-01 4.38e+00 ... (remaining 38170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 16338 17.05 - 34.10: 450 34.10 - 51.15: 82 51.15 - 68.20: 14 68.20 - 85.25: 4 Dihedral angle restraints: 16888 sinusoidal: 6499 harmonic: 10389 Sorted by residual: dihedral pdb=" CB CYS C 474 " pdb=" SG CYS C 474 " pdb=" SG CYS C 565 " pdb=" CB CYS C 565 " ideal model delta sinusoidal sigma weight residual 93.00 176.79 -83.79 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS C 474 " pdb=" SG CYS C 474 " pdb=" SG CYS C 495 " pdb=" CB CYS C 495 " ideal model delta sinusoidal sigma weight residual 93.00 28.67 64.33 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS C 474 " pdb=" SG CYS C 474 " pdb=" SG CYS C 476 " pdb=" CB CYS C 476 " ideal model delta sinusoidal sigma weight residual -86.00 -28.29 -57.71 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 16885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2645 0.027 - 0.054: 1094 0.054 - 0.081: 288 0.081 - 0.108: 256 0.108 - 0.135: 85 Chirality restraints: 4368 Sorted by residual: chirality pdb=" CA ILE C 790 " pdb=" N ILE C 790 " pdb=" C ILE C 790 " pdb=" CB ILE C 790 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-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 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 4365 not shown) Planarity restraints: 4939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A1067 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C1067 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 901 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.63e+00 pdb=" N PRO B 902 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 902 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 902 " 0.018 5.00e-02 4.00e+02 ... (remaining 4936 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4063 2.76 - 3.30: 25829 3.30 - 3.83: 42642 3.83 - 4.37: 49219 4.37 - 4.90: 84298 Nonbonded interactions: 206051 Sorted by model distance: nonbonded pdb=" O THR A 161 " pdb=" OG1 THR A 241 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.226 3.040 nonbonded pdb=" O THR B 161 " pdb=" OG1 THR B 241 " model vdw 2.244 3.040 nonbonded pdb=" O VAL B 636 " pdb=" OG1 THR B 666 " model vdw 2.245 3.040 nonbonded pdb=" OG SER C 715 " pdb=" O GLY C 718 " model vdw 2.248 3.040 ... (remaining 206046 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 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 (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 58 and (name N or name CA or name C or name O or name CB )) or resid 59 thr \ ough 73 or (resid 74 through 75 and (name N or name CA or name C or name O or na \ me CB )) or resid 76 through 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 through 95 and (name N \ or name CA or name C or name O or name CB )) or resid 96 through 97 or (resid 9 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 99 through 1 \ 04 or (resid 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 through 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame 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 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 138 or (resid 139 \ and (name N or name CA or name C or name O or name CB )) or resid 140 through 1 \ 45 or (resid 146 and (name N or name CA or name C or name O or name CB )) or res \ id 147 or (resid 148 and (name N or name CA or name C or name O or name CB )) or \ resid 149 through 184 or (resid 185 and (name N or name CA or name C or name O \ or name CB )) or resid 186 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 211 or (resid 212 and (name N \ or name CA or name C or name O or name CB )) or resid 213 through 219 or (resid \ 220 and (name N or name CA or name C or name O or name CB )) or resid 221 or (r \ esid 222 and (name N or name CA or name C or name O or name CB )) or resid 223 t \ hrough 225 or (resid 226 and (name N or name CA or name C or name O or name CB ) \ ) or resid 227 through 234 or (resid 235 and (name N or name CA or name C or nam \ e O or name CB )) or resid 236 through 244 or resid 254 through 256 or (resid 25 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 258 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or re \ sid 271 through 279 or (resid 280 and (name N or name CA or name C or name O or \ name CB )) or resid 281 through 284 or (resid 285 through 286 and (name N or nam \ e CA or name C or name O or name CB )) or resid 287 through 317 or (resid 318 th \ rough 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 341 or (resid 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 366 or (resid 367 and (name N or name CA or name C or na \ me O or name CB )) or resid 368 through 407 or (resid 408 through 409 and (name \ N or name CA or name C or name O or name CB )) or resid 410 through 425 or (resi \ d 426 and (name N or name CA or name C or name O or name CB )) or resid 427 thro \ ugh 438 or (resid 439 through 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 445 or (resid 446 and (name N or name CA or name \ C or name O or name CB )) or resid 447 through 460 or (resid 461 through 462 an \ d (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 resid 494 through 553 or (resid 554 and (name N or name CA or name C or na \ me O or name CB )) or resid 555 through 557 or resid 563 through 608 or (resid 6 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 610 or (res \ id 611 through 612 and (name N or name CA or name C or name O or name CB )) or r \ esid 613 through 626 or (resid 627 and (name N or name CA or name C or name O or \ name CB )) or resid 628 through 657 or (resid 658 and (name N or name CA or nam \ e C or name O or name CB )) or resid 659 or (resid 660 through 661 and (name N o \ r name CA or name C or name O or name CB )) or resid 662 through 672 or (resid 6 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 674 through \ 682 or (resid 683 through 684 and (name N or name CA or name C or name O or nam \ e 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 resid 699 through 769 or (resid 770 and (name N or na \ me CA or name C or name O or name CB )) or resid 771 through 785 or (resid 786 a \ nd (name N or name CA or name C or name O or name CB )) or resid 787 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 nam \ e CB )) or resid 821 through 924 or (resid 925 through 926 and (name N or name C \ A or name C or name O or name CB )) or resid 927 through 957 or (resid 958 and ( \ name N or name CA or name C or name O or name CB )) or resid 959 through 998 or \ (resid 999 through 1000 and (name N or name CA or name C or name O or name CB )) \ or resid 1001 or (resid 1002 through 1007 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1008 through 1037 or (resid 1038 through 1039 and ( \ name N or name CA or name C or name O or name CB )) or resid 1040 through 1058 o \ r (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 n \ ame CB )) or resid 1063 through 1065 or (resid 1066 and (name N or name CA or na \ me C or name O or name CB )) or resid 1067 through 1070 or (resid 1071 through 1 \ 072 and (name N or name CA or name C or name O or name CB )) or resid 1073 throu \ gh 1151 or (resid 1152 and (name N or name CA or name C or name O or name CB )) \ or resid 1153 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 1185 and (name N or name CA or name C or name O or name CB )) or resid 1186 th \ rough 1221 or resid 1301 through 1303)) 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 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or (resid 52 and (name N or na \ me CA or name C or name O or name CB )) or resid 53 through 73 or (resid 74 thro \ ugh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 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 through 95 and (name N or name CA or name C or \ name O or name CB )) or resid 96 through 104 or (resid 105 and (name N or name C \ A or name C or name O or name CB )) or resid 106 through 120 or (resid 121 and ( \ name N or name CA or name C or name O or name 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 and (name N or name CA or name C or name O or name CB \ )) or resid 130 through 138 or (resid 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 through 145 or (resid 146 and (name N or name C \ A or name C or name O or name CB )) or resid 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB )) or resid 149 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )) or resid 158 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 or (resid 222 and (name N or name CA or nam \ e C or name O or name CB )) or resid 223 through 256 or (resid 257 and (name N o \ r name CA or name C or name O or name CB )) or resid 258 through 284 or (resid 2 \ 85 through 286 and (name N or name CA or name C or name O or name CB )) or resid \ 287 through 366 or (resid 367 and (name N or name CA or name C or name O or nam \ e CB )) or resid 368 through 390 or (resid 391 through 392 and (name N or name C \ A or name C or name O or name CB )) or resid 393 through 400 or (resid 401 and ( \ name N or name CA or name C or name O or name CB )) or resid 402 through 408 or \ (resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 413 or (resid 414 and (name N or name CA or name C or name O or name CB \ )) or resid 415 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 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 resid 519 throug \ h 520 or (resid 521 and (name N or name CA or name C or name O or name CB )) or \ resid 522 through 626 or (resid 627 and (name N or name CA or name C or name O o \ r name CB )) or resid 628 through 640 or (resid 641 and (name N or name CA or na \ me C or name O or name CB )) or resid 642 through 647 or (resid 648 through 649 \ and (name N or name CA or name C or name O or name CB )) or resid 650 through 65 \ 4 or (resid 655 and (name N or name CA or name C or name O or name CB )) or resi \ d 656 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 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 and \ (name N or name CA or name C or name O or name CB )) or resid 745 through 763 or \ (resid 764 and (name N or name CA or name C or name O or name CB )) or resid 76 \ 5 through 769 or (resid 770 and (name N or name CA or name C or name O or name C \ B )) or resid 771 through 785 or (resid 786 and (name N or name CA or name C or \ name O or name CB )) or resid 787 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 858 or \ (resid 859 through 860 and (name N or name CA or name C or name O or name CB )) \ or resid 861 through 924 or (resid 925 through 926 and (name N or name CA or na \ me C or name O or name CB )) or resid 927 through 957 or (resid 958 and (name N \ or name CA or name C or name O or name CB )) or resid 959 through 998 or (resid \ 999 through 1000 and (name N or name CA or name C or name O or name CB )) or res \ id 1001 or (resid 1002 through 1007 and (name N or name CA or name C or name O o \ r name CB )) or resid 1008 through 1058 or (resid 1059 and (name N or name CA or \ name C or name O or name CB )) or resid 1060 through 1065 or (resid 1066 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1067 through 1070 or \ (resid 1071 through 1072 and (name N or name CA or name C or name O or name CB \ )) or resid 1073 through 1151 or (resid 1152 and (name N or name CA or name C or \ name O or name CB )) or resid 1153 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 through 1185 and (name N or name CA or name C or name O or name \ CB )) or resid 1186 through 1221 or resid 1301 through 1303)) selection = (chain 'C' and ((resid 14 and (name N or name CA or name C or name O or name CB \ )) or resid 15 through 37 or (resid 38 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 41 or (resid 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 48 or (resid 49 and \ (name N or name CA or name C or name O or name CB )) or resid 50 through 53 or ( \ resid 54 through 58 and (name N or name CA or name C or name O or name CB )) or \ resid 59 through 97 or (resid 98 and (name N or name CA or name C or name O or n \ ame CB )) or resid 99 through 156 or (resid 157 and (name N or name CA or name C \ or name O or name CB )) or resid 158 through 184 or (resid 185 and (name N or n \ ame CA or name C or name O or name CB )) or resid 186 through 234 or (resid 235 \ and (name N or name CA or name C or name O or name CB )) or resid 236 through 24 \ 4 or resid 254 through 269 or (resid 270 and (name N or name CA or name C or nam \ e O or name CB )) or resid 271 through 279 or (resid 280 and (name N or name CA \ or name C or name O or name CB )) or resid 281 through 311 or (resid 312 and (na \ me N or name CA or name C or name O or name CB )) or resid 313 through 317 or (r \ esid 318 through 319 and (name N or name CA or name C or name O or name CB )) or \ resid 320 through 341 or (resid 342 and (name N or name CA or name C or name O \ or name CB )) or resid 343 through 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 400 or (resid 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 409 and (name N or name CA or name C or name O or name \ CB )) or resid 410 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 438 or (resid 439 through \ 440 and (name N or name CA or name C or name O or name CB )) or resid 441 throu \ gh 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) or \ resid 447 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 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 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 608 or (resid 609 and (name N or name CA or name C or na \ me 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 640 or (resid 641 and (n \ ame N or name CA or name C or name O or name CB )) or resid 642 through 647 or ( \ resid 648 through 649 and (name N or name CA or name C or name O or name CB )) o \ r resid 650 through 654 or (resid 655 and (name N or name CA or name C or name O \ or name CB )) or resid 656 through 657 or (resid 658 and (name N or name CA or \ name C or name O or name CB )) or resid 659 or (resid 660 through 661 and (name \ N or name CA or name C or name O or name CB )) or resid 662 through 672 or (resi \ d 673 and (name N or name CA or name C or name O or name CB )) or resid 674 thro \ ugh 734 or (resid 735 and (name N or name CA or name C or name O or name CB )) o \ r resid 736 through 743 or (resid 744 and (name N or name CA or name C or name O \ or name CB )) or resid 745 through 763 or (resid 764 and (name N or name CA or \ name C or name O or name CB )) or resid 765 through 858 or (resid 859 through 86 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 861 through \ 1037 or (resid 1038 through 1039 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1040 through 1061 or (resid 1062 and (name N or name CA or na \ me C or name O or name CB )) or resid 1063 through 1221 or resid 1301 through 13 \ 03)) } 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: 3.480 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: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 60.610 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 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 0.032 28084 Z= 0.087 Angle : 0.434 13.189 38346 Z= 0.229 Chirality : 0.040 0.135 4368 Planarity : 0.003 0.038 4928 Dihedral : 7.607 85.255 9999 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.54 % Allowed : 5.93 % Favored : 92.53 % 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: -3.71 (0.11), residues: 3519 helix: -3.29 (0.12), residues: 640 sheet: -1.60 (0.21), residues: 547 loop : -2.58 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.001 0.000 HIS B 234 PHE 0.007 0.001 PHE C 202 TYR 0.008 0.001 TYR B 622 ARG 0.001 0.000 ARG C1120 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 11) link_NAG-ASN : angle 0.84343 ( 33) hydrogen bonds : bond 0.31252 ( 706) hydrogen bonds : angle 9.32116 ( 1986) SS BOND : bond 0.00188 ( 69) SS BOND : angle 1.85223 ( 138) covalent geometry : bond 0.00168 (28004) covalent geometry : angle 0.41925 (38175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 562 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7052 (tm-30) REVERT: C 307 SER cc_start: 0.8789 (t) cc_final: 0.8455 (m) REVERT: C 362 LEU cc_start: 0.7301 (mp) cc_final: 0.7008 (pp) REVERT: C 724 VAL cc_start: 0.7723 (t) cc_final: 0.7491 (m) REVERT: C 736 LEU cc_start: 0.5375 (mt) cc_final: 0.5171 (mp) REVERT: C 765 VAL cc_start: 0.7622 (t) cc_final: 0.7248 (p) REVERT: C 792 THR cc_start: 0.7391 (p) cc_final: 0.7173 (t) REVERT: C 795 THR cc_start: 0.4094 (OUTLIER) cc_final: 0.2695 (p) REVERT: C 835 PHE cc_start: 0.7647 (t80) cc_final: 0.7373 (t80) REVERT: C 845 GLU cc_start: 0.5977 (tm-30) cc_final: 0.5688 (tm-30) REVERT: C 994 MET cc_start: 0.4223 (tpp) cc_final: 0.3890 (tpp) REVERT: C 1008 PHE cc_start: 0.7062 (m-80) cc_final: 0.6590 (m-80) REVERT: C 1057 SER cc_start: 0.7456 (p) cc_final: 0.6273 (p) REVERT: C 1058 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.5561 (mp) REVERT: C 1060 GLU cc_start: 0.5928 (tt0) cc_final: 0.5667 (tt0) REVERT: C 1061 ILE cc_start: 0.7839 (pt) cc_final: 0.6668 (mt) REVERT: C 1075 ASP cc_start: 0.7545 (t0) cc_final: 0.7297 (t0) REVERT: C 1082 LEU cc_start: 0.8310 (mt) cc_final: 0.7683 (mt) REVERT: C 1149 LYS cc_start: 0.7158 (tmtt) cc_final: 0.6864 (tmtt) REVERT: C 1154 LYS cc_start: 0.7532 (tttm) cc_final: 0.6916 (tttm) REVERT: C 1195 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6692 (mt-10) REVERT: B 100 ASN cc_start: 0.7904 (t0) cc_final: 0.7539 (t0) REVERT: B 102 ILE cc_start: 0.7121 (mm) cc_final: 0.6864 (tt) REVERT: B 122 SER cc_start: 0.7760 (m) cc_final: 0.7438 (p) REVERT: B 125 VAL cc_start: 0.7740 (t) cc_final: 0.7424 (p) REVERT: B 135 TYR cc_start: 0.7412 (m-80) cc_final: 0.5857 (m-80) REVERT: B 184 LEU cc_start: 0.7319 (mt) cc_final: 0.6777 (mt) REVERT: B 232 LEU cc_start: 0.8315 (mp) cc_final: 0.8042 (mm) REVERT: B 257 TRP cc_start: 0.4792 (m-90) cc_final: 0.3727 (m-90) REVERT: B 269 ASN cc_start: 0.7795 (t0) cc_final: 0.7486 (t0) REVERT: B 293 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7657 (ttmt) REVERT: B 295 GLN cc_start: 0.7802 (mt0) cc_final: 0.7409 (mp10) REVERT: B 375 LYS cc_start: 0.8099 (ptmm) cc_final: 0.7797 (tttp) REVERT: B 632 ILE cc_start: 0.8357 (mt) cc_final: 0.8095 (mp) REVERT: B 670 LEU cc_start: 0.7337 (mt) cc_final: 0.7124 (mm) REVERT: B 676 ARG cc_start: 0.6005 (tmm160) cc_final: 0.5607 (tmm160) REVERT: B 677 VAL cc_start: 0.8014 (t) cc_final: 0.7481 (t) REVERT: B 682 TYR cc_start: 0.6262 (t80) cc_final: 0.5130 (t80) REVERT: B 683 GLN cc_start: 0.6813 (pp30) cc_final: 0.6372 (pp30) REVERT: B 762 TYR cc_start: 0.4468 (m-10) cc_final: 0.3624 (m-10) REVERT: B 764 PHE cc_start: 0.5742 (OUTLIER) cc_final: 0.5280 (t80) REVERT: B 829 LEU cc_start: 0.7971 (tp) cc_final: 0.7652 (mt) REVERT: B 830 SER cc_start: 0.8546 (m) cc_final: 0.8196 (p) REVERT: B 834 THR cc_start: 0.7059 (p) cc_final: 0.6800 (p) REVERT: B 838 ASN cc_start: 0.7187 (m110) cc_final: 0.6757 (m110) REVERT: B 839 ILE cc_start: 0.8491 (mm) cc_final: 0.8270 (tp) REVERT: B 845 GLU cc_start: 0.6782 (tt0) cc_final: 0.6507 (tt0) REVERT: B 944 LYS cc_start: 0.7604 (tttp) cc_final: 0.7316 (tppt) REVERT: B 959 THR cc_start: 0.5806 (p) cc_final: 0.5573 (p) REVERT: B 1030 GLN cc_start: 0.6948 (mm110) cc_final: 0.6688 (mp10) REVERT: B 1050 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7612 (mtmm) REVERT: A 48 THR cc_start: 0.7897 (p) cc_final: 0.7666 (t) REVERT: A 105 LYS cc_start: 0.7115 (tptt) cc_final: 0.6675 (tptt) REVERT: A 114 ASN cc_start: 0.7062 (t0) cc_final: 0.6701 (t0) REVERT: A 226 LEU cc_start: 0.7403 (tp) cc_final: 0.7033 (tt) REVERT: A 264 ARG cc_start: 0.7278 (ttm110) cc_final: 0.7028 (ptp-170) REVERT: A 283 SER cc_start: 0.7229 (m) cc_final: 0.6904 (p) REVERT: A 289 GLU cc_start: 0.6644 (tp30) cc_final: 0.6391 (tp30) REVERT: A 291 GLN cc_start: 0.7298 (mt0) cc_final: 0.7092 (mm-40) REVERT: A 293 LYS cc_start: 0.7429 (mtpp) cc_final: 0.7136 (ttmm) REVERT: A 305 ASP cc_start: 0.6711 (t0) cc_final: 0.6422 (t0) REVERT: A 329 ILE cc_start: 0.7695 (mp) cc_final: 0.6922 (mm) REVERT: A 331 ASN cc_start: 0.8365 (m110) cc_final: 0.8137 (m110) REVERT: A 347 ARG cc_start: 0.6580 (ttm170) cc_final: 0.6125 (ttm170) REVERT: A 622 TYR cc_start: 0.5301 (p90) cc_final: 0.4420 (p90) REVERT: A 683 GLN cc_start: 0.7679 (pt0) cc_final: 0.7406 (pt0) REVERT: A 738 MET cc_start: 0.6661 (mmp) cc_final: 0.6331 (mmp) REVERT: A 922 TYR cc_start: 0.7785 (m-10) cc_final: 0.7526 (m-80) REVERT: A 940 PHE cc_start: 0.7865 (m-10) cc_final: 0.7647 (m-80) REVERT: A 1019 PHE cc_start: 0.5699 (m-80) cc_final: 0.5424 (m-10) REVERT: A 1134 VAL cc_start: 0.8064 (t) cc_final: 0.7511 (m) outliers start: 47 outliers final: 16 residues processed: 599 average time/residue: 0.3798 time to fit residues: 358.0278 Evaluate side-chains 484 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 465 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 609 TYR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 0.0570 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 276 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 320 optimal weight: 9.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN C 273 HIS C 295 GLN C 605 ASN C 870 ASN C 941 ASN C1036 ASN C1046 GLN B 132 ASN B 188 ASN B 323 ASN B 355 ASN B 410 GLN B 445 ASN B 587 ASN B 709 GLN ** B 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN B 872 ASN B1016 GLN B1030 GLN B1111 ASN B1135 GLN B1145 HIS B1181 ASN A 587 ASN A 591 ASN A 646 ASN A 694 ASN A 799 HIS A 847 ASN A 854 GLN A 870 ASN ** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1071 GLN A1181 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.214791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.174359 restraints weight = 59866.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.179802 restraints weight = 30452.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.183325 restraints weight = 18655.489| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28084 Z= 0.174 Angle : 0.606 13.555 38346 Z= 0.318 Chirality : 0.045 0.185 4368 Planarity : 0.004 0.044 4928 Dihedral : 4.840 80.536 4057 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.23 % Allowed : 10.15 % Favored : 87.62 % 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: -2.80 (0.13), residues: 3519 helix: -1.22 (0.18), residues: 685 sheet: -1.32 (0.21), residues: 586 loop : -2.34 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 444 HIS 0.007 0.001 HIS A 201 PHE 0.025 0.002 PHE A 908 TYR 0.027 0.002 TYR B 622 ARG 0.007 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 11) link_NAG-ASN : angle 1.28781 ( 33) hydrogen bonds : bond 0.06075 ( 706) hydrogen bonds : angle 6.27284 ( 1986) SS BOND : bond 0.00328 ( 69) SS BOND : angle 1.82014 ( 138) covalent geometry : bond 0.00362 (28004) covalent geometry : angle 0.59651 (38175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 484 time to evaluate : 2.655 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 305 ASP cc_start: 0.7580 (p0) cc_final: 0.7360 (p0) REVERT: C 362 LEU cc_start: 0.7556 (mp) cc_final: 0.7114 (pp) REVERT: C 644 TRP cc_start: 0.7242 (p-90) cc_final: 0.6936 (p-90) REVERT: C 724 VAL cc_start: 0.7997 (t) cc_final: 0.7786 (m) REVERT: C 736 LEU cc_start: 0.5738 (mt) cc_final: 0.5480 (mp) REVERT: C 835 PHE cc_start: 0.7840 (t80) cc_final: 0.7497 (t80) REVERT: C 845 GLU cc_start: 0.6300 (tm-30) cc_final: 0.6024 (tm-30) REVERT: C 994 MET cc_start: 0.4144 (tpp) cc_final: 0.3859 (tpp) REVERT: C 1008 PHE cc_start: 0.7185 (m-80) cc_final: 0.6622 (m-80) REVERT: C 1057 SER cc_start: 0.7903 (p) cc_final: 0.7545 (p) REVERT: C 1077 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8683 (mp) REVERT: C 1082 LEU cc_start: 0.8416 (mt) cc_final: 0.7889 (mt) REVERT: C 1091 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: C 1195 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6887 (mt-10) REVERT: B 75 ARG cc_start: 0.7018 (tmm-80) cc_final: 0.6728 (tmm-80) REVERT: B 100 ASN cc_start: 0.8036 (t0) cc_final: 0.7680 (t0) REVERT: B 102 ILE cc_start: 0.7308 (mm) cc_final: 0.7021 (tp) REVERT: B 125 VAL cc_start: 0.8117 (t) cc_final: 0.7865 (p) REVERT: B 232 LEU cc_start: 0.8395 (mp) cc_final: 0.8119 (mm) REVERT: B 236 TYR cc_start: 0.6387 (t80) cc_final: 0.5075 (t80) REVERT: B 257 TRP cc_start: 0.5113 (m-90) cc_final: 0.3852 (m-90) REVERT: B 269 ASN cc_start: 0.7706 (t0) cc_final: 0.7324 (t0) REVERT: B 414 TYR cc_start: 0.3065 (t80) cc_final: 0.2793 (t80) REVERT: B 632 ILE cc_start: 0.8469 (mt) cc_final: 0.8233 (mp) REVERT: B 647 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5759 (mt) REVERT: B 670 LEU cc_start: 0.8131 (mt) cc_final: 0.7832 (mt) REVERT: B 676 ARG cc_start: 0.6560 (tmm160) cc_final: 0.6060 (tmm160) REVERT: B 677 VAL cc_start: 0.8036 (t) cc_final: 0.7692 (t) REVERT: B 682 TYR cc_start: 0.5924 (t80) cc_final: 0.5699 (t80) REVERT: B 683 GLN cc_start: 0.6877 (pp30) cc_final: 0.6568 (pp30) REVERT: B 762 TYR cc_start: 0.4401 (m-10) cc_final: 0.3438 (m-10) REVERT: B 764 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.5725 (t80) REVERT: B 782 VAL cc_start: 0.0025 (OUTLIER) cc_final: -0.0332 (p) REVERT: B 806 SER cc_start: 0.6948 (m) cc_final: 0.6674 (p) REVERT: B 809 LYS cc_start: 0.7145 (pttt) cc_final: 0.6877 (pttm) REVERT: B 829 LEU cc_start: 0.8061 (tp) cc_final: 0.7697 (mt) REVERT: B 830 SER cc_start: 0.8521 (m) cc_final: 0.8148 (p) REVERT: B 838 ASN cc_start: 0.7273 (m110) cc_final: 0.6870 (m110) REVERT: B 944 LYS cc_start: 0.8010 (tttp) cc_final: 0.7740 (tppt) REVERT: B 1030 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7086 (mp10) REVERT: B 1050 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7673 (mtpp) REVERT: B 1060 GLU cc_start: 0.6842 (tt0) cc_final: 0.6598 (tt0) REVERT: B 1069 GLU cc_start: 0.6564 (pm20) cc_final: 0.6255 (pm20) REVERT: B 1109 LYS cc_start: 0.6005 (tptp) cc_final: 0.5599 (tptm) REVERT: B 1143 PHE cc_start: 0.6482 (m-80) cc_final: 0.6215 (m-10) REVERT: B 1144 ILE cc_start: 0.6565 (mm) cc_final: 0.6211 (mp) REVERT: B 1149 LYS cc_start: 0.7373 (tptt) cc_final: 0.7085 (tppt) REVERT: A 114 ASN cc_start: 0.7063 (t0) cc_final: 0.6777 (t0) REVERT: A 226 LEU cc_start: 0.7607 (tp) cc_final: 0.7179 (tp) REVERT: A 289 GLU cc_start: 0.6858 (tp30) cc_final: 0.6554 (tp30) REVERT: A 293 LYS cc_start: 0.7607 (mtpp) cc_final: 0.7245 (ttmm) REVERT: A 305 ASP cc_start: 0.7009 (t0) cc_final: 0.6611 (t0) REVERT: A 319 ARG cc_start: 0.7051 (tpp-160) cc_final: 0.6448 (tpp-160) REVERT: A 329 ILE cc_start: 0.7684 (mp) cc_final: 0.7417 (mp) REVERT: A 622 TYR cc_start: 0.5829 (p90) cc_final: 0.5148 (p90) REVERT: A 634 LYS cc_start: 0.8373 (tttp) cc_final: 0.8063 (tttp) REVERT: A 681 PHE cc_start: 0.8144 (t80) cc_final: 0.7894 (t80) REVERT: A 812 ILE cc_start: 0.7938 (mt) cc_final: 0.7673 (mm) REVERT: A 952 GLU cc_start: 0.6835 (tp30) cc_final: 0.6474 (tp30) REVERT: A 998 ASN cc_start: 0.5811 (m-40) cc_final: 0.5491 (m110) REVERT: A 1092 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7583 (mm-40) REVERT: A 1205 MET cc_start: 0.5008 (ttt) cc_final: 0.4440 (ptt) REVERT: A 1207 SER cc_start: 0.7058 (p) cc_final: 0.6728 (t) outliers start: 68 outliers final: 39 residues processed: 533 average time/residue: 0.3627 time to fit residues: 309.6118 Evaluate side-chains 497 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 453 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1091 GLN Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 83 optimal weight: 0.0040 chunk 254 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 308 optimal weight: 0.7980 chunk 352 optimal weight: 7.9990 chunk 104 optimal weight: 0.2980 chunk 67 optimal weight: 0.0980 chunk 263 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 302 optimal weight: 6.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 273 HIS C 445 ASN C 856 GLN C1036 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 ASN B 854 GLN B1111 ASN B1136 ASN A 870 ASN A 954 GLN A1016 GLN A1049 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.216260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.176806 restraints weight = 60456.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.183685 restraints weight = 30949.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.187070 restraints weight = 16468.485| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28084 Z= 0.100 Angle : 0.527 12.119 38346 Z= 0.270 Chirality : 0.043 0.255 4368 Planarity : 0.004 0.046 4928 Dihedral : 4.217 71.219 4048 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.32 % Allowed : 12.25 % 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: -2.28 (0.13), residues: 3519 helix: -0.28 (0.20), residues: 685 sheet: -1.13 (0.21), residues: 565 loop : -2.13 (0.12), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 444 HIS 0.005 0.001 HIS A 201 PHE 0.034 0.001 PHE C 713 TYR 0.019 0.001 TYR A 729 ARG 0.007 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 11) link_NAG-ASN : angle 1.02428 ( 33) hydrogen bonds : bond 0.04819 ( 706) hydrogen bonds : angle 5.54103 ( 1986) SS BOND : bond 0.00312 ( 69) SS BOND : angle 1.81190 ( 138) covalent geometry : bond 0.00208 (28004) covalent geometry : angle 0.51584 (38175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 467 time to evaluate : 2.770 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 157 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7170 (tm-30) REVERT: C 362 LEU cc_start: 0.7628 (mp) cc_final: 0.7204 (pp) REVERT: C 644 TRP cc_start: 0.7186 (p-90) cc_final: 0.6928 (p-90) REVERT: C 724 VAL cc_start: 0.7891 (t) cc_final: 0.7653 (m) REVERT: C 736 LEU cc_start: 0.5662 (mt) cc_final: 0.5401 (mp) REVERT: C 835 PHE cc_start: 0.7659 (t80) cc_final: 0.7325 (t80) REVERT: C 845 GLU cc_start: 0.6284 (tm-30) cc_final: 0.6003 (tm-30) REVERT: C 885 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7639 (tppt) REVERT: C 994 MET cc_start: 0.3894 (tpp) cc_final: 0.3565 (tpp) REVERT: C 1057 SER cc_start: 0.7751 (p) cc_final: 0.7112 (p) REVERT: C 1082 LEU cc_start: 0.8394 (mt) cc_final: 0.7885 (mt) REVERT: C 1149 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7365 (pttm) REVERT: C 1195 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 100 ASN cc_start: 0.8011 (t0) cc_final: 0.7661 (t0) REVERT: B 125 VAL cc_start: 0.8142 (t) cc_final: 0.7890 (p) REVERT: B 135 TYR cc_start: 0.7501 (m-80) cc_final: 0.7041 (m-80) REVERT: B 153 TYR cc_start: 0.6937 (m-80) cc_final: 0.6713 (m-80) REVERT: B 232 LEU cc_start: 0.8352 (mp) cc_final: 0.8074 (mm) REVERT: B 257 TRP cc_start: 0.5221 (m-90) cc_final: 0.3945 (m-90) REVERT: B 269 ASN cc_start: 0.7679 (t0) cc_final: 0.7246 (t0) REVERT: B 414 TYR cc_start: 0.3291 (t80) cc_final: 0.2998 (t80) REVERT: B 633 PHE cc_start: 0.7950 (m-10) cc_final: 0.7685 (m-10) REVERT: B 642 ASN cc_start: 0.7405 (t0) cc_final: 0.6752 (t0) REVERT: B 676 ARG cc_start: 0.6434 (tmm160) cc_final: 0.5976 (tmm160) REVERT: B 677 VAL cc_start: 0.8063 (t) cc_final: 0.7695 (t) REVERT: B 682 TYR cc_start: 0.6096 (t80) cc_final: 0.5776 (t80) REVERT: B 683 GLN cc_start: 0.6808 (pp30) cc_final: 0.6462 (pp30) REVERT: B 762 TYR cc_start: 0.4454 (m-10) cc_final: 0.4063 (m-10) REVERT: B 764 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5650 (t80) REVERT: B 828 LEU cc_start: 0.8455 (mt) cc_final: 0.7858 (mt) REVERT: B 829 LEU cc_start: 0.8056 (tp) cc_final: 0.7712 (mt) REVERT: B 830 SER cc_start: 0.8345 (m) cc_final: 0.8053 (p) REVERT: B 863 GLN cc_start: 0.6713 (mm110) cc_final: 0.6413 (mm110) REVERT: B 944 LYS cc_start: 0.8034 (tttp) cc_final: 0.7706 (tppt) REVERT: B 1030 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7068 (mp10) REVERT: B 1050 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7661 (mtpp) REVERT: B 1075 ASP cc_start: 0.7472 (m-30) cc_final: 0.7181 (m-30) REVERT: B 1109 LYS cc_start: 0.5922 (tptp) cc_final: 0.5116 (tptp) REVERT: B 1112 GLU cc_start: 0.6390 (mt-10) cc_final: 0.5911 (tt0) REVERT: B 1143 PHE cc_start: 0.6405 (m-80) cc_final: 0.6170 (m-10) REVERT: B 1144 ILE cc_start: 0.6457 (mm) cc_final: 0.6124 (mp) REVERT: B 1149 LYS cc_start: 0.7339 (tptt) cc_final: 0.7011 (tppt) REVERT: A 114 ASN cc_start: 0.7297 (t0) cc_final: 0.6995 (t0) REVERT: A 186 LYS cc_start: 0.6606 (mmmt) cc_final: 0.5893 (mmtt) REVERT: A 187 LYS cc_start: 0.6322 (mtpp) cc_final: 0.6077 (mttm) REVERT: A 226 LEU cc_start: 0.7550 (tp) cc_final: 0.6575 (pp) REVERT: A 289 GLU cc_start: 0.6740 (tp30) cc_final: 0.6480 (tp30) REVERT: A 305 ASP cc_start: 0.6859 (t0) cc_final: 0.6394 (t0) REVERT: A 319 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6713 (tpp-160) REVERT: A 622 TYR cc_start: 0.5604 (p90) cc_final: 0.4997 (p90) REVERT: A 634 LYS cc_start: 0.8383 (tttp) cc_final: 0.8065 (tttp) REVERT: A 702 ASN cc_start: 0.6251 (p0) cc_final: 0.5748 (p0) REVERT: A 812 ILE cc_start: 0.7974 (mt) cc_final: 0.7748 (mm) REVERT: A 885 LYS cc_start: 0.7124 (tppt) cc_final: 0.6802 (tttp) REVERT: A 952 GLU cc_start: 0.6763 (tp30) cc_final: 0.6182 (tp30) REVERT: A 1082 LEU cc_start: 0.8673 (mt) cc_final: 0.8362 (mt) REVERT: A 1095 ASP cc_start: 0.6842 (p0) cc_final: 0.6641 (p0) REVERT: A 1205 MET cc_start: 0.5342 (ttt) cc_final: 0.4730 (ptt) REVERT: A 1207 SER cc_start: 0.7400 (p) cc_final: 0.7175 (t) outliers start: 71 outliers final: 47 residues processed: 515 average time/residue: 0.3802 time to fit residues: 310.5427 Evaluate side-chains 497 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 449 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 837 ASP Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 SER Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 264 optimal weight: 0.5980 chunk 229 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 213 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 346 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 605 ASN C 856 GLN C1036 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN B 838 ASN B 854 GLN B1111 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A 954 GLN A1049 ASN A1117 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.214283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.173795 restraints weight = 60902.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.180467 restraints weight = 32831.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.182699 restraints weight = 20299.729| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 28084 Z= 0.114 Angle : 0.534 11.731 38346 Z= 0.277 Chirality : 0.043 0.206 4368 Planarity : 0.004 0.051 4928 Dihedral : 4.246 72.201 4046 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.95 % Allowed : 12.70 % Favored : 84.35 % 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: -2.07 (0.14), residues: 3519 helix: 0.01 (0.20), residues: 693 sheet: -1.03 (0.22), residues: 553 loop : -2.02 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 444 HIS 0.005 0.001 HIS A 201 PHE 0.035 0.001 PHE C 713 TYR 0.015 0.001 TYR C1193 ARG 0.008 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 11) link_NAG-ASN : angle 1.18662 ( 33) hydrogen bonds : bond 0.04331 ( 706) hydrogen bonds : angle 5.33455 ( 1986) SS BOND : bond 0.00265 ( 69) SS BOND : angle 1.95037 ( 138) covalent geometry : bond 0.00244 (28004) covalent geometry : angle 0.52140 (38175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 483 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7138 (tm-30) REVERT: C 575 TRP cc_start: 0.7153 (p-90) cc_final: 0.6698 (p90) REVERT: C 644 TRP cc_start: 0.7169 (p-90) cc_final: 0.6872 (p-90) REVERT: C 659 LYS cc_start: 0.7883 (mttt) cc_final: 0.7674 (mttt) REVERT: C 724 VAL cc_start: 0.7960 (t) cc_final: 0.7641 (m) REVERT: C 736 LEU cc_start: 0.5646 (mt) cc_final: 0.5317 (mp) REVERT: C 801 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7310 (pp20) REVERT: C 835 PHE cc_start: 0.7816 (t80) cc_final: 0.7516 (t80) REVERT: C 845 GLU cc_start: 0.6256 (tm-30) cc_final: 0.5994 (tm-30) REVERT: C 967 MET cc_start: 0.4142 (mmm) cc_final: 0.3810 (mmt) REVERT: C 994 MET cc_start: 0.3865 (tpp) cc_final: 0.3528 (tpp) REVERT: C 1076 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7421 (mtm110) REVERT: C 1077 LEU cc_start: 0.8831 (tp) cc_final: 0.8611 (mp) REVERT: C 1082 LEU cc_start: 0.8411 (mt) cc_final: 0.7951 (mt) REVERT: C 1149 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7404 (pttt) REVERT: C 1195 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6552 (mt-10) REVERT: B 100 ASN cc_start: 0.8037 (t0) cc_final: 0.7683 (t0) REVERT: B 125 VAL cc_start: 0.8149 (t) cc_final: 0.7907 (p) REVERT: B 135 TYR cc_start: 0.7515 (m-80) cc_final: 0.7009 (m-80) REVERT: B 232 LEU cc_start: 0.8347 (mp) cc_final: 0.8062 (mm) REVERT: B 257 TRP cc_start: 0.5392 (m-90) cc_final: 0.4120 (m-90) REVERT: B 414 TYR cc_start: 0.3328 (t80) cc_final: 0.3116 (t80) REVERT: B 642 ASN cc_start: 0.7518 (t0) cc_final: 0.6876 (t0) REVERT: B 659 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7267 (mtmm) REVERT: B 676 ARG cc_start: 0.6578 (tmm160) cc_final: 0.6168 (tmm160) REVERT: B 682 TYR cc_start: 0.6056 (t80) cc_final: 0.5717 (t80) REVERT: B 683 GLN cc_start: 0.6895 (pp30) cc_final: 0.6558 (pp30) REVERT: B 694 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B 745 ASP cc_start: 0.6173 (t0) cc_final: 0.5836 (p0) REVERT: B 762 TYR cc_start: 0.4527 (m-10) cc_final: 0.4119 (m-10) REVERT: B 809 LYS cc_start: 0.7157 (pttt) cc_final: 0.6915 (pttm) REVERT: B 828 LEU cc_start: 0.8414 (mt) cc_final: 0.7797 (mt) REVERT: B 830 SER cc_start: 0.8365 (m) cc_final: 0.8047 (p) REVERT: B 856 GLN cc_start: 0.6785 (mp10) cc_final: 0.6478 (mp10) REVERT: B 863 GLN cc_start: 0.6711 (mm110) cc_final: 0.6449 (mm110) REVERT: B 943 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7274 (mm) REVERT: B 944 LYS cc_start: 0.8087 (tttp) cc_final: 0.7873 (tppt) REVERT: B 953 THR cc_start: 0.5140 (t) cc_final: 0.4923 (t) REVERT: B 994 MET cc_start: 0.7599 (tpt) cc_final: 0.7146 (mmm) REVERT: B 1050 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7661 (mtpp) REVERT: B 1066 ASP cc_start: 0.7799 (t0) cc_final: 0.7321 (t70) REVERT: B 1075 ASP cc_start: 0.7476 (m-30) cc_final: 0.7202 (m-30) REVERT: B 1089 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 1109 LYS cc_start: 0.5927 (tptp) cc_final: 0.5620 (tptt) REVERT: B 1112 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: B 1143 PHE cc_start: 0.6452 (m-80) cc_final: 0.6124 (m-80) REVERT: B 1144 ILE cc_start: 0.6579 (mm) cc_final: 0.6221 (mp) REVERT: B 1149 LYS cc_start: 0.7334 (tptt) cc_final: 0.7090 (tppt) REVERT: A 60 THR cc_start: 0.8037 (m) cc_final: 0.7797 (p) REVERT: A 61 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7365 (tp) REVERT: A 69 LYS cc_start: 0.6811 (ttpp) cc_final: 0.6584 (ptpp) REVERT: A 114 ASN cc_start: 0.7245 (t0) cc_final: 0.6942 (t0) REVERT: A 186 LYS cc_start: 0.6530 (mmmt) cc_final: 0.6127 (mmtm) REVERT: A 187 LYS cc_start: 0.6378 (mtpp) cc_final: 0.6100 (mttm) REVERT: A 226 LEU cc_start: 0.7590 (tp) cc_final: 0.6556 (pp) REVERT: A 272 GLU cc_start: 0.8271 (tt0) cc_final: 0.7979 (mm-30) REVERT: A 289 GLU cc_start: 0.6732 (tp30) cc_final: 0.6414 (tp30) REVERT: A 305 ASP cc_start: 0.6922 (t0) cc_final: 0.6452 (t0) REVERT: A 319 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6322 (tpp-160) REVERT: A 622 TYR cc_start: 0.5809 (p90) cc_final: 0.5076 (p90) REVERT: A 634 LYS cc_start: 0.8352 (tttp) cc_final: 0.8048 (tttp) REVERT: A 800 GLU cc_start: 0.6355 (mp0) cc_final: 0.5646 (mp0) REVERT: A 812 ILE cc_start: 0.7929 (mt) cc_final: 0.7662 (mm) REVERT: A 908 PHE cc_start: 0.6667 (m-80) cc_final: 0.6195 (m-80) REVERT: A 952 GLU cc_start: 0.6723 (tp30) cc_final: 0.6456 (tp30) REVERT: A 1050 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7738 (mmmt) REVERT: A 1076 ARG cc_start: 0.7912 (tpp80) cc_final: 0.7560 (tpp80) REVERT: A 1082 LEU cc_start: 0.8655 (mt) cc_final: 0.8355 (mt) REVERT: A 1095 ASP cc_start: 0.6663 (p0) cc_final: 0.6444 (p0) REVERT: A 1117 GLN cc_start: 0.6228 (mm-40) cc_final: 0.5831 (mm-40) REVERT: A 1205 MET cc_start: 0.5843 (ttt) cc_final: 0.5182 (ptt) REVERT: A 1207 SER cc_start: 0.7781 (p) cc_final: 0.7517 (t) outliers start: 90 outliers final: 61 residues processed: 546 average time/residue: 0.3745 time to fit residues: 326.6485 Evaluate side-chains 526 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 459 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1093 LEU Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 694 ASN Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 234 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 167 optimal weight: 50.0000 chunk 265 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 211 optimal weight: 0.0030 chunk 343 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN C 140 GLN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 605 ASN C 856 GLN C 941 ASN C1036 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN B 847 ASN B 854 GLN B 954 GLN B1111 ASN A 545 HIS A 605 ASN A 870 ASN A 941 ASN A 954 GLN A1049 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.214551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172684 restraints weight = 58732.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178190 restraints weight = 30082.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.181530 restraints weight = 18526.844| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28084 Z= 0.140 Angle : 0.569 11.448 38346 Z= 0.295 Chirality : 0.044 0.326 4368 Planarity : 0.004 0.053 4928 Dihedral : 4.382 77.323 4044 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.14 % Allowed : 13.23 % Favored : 83.63 % 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: -2.02 (0.14), residues: 3519 helix: 0.02 (0.20), residues: 704 sheet: -0.98 (0.22), residues: 554 loop : -2.00 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 257 HIS 0.004 0.001 HIS C 201 PHE 0.029 0.001 PHE C 979 TYR 0.020 0.001 TYR B 203 ARG 0.009 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 11) link_NAG-ASN : angle 1.43987 ( 33) hydrogen bonds : bond 0.04250 ( 706) hydrogen bonds : angle 5.34064 ( 1986) SS BOND : bond 0.00393 ( 69) SS BOND : angle 2.04123 ( 138) covalent geometry : bond 0.00298 (28004) covalent geometry : angle 0.55498 (38175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 464 time to evaluate : 2.894 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 575 TRP cc_start: 0.7030 (p-90) cc_final: 0.6569 (p90) REVERT: C 612 THR cc_start: 0.6483 (p) cc_final: 0.6178 (m) REVERT: C 659 LYS cc_start: 0.7971 (mttt) cc_final: 0.7583 (mttt) REVERT: C 736 LEU cc_start: 0.5771 (mt) cc_final: 0.5138 (mp) REVERT: C 835 PHE cc_start: 0.7887 (t80) cc_final: 0.7571 (t80) REVERT: C 845 GLU cc_start: 0.6309 (tm-30) cc_final: 0.6027 (tm-30) REVERT: C 885 LYS cc_start: 0.7897 (tppt) cc_final: 0.7632 (mmtt) REVERT: C 967 MET cc_start: 0.3962 (mmm) cc_final: 0.3493 (mmt) REVERT: C 994 MET cc_start: 0.4211 (tpp) cc_final: 0.3821 (tpp) REVERT: C 1008 PHE cc_start: 0.7233 (m-80) cc_final: 0.6701 (m-80) REVERT: C 1015 ILE cc_start: 0.7730 (mm) cc_final: 0.7295 (mt) REVERT: C 1019 PHE cc_start: 0.6535 (m-10) cc_final: 0.6238 (m-80) REVERT: C 1047 LEU cc_start: 0.8429 (mt) cc_final: 0.8207 (mp) REVERT: C 1049 ASN cc_start: 0.8172 (m-40) cc_final: 0.7898 (m-40) REVERT: C 1082 LEU cc_start: 0.8414 (mt) cc_final: 0.8019 (mt) REVERT: C 1195 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6592 (mt-10) REVERT: B 75 ARG cc_start: 0.6998 (tmm-80) cc_final: 0.6537 (tmm-80) REVERT: B 100 ASN cc_start: 0.8004 (t0) cc_final: 0.7649 (t0) REVERT: B 125 VAL cc_start: 0.8159 (t) cc_final: 0.7955 (p) REVERT: B 237 VAL cc_start: 0.7111 (t) cc_final: 0.6752 (t) REVERT: B 257 TRP cc_start: 0.5709 (m-90) cc_final: 0.4313 (m-90) REVERT: B 269 ASN cc_start: 0.7503 (t0) cc_final: 0.7192 (t0) REVERT: B 621 ASN cc_start: 0.7250 (m-40) cc_final: 0.7043 (m110) REVERT: B 642 ASN cc_start: 0.7520 (t0) cc_final: 0.6906 (t0) REVERT: B 647 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5872 (mt) REVERT: B 659 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7241 (mtmm) REVERT: B 674 SER cc_start: 0.8252 (m) cc_final: 0.8050 (p) REVERT: B 676 ARG cc_start: 0.6693 (tmm160) cc_final: 0.6360 (tmm160) REVERT: B 682 TYR cc_start: 0.6098 (t80) cc_final: 0.5827 (t80) REVERT: B 683 GLN cc_start: 0.6968 (pp30) cc_final: 0.6631 (pp30) REVERT: B 762 TYR cc_start: 0.4663 (m-10) cc_final: 0.4172 (m-10) REVERT: B 809 LYS cc_start: 0.7154 (pttt) cc_final: 0.6937 (ptpp) REVERT: B 830 SER cc_start: 0.8295 (m) cc_final: 0.8034 (p) REVERT: B 856 GLN cc_start: 0.6810 (mt0) cc_final: 0.6165 (mp10) REVERT: B 863 GLN cc_start: 0.6787 (mm110) cc_final: 0.6487 (mm110) REVERT: B 920 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7267 (mt-10) REVERT: B 944 LYS cc_start: 0.8159 (tttp) cc_final: 0.7938 (tppt) REVERT: B 1050 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7683 (mtpp) REVERT: B 1064 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6495 (ttp-170) REVERT: B 1109 LYS cc_start: 0.5916 (tptp) cc_final: 0.5558 (tptt) REVERT: B 1112 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5763 (tt0) REVERT: B 1143 PHE cc_start: 0.6536 (m-80) cc_final: 0.6145 (m-80) REVERT: B 1144 ILE cc_start: 0.6609 (mm) cc_final: 0.6233 (mp) REVERT: A 60 THR cc_start: 0.8110 (m) cc_final: 0.7867 (p) REVERT: A 69 LYS cc_start: 0.6984 (ttpp) cc_final: 0.6774 (ptpp) REVERT: A 105 LYS cc_start: 0.7642 (tptt) cc_final: 0.7144 (tptm) REVERT: A 114 ASN cc_start: 0.7309 (t0) cc_final: 0.7084 (t0) REVERT: A 187 LYS cc_start: 0.6437 (mtpp) cc_final: 0.6066 (mmmt) REVERT: A 226 LEU cc_start: 0.7605 (tp) cc_final: 0.6583 (pp) REVERT: A 272 GLU cc_start: 0.8316 (tt0) cc_final: 0.7914 (mm-30) REVERT: A 289 GLU cc_start: 0.6825 (tp30) cc_final: 0.6515 (tp30) REVERT: A 305 ASP cc_start: 0.6971 (t0) cc_final: 0.6507 (t0) REVERT: A 319 ARG cc_start: 0.7025 (tpp-160) cc_final: 0.6563 (tpp-160) REVERT: A 634 LYS cc_start: 0.8359 (tttp) cc_final: 0.8057 (tttp) REVERT: A 800 GLU cc_start: 0.6491 (mp0) cc_final: 0.4687 (tt0) REVERT: A 908 PHE cc_start: 0.6833 (m-80) cc_final: 0.6324 (m-80) REVERT: A 952 GLU cc_start: 0.6863 (tp30) cc_final: 0.6554 (tp30) REVERT: A 1076 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7463 (mtp85) REVERT: A 1082 LEU cc_start: 0.8635 (mt) cc_final: 0.8354 (mt) REVERT: A 1095 ASP cc_start: 0.6789 (p0) cc_final: 0.6563 (p0) REVERT: A 1117 GLN cc_start: 0.6226 (mm-40) cc_final: 0.5765 (mm-40) REVERT: A 1205 MET cc_start: 0.5920 (ttt) cc_final: 0.5300 (ptt) REVERT: A 1207 SER cc_start: 0.7963 (p) cc_final: 0.7611 (t) outliers start: 96 outliers final: 76 residues processed: 531 average time/residue: 0.3767 time to fit residues: 319.8977 Evaluate side-chains 535 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 456 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1093 LEU Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 951 SER Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 237 optimal weight: 4.9990 chunk 286 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 235 optimal weight: 0.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 ASN C1049 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN B 854 GLN B1111 ASN A 630 GLN A 870 ASN A 954 GLN A1049 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.212222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.172013 restraints weight = 60267.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177228 restraints weight = 31391.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.180579 restraints weight = 19610.439| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28084 Z= 0.130 Angle : 0.564 11.279 38346 Z= 0.291 Chirality : 0.044 0.273 4368 Planarity : 0.004 0.052 4928 Dihedral : 4.422 77.121 4043 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.91 % Allowed : 14.11 % Favored : 82.97 % 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: -1.93 (0.14), residues: 3519 helix: 0.15 (0.20), residues: 695 sheet: -0.90 (0.22), residues: 549 loop : -1.95 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 197 HIS 0.009 0.001 HIS A 175 PHE 0.025 0.001 PHE B 209 TYR 0.020 0.001 TYR A 746 ARG 0.007 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 11) link_NAG-ASN : angle 1.48050 ( 33) hydrogen bonds : bond 0.04059 ( 706) hydrogen bonds : angle 5.22021 ( 1986) SS BOND : bond 0.00270 ( 69) SS BOND : angle 1.95431 ( 138) covalent geometry : bond 0.00278 (28004) covalent geometry : angle 0.55084 (38175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 464 time to evaluate : 2.757 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 157 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 309 PHE cc_start: 0.4870 (OUTLIER) cc_final: 0.4464 (t80) REVERT: C 321 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7578 (tt) REVERT: C 575 TRP cc_start: 0.6949 (p-90) cc_final: 0.6627 (p90) REVERT: C 736 LEU cc_start: 0.5777 (mt) cc_final: 0.5069 (mp) REVERT: C 835 PHE cc_start: 0.7881 (t80) cc_final: 0.7613 (t80) REVERT: C 845 GLU cc_start: 0.6302 (tm-30) cc_final: 0.6051 (tm-30) REVERT: C 885 LYS cc_start: 0.7890 (tppt) cc_final: 0.7612 (tptt) REVERT: C 967 MET cc_start: 0.3933 (mmm) cc_final: 0.3520 (mmt) REVERT: C 1008 PHE cc_start: 0.7217 (m-80) cc_final: 0.6716 (m-80) REVERT: C 1019 PHE cc_start: 0.6489 (m-10) cc_final: 0.6188 (m-80) REVERT: C 1082 LEU cc_start: 0.8427 (mt) cc_final: 0.8097 (mt) REVERT: C 1149 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7750 (pttt) REVERT: B 100 ASN cc_start: 0.8011 (t0) cc_final: 0.7658 (t0) REVERT: B 125 VAL cc_start: 0.8209 (t) cc_final: 0.7986 (p) REVERT: B 135 TYR cc_start: 0.7521 (m-80) cc_final: 0.7185 (m-80) REVERT: B 232 LEU cc_start: 0.8348 (mp) cc_final: 0.8078 (mm) REVERT: B 257 TRP cc_start: 0.5716 (m-90) cc_final: 0.4285 (m-90) REVERT: B 269 ASN cc_start: 0.7471 (t0) cc_final: 0.7209 (t0) REVERT: B 297 PHE cc_start: 0.5269 (m-80) cc_final: 0.4980 (m-80) REVERT: B 640 TYR cc_start: 0.8005 (p90) cc_final: 0.7761 (p90) REVERT: B 641 TYR cc_start: 0.6845 (m-80) cc_final: 0.6478 (m-80) REVERT: B 642 ASN cc_start: 0.7539 (t0) cc_final: 0.6936 (t0) REVERT: B 647 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.5835 (mt) REVERT: B 659 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7222 (mtmm) REVERT: B 676 ARG cc_start: 0.6671 (tmm160) cc_final: 0.6423 (tmm160) REVERT: B 682 TYR cc_start: 0.6100 (t80) cc_final: 0.5651 (t80) REVERT: B 683 GLN cc_start: 0.6954 (pp30) cc_final: 0.6581 (pp30) REVERT: B 719 CYS cc_start: 0.4477 (t) cc_final: 0.4178 (t) REVERT: B 762 TYR cc_start: 0.4684 (m-10) cc_final: 0.4176 (m-10) REVERT: B 809 LYS cc_start: 0.7144 (ptpt) cc_final: 0.6918 (ptpp) REVERT: B 838 ASN cc_start: 0.7342 (m-40) cc_final: 0.7141 (m110) REVERT: B 856 GLN cc_start: 0.6856 (mt0) cc_final: 0.6127 (mp10) REVERT: B 863 GLN cc_start: 0.6790 (mm110) cc_final: 0.6479 (mm110) REVERT: B 920 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 1050 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7697 (mtpp) REVERT: B 1064 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6379 (ttp-170) REVERT: B 1066 ASP cc_start: 0.7882 (t0) cc_final: 0.7510 (t0) REVERT: B 1109 LYS cc_start: 0.5934 (tptp) cc_final: 0.5201 (tptt) REVERT: B 1112 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5785 (tt0) REVERT: B 1144 ILE cc_start: 0.6665 (mm) cc_final: 0.6265 (mp) REVERT: B 1149 LYS cc_start: 0.7479 (tptt) cc_final: 0.7247 (tppt) REVERT: B 1177 PHE cc_start: 0.6710 (m-10) cc_final: 0.6510 (m-80) REVERT: A 60 THR cc_start: 0.8083 (m) cc_final: 0.7832 (p) REVERT: A 63 PHE cc_start: 0.7627 (t80) cc_final: 0.7427 (t80) REVERT: A 186 LYS cc_start: 0.6172 (tppt) cc_final: 0.5793 (mmtm) REVERT: A 226 LEU cc_start: 0.7601 (tp) cc_final: 0.7165 (tp) REVERT: A 272 GLU cc_start: 0.8357 (tt0) cc_final: 0.7955 (tt0) REVERT: A 289 GLU cc_start: 0.6798 (tp30) cc_final: 0.6528 (tp30) REVERT: A 305 ASP cc_start: 0.6853 (t0) cc_final: 0.6426 (t0) REVERT: A 319 ARG cc_start: 0.6995 (tpp-160) cc_final: 0.6541 (tpp-160) REVERT: A 634 LYS cc_start: 0.8342 (tttp) cc_final: 0.8046 (tttp) REVERT: A 656 ILE cc_start: 0.8045 (pt) cc_final: 0.7761 (mm) REVERT: A 800 GLU cc_start: 0.6420 (mp0) cc_final: 0.4502 (tt0) REVERT: A 818 VAL cc_start: 0.7334 (t) cc_final: 0.6827 (p) REVERT: A 1076 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7439 (mtp85) REVERT: A 1082 LEU cc_start: 0.8686 (mt) cc_final: 0.8411 (mt) REVERT: A 1095 ASP cc_start: 0.6741 (p0) cc_final: 0.6512 (p0) REVERT: A 1205 MET cc_start: 0.6129 (ttt) cc_final: 0.5417 (ptt) REVERT: A 1207 SER cc_start: 0.7991 (p) cc_final: 0.7683 (p) outliers start: 89 outliers final: 64 residues processed: 529 average time/residue: 0.3947 time to fit residues: 336.6701 Evaluate side-chains 519 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 450 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1057 SER Chi-restraints excluded: chain C residue 1093 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 959 THR Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1203 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 142 optimal weight: 6.9990 chunk 187 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 179 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 341 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 826 HIS C 872 ASN C 923 ASN C1036 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 621 ASN B 847 ASN B 854 GLN B1049 ASN B1111 ASN B1122 ASN A 870 ASN A 954 GLN A1049 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.248841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.233829 restraints weight = 80778.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.233627 restraints weight = 87390.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.234298 restraints weight = 79136.913| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28084 Z= 0.111 Angle : 0.553 11.219 38346 Z= 0.284 Chirality : 0.044 0.233 4368 Planarity : 0.004 0.054 4928 Dihedral : 4.337 78.394 4042 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.69 % Allowed : 15.00 % Favored : 82.32 % 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: -1.82 (0.14), residues: 3519 helix: 0.27 (0.20), residues: 707 sheet: -0.76 (0.22), residues: 539 loop : -1.92 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 197 HIS 0.005 0.001 HIS B 160 PHE 0.031 0.001 PHE C 658 TYR 0.017 0.001 TYR B 203 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 11) link_NAG-ASN : angle 1.18263 ( 33) hydrogen bonds : bond 0.03785 ( 706) hydrogen bonds : angle 5.05359 ( 1986) SS BOND : bond 0.00224 ( 69) SS BOND : angle 1.87022 ( 138) covalent geometry : bond 0.00240 (28004) covalent geometry : angle 0.54158 (38175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 454 time to evaluate : 2.878 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 157 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6862 (tm-30) REVERT: C 309 PHE cc_start: 0.4945 (OUTLIER) cc_final: 0.4575 (t80) REVERT: C 659 LYS cc_start: 0.7951 (mttt) cc_final: 0.7561 (mttp) REVERT: C 736 LEU cc_start: 0.5830 (mt) cc_final: 0.5538 (mp) REVERT: C 839 ILE cc_start: 0.8381 (tt) cc_final: 0.8068 (pt) REVERT: C 845 GLU cc_start: 0.6442 (tm-30) cc_final: 0.6196 (tm-30) REVERT: C 885 LYS cc_start: 0.7782 (tppt) cc_final: 0.7508 (tptt) REVERT: C 967 MET cc_start: 0.4161 (mmm) cc_final: 0.3705 (mmt) REVERT: C 1008 PHE cc_start: 0.7133 (m-80) cc_final: 0.6656 (m-80) REVERT: C 1019 PHE cc_start: 0.6292 (m-10) cc_final: 0.6012 (m-80) REVERT: C 1109 LYS cc_start: 0.6322 (ttmm) cc_final: 0.5695 (mtpp) REVERT: C 1149 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7749 (tmtt) REVERT: C 1195 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 100 ASN cc_start: 0.7989 (t0) cc_final: 0.7641 (t0) REVERT: B 135 TYR cc_start: 0.7468 (m-80) cc_final: 0.7233 (m-80) REVERT: B 232 LEU cc_start: 0.8272 (mp) cc_final: 0.8059 (mm) REVERT: B 257 TRP cc_start: 0.5660 (m-90) cc_final: 0.4280 (m-90) REVERT: B 269 ASN cc_start: 0.7391 (t0) cc_final: 0.6948 (t0) REVERT: B 621 ASN cc_start: 0.7307 (m-40) cc_final: 0.7049 (m110) REVERT: B 640 TYR cc_start: 0.8055 (p90) cc_final: 0.7802 (p90) REVERT: B 641 TYR cc_start: 0.6907 (m-80) cc_final: 0.6481 (m-80) REVERT: B 642 ASN cc_start: 0.7520 (t0) cc_final: 0.6940 (t0) REVERT: B 647 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.5860 (mt) REVERT: B 676 ARG cc_start: 0.6654 (tmm160) cc_final: 0.6276 (tmm160) REVERT: B 682 TYR cc_start: 0.6171 (t80) cc_final: 0.5754 (t80) REVERT: B 683 GLN cc_start: 0.6980 (pp30) cc_final: 0.6597 (pp30) REVERT: B 762 TYR cc_start: 0.4647 (m-10) cc_final: 0.4196 (m-10) REVERT: B 809 LYS cc_start: 0.7013 (ptpt) cc_final: 0.6705 (ptpp) REVERT: B 838 ASN cc_start: 0.7370 (m-40) cc_final: 0.7101 (m110) REVERT: B 863 GLN cc_start: 0.6918 (mm110) cc_final: 0.6571 (mm110) REVERT: B 920 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 1050 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7687 (mtpp) REVERT: B 1064 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6303 (ttp-170) REVERT: B 1071 GLN cc_start: 0.7156 (pm20) cc_final: 0.6900 (pm20) REVERT: B 1109 LYS cc_start: 0.5697 (tptp) cc_final: 0.4904 (tptm) REVERT: B 1112 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5812 (tt0) REVERT: B 1143 PHE cc_start: 0.6396 (m-80) cc_final: 0.6097 (m-80) REVERT: B 1144 ILE cc_start: 0.6610 (mm) cc_final: 0.6194 (mp) REVERT: B 1177 PHE cc_start: 0.6339 (m-10) cc_final: 0.6096 (m-80) REVERT: A 63 PHE cc_start: 0.7597 (t80) cc_final: 0.7354 (t80) REVERT: A 186 LYS cc_start: 0.5965 (tppt) cc_final: 0.5629 (mmtm) REVERT: A 226 LEU cc_start: 0.7617 (tp) cc_final: 0.7179 (tp) REVERT: A 255 GLU cc_start: 0.6783 (tt0) cc_final: 0.6075 (tt0) REVERT: A 257 TRP cc_start: 0.4096 (OUTLIER) cc_final: 0.3798 (m100) REVERT: A 272 GLU cc_start: 0.8499 (tt0) cc_final: 0.8025 (tt0) REVERT: A 289 GLU cc_start: 0.6889 (tp30) cc_final: 0.6565 (tp30) REVERT: A 305 ASP cc_start: 0.6350 (t0) cc_final: 0.6026 (t0) REVERT: A 319 ARG cc_start: 0.6943 (tpp-160) cc_final: 0.6588 (tpp-160) REVERT: A 634 LYS cc_start: 0.8333 (tttp) cc_final: 0.8043 (tttp) REVERT: A 800 GLU cc_start: 0.6406 (mp0) cc_final: 0.4490 (tm-30) REVERT: A 818 VAL cc_start: 0.7289 (t) cc_final: 0.6772 (p) REVERT: A 994 MET cc_start: 0.4627 (tpp) cc_final: 0.4374 (tpp) REVERT: A 1050 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7720 (mmmt) REVERT: A 1076 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7526 (mtp85) REVERT: A 1082 LEU cc_start: 0.8618 (mt) cc_final: 0.8415 (mt) REVERT: A 1095 ASP cc_start: 0.6837 (p0) cc_final: 0.6618 (p0) REVERT: A 1205 MET cc_start: 0.5037 (ttt) cc_final: 0.4810 (ptt) REVERT: A 1207 SER cc_start: 0.7264 (p) cc_final: 0.6810 (p) outliers start: 82 outliers final: 64 residues processed: 511 average time/residue: 0.3672 time to fit residues: 299.0058 Evaluate side-chains 510 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 441 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 837 ASP Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 923 ASN Chi-restraints excluded: chain C residue 1093 LEU Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1079 ASN Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 330 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 241 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 54 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 847 ASN B 854 GLN B1049 ASN B1111 ASN B1122 ASN ** B1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A 954 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.248762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.233819 restraints weight = 81090.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.233603 restraints weight = 90742.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.234376 restraints weight = 79278.437| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28084 Z= 0.111 Angle : 0.561 11.196 38346 Z= 0.289 Chirality : 0.044 0.340 4368 Planarity : 0.004 0.082 4928 Dihedral : 4.335 78.389 4042 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.69 % Allowed : 15.09 % Favored : 82.22 % 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: -1.77 (0.14), residues: 3519 helix: 0.37 (0.20), residues: 701 sheet: -0.87 (0.21), residues: 572 loop : -1.87 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 174 HIS 0.004 0.001 HIS B 160 PHE 0.026 0.001 PHE C 979 TYR 0.023 0.001 TYR A 682 ARG 0.009 0.000 ARG B 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 11) link_NAG-ASN : angle 1.28357 ( 33) hydrogen bonds : bond 0.03707 ( 706) hydrogen bonds : angle 5.00107 ( 1986) SS BOND : bond 0.00212 ( 69) SS BOND : angle 1.84252 ( 138) covalent geometry : bond 0.00240 (28004) covalent geometry : angle 0.54963 (38175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 448 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6807 (tm-30) REVERT: C 309 PHE cc_start: 0.4979 (OUTLIER) cc_final: 0.4596 (t80) REVERT: C 659 LYS cc_start: 0.7924 (mttt) cc_final: 0.7644 (mttp) REVERT: C 736 LEU cc_start: 0.5798 (mt) cc_final: 0.5507 (mp) REVERT: C 839 ILE cc_start: 0.8357 (tt) cc_final: 0.8023 (pt) REVERT: C 845 GLU cc_start: 0.6509 (tm-30) cc_final: 0.6282 (tm-30) REVERT: C 885 LYS cc_start: 0.7774 (tppt) cc_final: 0.7477 (tptt) REVERT: C 967 MET cc_start: 0.4189 (mmm) cc_final: 0.3736 (mmt) REVERT: C 1008 PHE cc_start: 0.7120 (m-80) cc_final: 0.6660 (m-80) REVERT: C 1049 ASN cc_start: 0.8112 (m-40) cc_final: 0.7894 (m-40) REVERT: C 1076 ARG cc_start: 0.7582 (mtm110) cc_final: 0.7377 (mtm110) REVERT: C 1109 LYS cc_start: 0.6277 (ttmm) cc_final: 0.5659 (mtpp) REVERT: C 1149 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7737 (tmtt) REVERT: C 1195 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 100 ASN cc_start: 0.7980 (t0) cc_final: 0.7650 (t0) REVERT: B 135 TYR cc_start: 0.7505 (m-80) cc_final: 0.7265 (m-80) REVERT: B 140 GLN cc_start: 0.8148 (tp40) cc_final: 0.7718 (tp-100) REVERT: B 232 LEU cc_start: 0.8292 (mp) cc_final: 0.8080 (mm) REVERT: B 264 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5981 (mtm180) REVERT: B 269 ASN cc_start: 0.7370 (t0) cc_final: 0.6966 (t0) REVERT: B 621 ASN cc_start: 0.7259 (m-40) cc_final: 0.7039 (m110) REVERT: B 640 TYR cc_start: 0.8033 (p90) cc_final: 0.7771 (p90) REVERT: B 642 ASN cc_start: 0.7534 (t0) cc_final: 0.6956 (t0) REVERT: B 647 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.5839 (mt) REVERT: B 676 ARG cc_start: 0.6615 (tmm160) cc_final: 0.6264 (tmm160) REVERT: B 682 TYR cc_start: 0.6092 (t80) cc_final: 0.5844 (t80) REVERT: B 683 GLN cc_start: 0.6942 (pp30) cc_final: 0.6544 (pp30) REVERT: B 762 TYR cc_start: 0.4682 (m-10) cc_final: 0.4249 (m-10) REVERT: B 809 LYS cc_start: 0.6983 (ptpt) cc_final: 0.6712 (ptpp) REVERT: B 838 ASN cc_start: 0.7389 (m-40) cc_final: 0.7128 (m110) REVERT: B 920 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 1050 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7693 (mtpp) REVERT: B 1064 ARG cc_start: 0.6597 (ttp-170) cc_final: 0.6251 (ttp-170) REVERT: B 1109 LYS cc_start: 0.5710 (tptp) cc_final: 0.4930 (tptm) REVERT: B 1112 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5803 (tt0) REVERT: B 1143 PHE cc_start: 0.6426 (m-80) cc_final: 0.6029 (m-80) REVERT: B 1144 ILE cc_start: 0.6617 (mm) cc_final: 0.6240 (mp) REVERT: B 1177 PHE cc_start: 0.6322 (m-10) cc_final: 0.6096 (m-80) REVERT: A 63 PHE cc_start: 0.7601 (t80) cc_final: 0.7359 (t80) REVERT: A 186 LYS cc_start: 0.5953 (tppt) cc_final: 0.5672 (mmtm) REVERT: A 226 LEU cc_start: 0.7588 (tp) cc_final: 0.7147 (tp) REVERT: A 272 GLU cc_start: 0.8470 (tt0) cc_final: 0.8011 (tt0) REVERT: A 289 GLU cc_start: 0.6855 (tp30) cc_final: 0.6534 (tp30) REVERT: A 305 ASP cc_start: 0.6330 (t0) cc_final: 0.5982 (t0) REVERT: A 319 ARG cc_start: 0.6933 (tpp-160) cc_final: 0.6608 (tpp-160) REVERT: A 634 LYS cc_start: 0.8304 (tttp) cc_final: 0.8031 (tttp) REVERT: A 656 ILE cc_start: 0.8071 (pt) cc_final: 0.7780 (mm) REVERT: A 800 GLU cc_start: 0.6383 (mp0) cc_final: 0.4434 (tm-30) REVERT: A 818 VAL cc_start: 0.7310 (t) cc_final: 0.6796 (p) REVERT: A 1076 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7494 (mtp85) REVERT: A 1095 ASP cc_start: 0.6815 (p0) cc_final: 0.6594 (p0) REVERT: A 1205 MET cc_start: 0.5086 (ttt) cc_final: 0.4680 (ptp) REVERT: A 1207 SER cc_start: 0.7266 (p) cc_final: 0.6763 (p) outliers start: 82 outliers final: 67 residues processed: 505 average time/residue: 0.3711 time to fit residues: 298.0400 Evaluate side-chains 511 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 440 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 837 ASP Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 923 ASN Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1134 VAL Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1185 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 339 optimal weight: 0.9990 chunk 316 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 chunk 201 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 334 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 190 optimal weight: 0.3980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN C1036 ASN C1049 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 854 GLN B1049 ASN B1111 ASN B1122 ASN ** B1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A 954 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.214026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.173417 restraints weight = 58551.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.178601 restraints weight = 31034.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181727 restraints weight = 19514.804| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28084 Z= 0.112 Angle : 0.573 11.178 38346 Z= 0.294 Chirality : 0.045 0.356 4368 Planarity : 0.004 0.068 4928 Dihedral : 4.329 79.097 4041 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.49 % Allowed : 15.72 % Favored : 81.79 % 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: -1.75 (0.14), residues: 3519 helix: 0.40 (0.20), residues: 700 sheet: -0.74 (0.22), residues: 546 loop : -1.89 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 575 HIS 0.005 0.001 HIS B 160 PHE 0.027 0.001 PHE C 979 TYR 0.023 0.001 TYR A 84 ARG 0.007 0.000 ARG B 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 11) link_NAG-ASN : angle 1.29923 ( 33) hydrogen bonds : bond 0.03667 ( 706) hydrogen bonds : angle 4.96839 ( 1986) SS BOND : bond 0.00208 ( 69) SS BOND : angle 1.92641 ( 138) covalent geometry : bond 0.00245 (28004) covalent geometry : angle 0.56110 (38175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 450 time to evaluate : 2.690 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 157 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 309 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4620 (t80) REVERT: C 659 LYS cc_start: 0.7970 (mttt) cc_final: 0.7529 (mttp) REVERT: C 736 LEU cc_start: 0.5740 (mt) cc_final: 0.5424 (mp) REVERT: C 845 GLU cc_start: 0.6256 (tm-30) cc_final: 0.6047 (tm-30) REVERT: C 885 LYS cc_start: 0.7831 (tppt) cc_final: 0.7518 (tptt) REVERT: C 967 MET cc_start: 0.3932 (mmm) cc_final: 0.3496 (mmt) REVERT: C 1008 PHE cc_start: 0.7196 (m-80) cc_final: 0.6729 (m-80) REVERT: C 1055 SER cc_start: 0.8555 (m) cc_final: 0.8224 (t) REVERT: C 1109 LYS cc_start: 0.6377 (ttmm) cc_final: 0.5719 (mtpp) REVERT: C 1149 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7596 (tmtt) REVERT: C 1195 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 100 ASN cc_start: 0.7964 (t0) cc_final: 0.7619 (t0) REVERT: B 135 TYR cc_start: 0.7547 (m-80) cc_final: 0.7191 (m-80) REVERT: B 140 GLN cc_start: 0.8158 (tp40) cc_final: 0.7764 (tp-100) REVERT: B 232 LEU cc_start: 0.8349 (mp) cc_final: 0.8109 (mm) REVERT: B 269 ASN cc_start: 0.7411 (t0) cc_final: 0.7026 (t0) REVERT: B 640 TYR cc_start: 0.7975 (p90) cc_final: 0.7765 (p90) REVERT: B 642 ASN cc_start: 0.7512 (t0) cc_final: 0.6891 (t0) REVERT: B 647 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.5922 (mt) REVERT: B 676 ARG cc_start: 0.6609 (tmm160) cc_final: 0.6335 (tmm160) REVERT: B 682 TYR cc_start: 0.6078 (t80) cc_final: 0.5795 (t80) REVERT: B 683 GLN cc_start: 0.6978 (pp30) cc_final: 0.6615 (pp30) REVERT: B 719 CYS cc_start: 0.4281 (t) cc_final: 0.4058 (t) REVERT: B 762 TYR cc_start: 0.4713 (m-10) cc_final: 0.4280 (m-10) REVERT: B 809 LYS cc_start: 0.7133 (ptpt) cc_final: 0.6916 (ptpp) REVERT: B 838 ASN cc_start: 0.7359 (m-40) cc_final: 0.7127 (m110) REVERT: B 920 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 1050 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7687 (mtpp) REVERT: B 1064 ARG cc_start: 0.6704 (ttp-170) cc_final: 0.6344 (ttp-170) REVERT: B 1109 LYS cc_start: 0.5731 (tptp) cc_final: 0.5038 (tptm) REVERT: B 1112 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5810 (tt0) REVERT: B 1143 PHE cc_start: 0.6427 (m-80) cc_final: 0.6046 (m-10) REVERT: B 1144 ILE cc_start: 0.6596 (mm) cc_final: 0.6246 (mp) REVERT: A 63 PHE cc_start: 0.7595 (t80) cc_final: 0.7366 (t80) REVERT: A 186 LYS cc_start: 0.6153 (tppt) cc_final: 0.5730 (mmtm) REVERT: A 226 LEU cc_start: 0.7534 (tp) cc_final: 0.7078 (tp) REVERT: A 272 GLU cc_start: 0.8284 (tt0) cc_final: 0.7964 (mm-30) REVERT: A 289 GLU cc_start: 0.6776 (tp30) cc_final: 0.6527 (tp30) REVERT: A 305 ASP cc_start: 0.6753 (t0) cc_final: 0.6368 (t0) REVERT: A 319 ARG cc_start: 0.6951 (tpp-160) cc_final: 0.6515 (tpp-160) REVERT: A 634 LYS cc_start: 0.8247 (tttp) cc_final: 0.7961 (tttp) REVERT: A 656 ILE cc_start: 0.8092 (pt) cc_final: 0.7803 (mm) REVERT: A 800 GLU cc_start: 0.6304 (mp0) cc_final: 0.4414 (tm-30) REVERT: A 818 VAL cc_start: 0.7330 (t) cc_final: 0.6860 (p) REVERT: A 952 GLU cc_start: 0.6952 (tp30) cc_final: 0.6485 (tp30) REVERT: A 994 MET cc_start: 0.4495 (tpp) cc_final: 0.4160 (tpp) REVERT: A 1076 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7307 (mtp85) REVERT: A 1082 LEU cc_start: 0.8691 (mt) cc_final: 0.8482 (mt) REVERT: A 1095 ASP cc_start: 0.6698 (p0) cc_final: 0.6467 (p0) REVERT: A 1205 MET cc_start: 0.6193 (ttt) cc_final: 0.5102 (ptp) REVERT: A 1207 SER cc_start: 0.7935 (p) cc_final: 0.7499 (p) outliers start: 76 outliers final: 67 residues processed: 500 average time/residue: 0.3851 time to fit residues: 306.2268 Evaluate side-chains 511 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 441 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 837 ASP Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 923 ASN Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 162 optimal weight: 3.9990 chunk 102 optimal weight: 0.0970 chunk 306 optimal weight: 0.2980 chunk 201 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 267 optimal weight: 0.4980 chunk 133 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 854 GLN B1049 ASN B1111 ASN B1122 ASN ** B1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A 954 GLN A1211 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.212714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171618 restraints weight = 58289.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.176729 restraints weight = 30849.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.180025 restraints weight = 19420.146| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28084 Z= 0.158 Angle : 0.618 11.083 38346 Z= 0.320 Chirality : 0.046 0.318 4368 Planarity : 0.004 0.079 4928 Dihedral : 4.593 79.932 4041 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.39 % Allowed : 16.11 % Favored : 81.50 % 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: -1.89 (0.14), residues: 3519 helix: 0.16 (0.20), residues: 710 sheet: -0.76 (0.22), residues: 530 loop : -1.96 (0.12), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 174 HIS 0.006 0.001 HIS B 160 PHE 0.027 0.001 PHE B 209 TYR 0.021 0.002 TYR A 682 ARG 0.008 0.000 ARG B 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 11) link_NAG-ASN : angle 1.58928 ( 33) hydrogen bonds : bond 0.04085 ( 706) hydrogen bonds : angle 5.20689 ( 1986) SS BOND : bond 0.00240 ( 69) SS BOND : angle 2.04596 ( 138) covalent geometry : bond 0.00336 (28004) covalent geometry : angle 0.60515 (38175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 452 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 309 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.4698 (t80) REVERT: C 736 LEU cc_start: 0.5823 (mt) cc_final: 0.5159 (mp) REVERT: C 885 LYS cc_start: 0.7799 (tppt) cc_final: 0.7482 (tptt) REVERT: C 907 LEU cc_start: 0.7841 (mt) cc_final: 0.7555 (tp) REVERT: C 967 MET cc_start: 0.4050 (mmm) cc_final: 0.3597 (mmt) REVERT: C 1008 PHE cc_start: 0.7144 (m-80) cc_final: 0.6676 (m-80) REVERT: C 1055 SER cc_start: 0.8605 (m) cc_final: 0.8250 (t) REVERT: C 1149 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7637 (tmtt) REVERT: C 1195 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6882 (mt-10) REVERT: B 100 ASN cc_start: 0.8056 (t0) cc_final: 0.7684 (t0) REVERT: B 135 TYR cc_start: 0.7559 (m-80) cc_final: 0.7255 (m-80) REVERT: B 140 GLN cc_start: 0.8175 (tp40) cc_final: 0.7810 (tp-100) REVERT: B 232 LEU cc_start: 0.8379 (mp) cc_final: 0.8139 (mm) REVERT: B 269 ASN cc_start: 0.7433 (t0) cc_final: 0.7074 (t0) REVERT: B 621 ASN cc_start: 0.7217 (m-40) cc_final: 0.6996 (m110) REVERT: B 640 TYR cc_start: 0.8006 (p90) cc_final: 0.7796 (p90) REVERT: B 642 ASN cc_start: 0.7590 (t0) cc_final: 0.7239 (t0) REVERT: B 644 TRP cc_start: 0.6044 (p90) cc_final: 0.5741 (p90) REVERT: B 647 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6020 (mt) REVERT: B 676 ARG cc_start: 0.6632 (tmm160) cc_final: 0.6400 (tmm160) REVERT: B 683 GLN cc_start: 0.6985 (pp30) cc_final: 0.6597 (pp30) REVERT: B 762 TYR cc_start: 0.4744 (m-10) cc_final: 0.4219 (m-10) REVERT: B 809 LYS cc_start: 0.7188 (ptpt) cc_final: 0.6984 (ptpp) REVERT: B 838 ASN cc_start: 0.7403 (m-40) cc_final: 0.7178 (m110) REVERT: B 887 LEU cc_start: 0.5987 (mp) cc_final: 0.5749 (tp) REVERT: B 1050 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7674 (mtpp) REVERT: B 1057 SER cc_start: 0.8628 (t) cc_final: 0.8369 (t) REVERT: B 1064 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6342 (ttp-170) REVERT: B 1109 LYS cc_start: 0.5952 (tptp) cc_final: 0.5191 (tptm) REVERT: B 1112 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5798 (tt0) REVERT: B 1143 PHE cc_start: 0.6423 (m-80) cc_final: 0.6019 (m-80) REVERT: B 1144 ILE cc_start: 0.6645 (mm) cc_final: 0.6401 (mm) REVERT: A 186 LYS cc_start: 0.6161 (tppt) cc_final: 0.5799 (mmtm) REVERT: A 199 TYR cc_start: 0.6618 (m-80) cc_final: 0.6347 (m-80) REVERT: A 226 LEU cc_start: 0.7541 (tp) cc_final: 0.7082 (tp) REVERT: A 272 GLU cc_start: 0.8279 (tt0) cc_final: 0.7965 (mm-30) REVERT: A 289 GLU cc_start: 0.6816 (tp30) cc_final: 0.6560 (tp30) REVERT: A 305 ASP cc_start: 0.6799 (t0) cc_final: 0.6351 (t0) REVERT: A 319 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6500 (tpp-160) REVERT: A 634 LYS cc_start: 0.8240 (tttp) cc_final: 0.7961 (tttp) REVERT: A 656 ILE cc_start: 0.8131 (pt) cc_final: 0.7816 (mm) REVERT: A 800 GLU cc_start: 0.6410 (mp0) cc_final: 0.4427 (tt0) REVERT: A 818 VAL cc_start: 0.7341 (t) cc_final: 0.6878 (p) REVERT: A 831 GLU cc_start: 0.4449 (tm-30) cc_final: 0.3575 (tm-30) REVERT: A 994 MET cc_start: 0.4756 (tpp) cc_final: 0.4458 (tpp) REVERT: A 1076 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7292 (mtp85) REVERT: A 1082 LEU cc_start: 0.8654 (mt) cc_final: 0.8413 (mt) REVERT: A 1095 ASP cc_start: 0.6731 (p0) cc_final: 0.6511 (p0) REVERT: A 1205 MET cc_start: 0.6402 (ttt) cc_final: 0.5463 (ptt) REVERT: A 1207 SER cc_start: 0.8050 (p) cc_final: 0.7631 (p) outliers start: 73 outliers final: 64 residues processed: 497 average time/residue: 0.3672 time to fit residues: 290.9845 Evaluate side-chains 512 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 444 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 923 ASN Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1061 ILE Chi-restraints excluded: chain C residue 1113 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 923 ASN Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1139 TYR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 734 CYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 30 optimal weight: 0.0970 chunk 242 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 348 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 265 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 244 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 ASN C1036 ASN C1129 HIS B 132 ASN B 854 GLN B1049 ASN B1111 ASN B1122 ASN ** B1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A 954 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.248875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.234070 restraints weight = 80921.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.233835 restraints weight = 89745.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.234610 restraints weight = 81136.944| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28084 Z= 0.102 Angle : 0.577 11.273 38346 Z= 0.296 Chirality : 0.044 0.307 4368 Planarity : 0.004 0.053 4928 Dihedral : 4.369 81.265 4041 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.29 % Allowed : 16.27 % Favored : 81.43 % 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: -1.73 (0.14), residues: 3519 helix: 0.42 (0.20), residues: 710 sheet: -0.87 (0.21), residues: 579 loop : -1.85 (0.12), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 257 HIS 0.005 0.001 HIS B 160 PHE 0.037 0.001 PHE C 713 TYR 0.020 0.001 TYR A 199 ARG 0.006 0.000 ARG B 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 11) link_NAG-ASN : angle 1.32328 ( 33) hydrogen bonds : bond 0.03489 ( 706) hydrogen bonds : angle 4.89818 ( 1986) SS BOND : bond 0.00261 ( 69) SS BOND : angle 1.99691 ( 138) covalent geometry : bond 0.00225 (28004) covalent geometry : angle 0.56477 (38175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10069.59 seconds wall clock time: 176 minutes 55.50 seconds (10615.50 seconds total)