Starting phenix.real_space_refine on Mon Aug 25 10:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqc_41502/08_2025/8tqc_41502_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqc_41502/08_2025/8tqc_41502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tqc_41502/08_2025/8tqc_41502_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqc_41502/08_2025/8tqc_41502_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tqc_41502/08_2025/8tqc_41502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqc_41502/08_2025/8tqc_41502.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4357 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 172 5.16 5 C 15113 2.51 5 N 4054 2.21 5 O 4279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23620 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 11147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11147 Classifications: {'peptide': 1400} Link IDs: {'PTRANS': 64, 'TRANS': 1335} Chain breaks: 16 Chain: "D" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 7714 Classifications: {'peptide': 969} Link IDs: {'PTRANS': 60, 'TRANS': 908} Chain breaks: 22 Chain: "A" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2561 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 5 Chain: "B" Number of atoms: 2196 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 2189 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 2189 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 2238 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17555 SG CYS D1896 60.817 46.935 171.164 1.00 34.39 S ATOM 17580 SG CYS D1899 57.145 45.793 170.359 1.00 28.01 S ATOM 13454 SG CYS D1096 59.536 28.023 132.056 1.00 24.58 S ATOM 13467 SG CYS D1098 56.707 25.689 132.971 1.00 33.93 S ATOM 13631 SG CYS D1122 57.243 27.174 129.311 1.00 33.02 S ATOM 13644 SG CYS D1124 55.857 29.240 132.023 1.00 27.93 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AVAL B 163 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 163 " occ=0.50 Time building chain proxies: 4.54, per 1000 atoms: 0.19 Number of scatterers: 23620 At special positions: 0 Unit cell: (95.2389, 141.253, 233.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 172 16.00 O 4279 8.00 N 4054 7.00 C 15113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D1232 " - pdb=" SG CYS D1260 " distance=2.03 Simple disulfide: pdb=" SG CYS D1456 " - pdb=" SG CYS D1669 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C2201 " pdb="ZN ZN C2201 " - pdb=" NE2 HIS C1729 " pdb="ZN ZN C2201 " - pdb=" ND1 HIS C1727 " pdb="ZN ZN C2201 " - pdb=" SG CYS D1899 " pdb="ZN ZN C2201 " - pdb=" SG CYS D1896 " pdb=" ZN D2201 " pdb="ZN ZN D2201 " - pdb=" SG CYS D1096 " pdb="ZN ZN D2201 " - pdb=" SG CYS D1124 " pdb="ZN ZN D2201 " - pdb=" SG CYS D1122 " pdb="ZN ZN D2201 " - pdb=" SG CYS D1098 " Number of angles added : 7 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 14 sheets defined 55.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'C' and resid 37 through 44 removed outlier: 3.546A pdb=" N LYS C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 Processing helix chain 'C' and resid 105 through 108 removed outlier: 4.052A pdb=" N ARG C 108 " --> pdb=" O VAL C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 109 through 121 removed outlier: 3.936A pdb=" N ILE C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.772A pdb=" N LEU C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.891A pdb=" N GLY C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 149 " --> pdb=" O TYR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 171 removed outlier: 3.802A pdb=" N TRP C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 206 removed outlier: 3.624A pdb=" N GLU C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 199 " --> pdb=" O TRP C 195 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 247 removed outlier: 3.811A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.910A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.903A pdb=" N VAL C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 310 removed outlier: 3.618A pdb=" N SER C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.591A pdb=" N MET C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 removed outlier: 3.598A pdb=" N VAL C 359 " --> pdb=" O HIS C 355 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 410 through 437 Processing helix chain 'C' and resid 452 through 465 removed outlier: 3.981A pdb=" N VAL C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 462 " --> pdb=" O HIS C 458 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 removed outlier: 4.197A pdb=" N LEU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 483 " --> pdb=" O SER C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 removed outlier: 4.711A pdb=" N SER C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS C 508 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.684A pdb=" N LEU C 528 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 531 " --> pdb=" O LYS C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.799A pdb=" N LEU C 574 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 570 through 575' Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 587 through 606 removed outlier: 3.691A pdb=" N ILE C 604 " --> pdb=" O PHE C 600 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 605 " --> pdb=" O CYS C 601 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS C 606 " --> pdb=" O GLU C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 624 removed outlier: 3.655A pdb=" N THR C 617 " --> pdb=" O MET C 613 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY C 622 " --> pdb=" O LEU C 618 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 623 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 removed outlier: 3.584A pdb=" N ALA C 735 " --> pdb=" O VAL C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 754 removed outlier: 3.593A pdb=" N LEU C 754 " --> pdb=" O CYS C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 758 removed outlier: 3.633A pdb=" N PHE C 758 " --> pdb=" O VAL C 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 758' Processing helix chain 'C' and resid 761 through 772 removed outlier: 3.956A pdb=" N ASP C 765 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS C 772 " --> pdb=" O ARG C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 784 removed outlier: 3.545A pdb=" N ASP C 777 " --> pdb=" O LYS C 773 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE C 778 " --> pdb=" O ILE C 774 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 779 " --> pdb=" O THR C 775 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 782 " --> pdb=" O ILE C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 791 removed outlier: 3.605A pdb=" N THR C 790 " --> pdb=" O THR C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 813 removed outlier: 3.549A pdb=" N ASP C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 812 " --> pdb=" O GLY C 808 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 813 " --> pdb=" O GLY C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 816 No H-bonds generated for 'chain 'C' and resid 814 through 816' Processing helix chain 'C' and resid 826 through 835 Processing helix chain 'C' and resid 840 through 857 removed outlier: 3.571A pdb=" N VAL C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 851 " --> pdb=" O GLN C 847 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN C 855 " --> pdb=" O ASN C 851 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 856 " --> pdb=" O VAL C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 881 removed outlier: 3.516A pdb=" N ASP C 878 " --> pdb=" O GLN C 874 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 879 " --> pdb=" O PHE C 875 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 884 No H-bonds generated for 'chain 'C' and resid 882 through 884' Processing helix chain 'C' and resid 889 through 905 removed outlier: 3.807A pdb=" N LEU C 897 " --> pdb=" O ALA C 893 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 901 " --> pdb=" O LEU C 897 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 902 " --> pdb=" O ASN C 898 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 905 " --> pdb=" O SER C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 932 removed outlier: 3.628A pdb=" N CYS C 925 " --> pdb=" O SER C 921 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 934 No H-bonds generated for 'chain 'C' and resid 933 through 934' Processing helix chain 'C' and resid 935 through 939 removed outlier: 3.728A pdb=" N ILE C 938 " --> pdb=" O ALA C 935 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 939 " --> pdb=" O CYS C 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 935 through 939' Processing helix chain 'C' and resid 947 through 958 removed outlier: 3.640A pdb=" N VAL C 954 " --> pdb=" O GLY C 950 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL C 955 " --> pdb=" O LEU C 951 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS C 956 " --> pdb=" O CYS C 952 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY C 958 " --> pdb=" O VAL C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 975 Processing helix chain 'C' and resid 977 through 981 removed outlier: 3.547A pdb=" N SER C 981 " --> pdb=" O LEU C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1002 removed outlier: 3.982A pdb=" N PHE C 996 " --> pdb=" O LEU C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1046 removed outlier: 3.968A pdb=" N LYS C1041 " --> pdb=" O THR C1037 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C1042 " --> pdb=" O GLY C1038 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1062 removed outlier: 3.626A pdb=" N VAL C1054 " --> pdb=" O ARG C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.669A pdb=" N VAL C1071 " --> pdb=" O ASP C1067 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C1075 " --> pdb=" O VAL C1071 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C1080 " --> pdb=" O ILE C1076 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C1081 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C1082 " --> pdb=" O CYS C1078 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR C1084 " --> pdb=" O GLU C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1092 removed outlier: 3.533A pdb=" N ALA C1090 " --> pdb=" O SER C1087 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C1091 " --> pdb=" O LEU C1088 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP C1092 " --> pdb=" O SER C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1093 through 1101 removed outlier: 4.972A pdb=" N LEU C1099 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS C1101 " --> pdb=" O LYS C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1116 Processing helix chain 'C' and resid 1124 through 1137 removed outlier: 4.063A pdb=" N LEU C1128 " --> pdb=" O PHE C1124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C1133 " --> pdb=" O ALA C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1150 removed outlier: 4.443A pdb=" N ARG C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1161 removed outlier: 3.586A pdb=" N SER C1154 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C1155 " --> pdb=" O ALA C1151 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C1156 " --> pdb=" O ILE C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1180 removed outlier: 4.035A pdb=" N ALA C1169 " --> pdb=" O SER C1165 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG C1170 " --> pdb=" O GLU C1166 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C1176 " --> pdb=" O THR C1172 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C1177 " --> pdb=" O CYS C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1211 Processing helix chain 'C' and resid 1219 through 1232 removed outlier: 3.620A pdb=" N VAL C1223 " --> pdb=" O ALA C1219 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C1231 " --> pdb=" O VAL C1227 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C1232 " --> pdb=" O PHE C1228 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1289 removed outlier: 4.583A pdb=" N LEU C1283 " --> pdb=" O ALA C1279 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C1284 " --> pdb=" O LYS C1280 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN C1289 " --> pdb=" O SER C1285 " (cutoff:3.500A) Processing helix chain 'C' and resid 1289 through 1303 removed outlier: 3.705A pdb=" N CYS C1296 " --> pdb=" O VAL C1292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C1300 " --> pdb=" O CYS C1296 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS C1301 " --> pdb=" O LEU C1297 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU C1302 " --> pdb=" O LYS C1298 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C1303 " --> pdb=" O SER C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1319 removed outlier: 4.337A pdb=" N GLN C1318 " --> pdb=" O SER C1314 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C1319 " --> pdb=" O ALA C1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1314 through 1319' Processing helix chain 'C' and resid 1320 through 1326 removed outlier: 3.759A pdb=" N TYR C1326 " --> pdb=" O GLN C1322 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1346 removed outlier: 4.176A pdb=" N GLN C1342 " --> pdb=" O ASN C1338 " (cutoff:3.500A) Processing helix chain 'C' and resid 1355 through 1360 removed outlier: 4.387A pdb=" N SER C1360 " --> pdb=" O MET C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1370 removed outlier: 4.234A pdb=" N GLN C1364 " --> pdb=" O SER C1360 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C1365 " --> pdb=" O LEU C1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 1371 through 1375 removed outlier: 3.620A pdb=" N MET C1375 " --> pdb=" O ASN C1372 " (cutoff:3.500A) Processing helix chain 'C' and resid 1379 through 1386 removed outlier: 4.011A pdb=" N THR C1386 " --> pdb=" O ILE C1382 " (cutoff:3.500A) Processing helix chain 'C' and resid 1390 through 1395 Processing helix chain 'C' and resid 1424 through 1427 Processing helix chain 'C' and resid 1428 through 1434 Processing helix chain 'C' and resid 1436 through 1452 removed outlier: 3.728A pdb=" N HIS C1442 " --> pdb=" O SER C1438 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C1449 " --> pdb=" O LYS C1445 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C1450 " --> pdb=" O ALA C1446 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1475 removed outlier: 3.600A pdb=" N ARG C1465 " --> pdb=" O SER C1461 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP C1466 " --> pdb=" O ARG C1462 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C1467 " --> pdb=" O LYS C1463 " (cutoff:3.500A) Processing helix chain 'C' and resid 1479 through 1489 removed outlier: 3.505A pdb=" N VAL C1485 " --> pdb=" O PHE C1481 " (cutoff:3.500A) Processing helix chain 'C' and resid 1496 through 1513 removed outlier: 3.761A pdb=" N LEU C1500 " --> pdb=" O ARG C1496 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C1501 " --> pdb=" O GLU C1497 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C1502 " --> pdb=" O GLY C1498 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS C1508 " --> pdb=" O TYR C1504 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN C1509 " --> pdb=" O SER C1505 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C1511 " --> pdb=" O VAL C1507 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C1512 " --> pdb=" O HIS C1508 " (cutoff:3.500A) Processing helix chain 'C' and resid 1530 through 1543 removed outlier: 3.530A pdb=" N LEU C1535 " --> pdb=" O GLU C1531 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG C1536 " --> pdb=" O ALA C1532 " (cutoff:3.500A) Processing helix chain 'C' and resid 1543 through 1548 Processing helix chain 'C' and resid 1552 through 1567 removed outlier: 3.608A pdb=" N GLU C1556 " --> pdb=" O GLN C1552 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP C1557 " --> pdb=" O GLN C1553 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C1560 " --> pdb=" O GLU C1556 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C1561 " --> pdb=" O TRP C1557 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C1562 " --> pdb=" O ALA C1558 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C1564 " --> pdb=" O LEU C1560 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C1567 " --> pdb=" O GLU C1563 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1595 removed outlier: 3.760A pdb=" N THR C1580 " --> pdb=" O ASN C1576 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C1582 " --> pdb=" O LEU C1578 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C1583 " --> pdb=" O PHE C1579 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET C1585 " --> pdb=" O THR C1581 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C1588 " --> pdb=" O ASP C1584 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C1593 " --> pdb=" O LEU C1589 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C1594 " --> pdb=" O ILE C1590 " (cutoff:3.500A) Processing helix chain 'C' and resid 1610 through 1622 removed outlier: 3.750A pdb=" N LYS C1619 " --> pdb=" O ASN C1615 " (cutoff:3.500A) Processing helix chain 'C' and resid 1631 through 1639 removed outlier: 3.876A pdb=" N VAL C1635 " --> pdb=" O SER C1631 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C1638 " --> pdb=" O LYS C1634 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C1639 " --> pdb=" O VAL C1635 " (cutoff:3.500A) Processing helix chain 'C' and resid 1715 through 1724 removed outlier: 3.507A pdb=" N GLN C1721 " --> pdb=" O GLY C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1725 through 1727 No H-bonds generated for 'chain 'C' and resid 1725 through 1727' Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.533A pdb=" N ALA D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 112 through 134 removed outlier: 3.778A pdb=" N LYS D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 200 removed outlier: 3.542A pdb=" N ILE D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 197 " --> pdb=" O HIS D 193 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.911A pdb=" N GLN D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 349 Processing helix chain 'D' and resid 1071 through 1078 Processing helix chain 'D' and resid 1087 through 1092 removed outlier: 3.580A pdb=" N PHE D1090 " --> pdb=" O ASP D1087 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER D1092 " --> pdb=" O ASN D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1110 Processing helix chain 'D' and resid 1127 through 1135 removed outlier: 3.817A pdb=" N LYS D1133 " --> pdb=" O VAL D1129 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D1134 " --> pdb=" O MET D1130 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1150 removed outlier: 3.722A pdb=" N ASP D1147 " --> pdb=" O GLU D1143 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D1148 " --> pdb=" O ASP D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1155 through 1168 removed outlier: 3.619A pdb=" N ALA D1159 " --> pdb=" O CYS D1155 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D1167 " --> pdb=" O PHE D1163 " (cutoff:3.500A) Processing helix chain 'D' and resid 1185 through 1196 removed outlier: 3.515A pdb=" N ILE D1189 " --> pdb=" O SER D1185 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS D1196 " --> pdb=" O LEU D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1222 through 1244 removed outlier: 3.822A pdb=" N TYR D1233 " --> pdb=" O CYS D1229 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D1234 " --> pdb=" O ASN D1230 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D1242 " --> pdb=" O HIS D1238 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET D1243 " --> pdb=" O GLY D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1260 removed outlier: 3.571A pdb=" N SER D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1262 through 1267 removed outlier: 3.748A pdb=" N SER D1265 " --> pdb=" O HIS D1262 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1295 removed outlier: 3.513A pdb=" N GLN D1286 " --> pdb=" O LEU D1282 " (cutoff:3.500A) Proline residue: D1287 - end of helix removed outlier: 3.505A pdb=" N ILE D1293 " --> pdb=" O LEU D1289 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1316 Processing helix chain 'D' and resid 1348 through 1355 removed outlier: 3.561A pdb=" N LEU D1352 " --> pdb=" O PRO D1349 " (cutoff:3.500A) Proline residue: D1353 - end of helix Processing helix chain 'D' and resid 1378 through 1399 removed outlier: 3.615A pdb=" N GLY D1384 " --> pdb=" O ALA D1380 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D1387 " --> pdb=" O ASN D1383 " (cutoff:3.500A) Processing helix chain 'D' and resid 1448 through 1465 removed outlier: 4.001A pdb=" N VAL D1455 " --> pdb=" O LEU D1451 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N CYS D1456 " --> pdb=" O TYR D1452 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D1460 " --> pdb=" O CYS D1456 " (cutoff:3.500A) Proline residue: D1462 - end of helix removed outlier: 3.547A pdb=" N ALA D1465 " --> pdb=" O GLY D1461 " (cutoff:3.500A) Processing helix chain 'D' and resid 1619 through 1623 removed outlier: 3.692A pdb=" N VAL D1622 " --> pdb=" O ARG D1619 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D1623 " --> pdb=" O ASP D1620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1619 through 1623' Processing helix chain 'D' and resid 1663 through 1676 removed outlier: 4.616A pdb=" N CYS D1669 " --> pdb=" O GLY D1665 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE D1670 " --> pdb=" O LEU D1666 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D1675 " --> pdb=" O LEU D1671 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR D1676 " --> pdb=" O GLU D1672 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1683 Processing helix chain 'D' and resid 1692 through 1697 removed outlier: 3.518A pdb=" N LEU D1696 " --> pdb=" O CYS D1692 " (cutoff:3.500A) Processing helix chain 'D' and resid 1709 through 1721 Processing helix chain 'D' and resid 1739 through 1749 Processing helix chain 'D' and resid 1836 through 1852 Processing helix chain 'D' and resid 1871 through 1880 Processing helix chain 'D' and resid 1881 through 1896 removed outlier: 3.702A pdb=" N SER D1889 " --> pdb=" O LEU D1885 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D1890 " --> pdb=" O GLN D1886 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D1895 " --> pdb=" O ARG D1891 " (cutoff:3.500A) Processing helix chain 'D' and resid 1896 through 1902 removed outlier: 3.599A pdb=" N GLY D1900 " --> pdb=" O CYS D1896 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D1901 " --> pdb=" O ARG D1897 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D1902 " --> pdb=" O MET D1898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1896 through 1902' Processing helix chain 'D' and resid 1950 through 1955 removed outlier: 3.573A pdb=" N ASP D1954 " --> pdb=" O ASN D1950 " (cutoff:3.500A) Processing helix chain 'D' and resid 2078 through 2083 Processing helix chain 'D' and resid 2085 through 2090 removed outlier: 3.840A pdb=" N TYR D2090 " --> pdb=" O GLN D2087 " (cutoff:3.500A) Processing helix chain 'D' and resid 2119 through 2123 Processing helix chain 'D' and resid 2125 through 2142 removed outlier: 3.746A pdb=" N VAL D2129 " --> pdb=" O GLN D2125 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D2130 " --> pdb=" O THR D2126 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D2142 " --> pdb=" O ASN D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2143 through 2145 No H-bonds generated for 'chain 'D' and resid 2143 through 2145' Processing helix chain 'D' and resid 2157 through 2174 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.629A pdb=" N VAL A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.750A pdb=" N MET A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.714A pdb=" N HIS A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.950A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.600A pdb=" N ALA A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 58 through 75 removed outlier: 3.913A pdb=" N ILE B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 98 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.512A pdb=" N PHE B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 209 removed outlier: 3.535A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 removed outlier: 3.792A pdb=" N GLU B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.620A pdb=" N GLU B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.880A pdb=" N TRP C 103 " --> pdb=" O VAL C 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 1646 through 1650 removed outlier: 3.509A pdb=" N THR C1681 " --> pdb=" O THR C1650 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 15 through 16 removed outlier: 4.333A pdb=" N HIS D 16 " --> pdb=" O MET D1926 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D1926 " --> pdb=" O HIS D 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 24 removed outlier: 6.243A pdb=" N LEU D 19 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL D 178 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N CYS D 21 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR D 176 " --> pdb=" O CYS D 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 23 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 66 through 71 removed outlier: 3.872A pdb=" N GLU D 103 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL D 34 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU D 101 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 139 Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 188 Processing sheet with id=AA8, first strand: chain 'D' and resid 204 through 208 removed outlier: 4.593A pdb=" N PHE D 204 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 218 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU D 268 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN D 220 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA D 266 " --> pdb=" O GLN D 220 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE D 222 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU D 264 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1345 through 1347 removed outlier: 3.766A pdb=" N ILE D1765 " --> pdb=" O LEU D1337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 1415 through 1418 removed outlier: 7.583A pdb=" N MET D1416 " --> pdb=" O TYR D1371 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL D1373 " --> pdb=" O MET D1416 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL D1418 " --> pdb=" O VAL D1373 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N CYS D1375 " --> pdb=" O VAL D1418 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA D1370 " --> pdb=" O VAL D1640 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR D1642 " --> pdb=" O ALA D1370 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D1372 " --> pdb=" O TYR D1642 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D1644 " --> pdb=" O VAL D1372 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D1374 " --> pdb=" O ILE D1644 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D1639 " --> pdb=" O SER D1686 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN D1688 " --> pdb=" O ILE D1639 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL D1641 " --> pdb=" O GLN D1688 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE D1690 " --> pdb=" O VAL D1641 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE D1643 " --> pdb=" O ILE D1690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 1815 through 1821 removed outlier: 6.426A pdb=" N ASN D1788 " --> pdb=" O ARG D1859 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D1861 " --> pdb=" O ASN D1788 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D1790 " --> pdb=" O VAL D1861 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY D1863 " --> pdb=" O LEU D1790 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D1792 " --> pdb=" O GLY D1863 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL D1915 " --> pdb=" O VAL D1860 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE D1862 " --> pdb=" O VAL D1915 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N MET D1917 " --> pdb=" O ILE D1862 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG D1864 " --> pdb=" O MET D1917 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D1961 " --> pdb=" O TYR D2067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 26 through 29 removed outlier: 6.583A pdb=" N LYS A 26 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS A 37 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 93 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS A 92 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 86 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP A 94 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL A 84 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 96 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.430A pdb=" N MET A 160 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 168 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 147 through 148 933 hydrogen bonds defined for protein. 2677 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: 3.51 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7637 1.34 - 1.46: 5406 1.46 - 1.58: 10850 1.58 - 1.70: 0 1.70 - 1.82: 244 Bond restraints: 24137 Sorted by residual: bond pdb=" C GLN C1479 " pdb=" N PRO C1480 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.12e+00 bond pdb=" N ASP C 963 " pdb=" CA ASP C 963 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.00e+00 bond pdb=" N LEU D2156 " pdb=" CA LEU D2156 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.79e+00 bond pdb=" C GLY C 20 " pdb=" N PRO C 21 " ideal model delta sigma weight residual 1.331 1.346 -0.014 8.70e-03 1.32e+04 2.71e+00 bond pdb=" CA ARG D1367 " pdb=" C ARG D1367 " ideal model delta sigma weight residual 1.523 1.539 -0.017 1.23e-02 6.61e+03 1.82e+00 ... (remaining 24132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 32004 2.05 - 4.11: 537 4.11 - 6.16: 85 6.16 - 8.21: 29 8.21 - 10.27: 8 Bond angle restraints: 32663 Sorted by residual: angle pdb=" C GLY C 20 " pdb=" N PRO C 21 " pdb=" CA PRO C 21 " ideal model delta sigma weight residual 119.66 125.74 -6.08 7.30e-01 1.88e+00 6.94e+01 angle pdb=" C LEU A 340 " pdb=" N PRO A 341 " pdb=" CA PRO A 341 " ideal model delta sigma weight residual 119.89 127.08 -7.19 1.02e+00 9.61e-01 4.97e+01 angle pdb=" N SER D1365 " pdb=" CA SER D1365 " pdb=" C SER D1365 " ideal model delta sigma weight residual 111.74 119.84 -8.10 1.35e+00 5.49e-01 3.60e+01 angle pdb=" N GLN D1366 " pdb=" CA GLN D1366 " pdb=" C GLN D1366 " ideal model delta sigma weight residual 111.39 119.05 -7.66 1.38e+00 5.25e-01 3.08e+01 angle pdb=" N LYS D 347 " pdb=" CA LYS D 347 " pdb=" C LYS D 347 " ideal model delta sigma weight residual 111.28 116.71 -5.43 1.09e+00 8.42e-01 2.49e+01 ... (remaining 32658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 12984 17.59 - 35.17: 1336 35.17 - 52.76: 241 52.76 - 70.34: 31 70.34 - 87.93: 17 Dihedral angle restraints: 14609 sinusoidal: 5989 harmonic: 8620 Sorted by residual: dihedral pdb=" CB CYS D1456 " pdb=" SG CYS D1456 " pdb=" SG CYS D1669 " pdb=" CB CYS D1669 " ideal model delta sinusoidal sigma weight residual 93.00 140.95 -47.95 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" N LEU D2156 " pdb=" C LEU D2156 " pdb=" CA LEU D2156 " pdb=" CB LEU D2156 " ideal model delta harmonic sigma weight residual 122.80 132.51 -9.71 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" CA ASP C 942 " pdb=" C ASP C 942 " pdb=" N GLN C 943 " pdb=" CA GLN C 943 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 14606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3219 0.065 - 0.131: 407 0.131 - 0.196: 24 0.196 - 0.262: 5 0.262 - 0.327: 3 Chirality restraints: 3658 Sorted by residual: chirality pdb=" CA SER D1365 " pdb=" N SER D1365 " pdb=" C SER D1365 " pdb=" CB SER D1365 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA LEU D2156 " pdb=" N LEU D2156 " pdb=" C LEU D2156 " pdb=" CB LEU D2156 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ASN C1575 " pdb=" N ASN C1575 " pdb=" C ASN C1575 " pdb=" CB ASN C1575 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 3655 not shown) Planarity restraints: 4152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1479 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO C1480 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C1480 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1480 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1009 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO C1010 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C1010 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1010 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C1639 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO C1640 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C1640 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1640 " 0.031 5.00e-02 4.00e+02 ... (remaining 4149 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2524 2.75 - 3.29: 23639 3.29 - 3.82: 36804 3.82 - 4.36: 42976 4.36 - 4.90: 72669 Nonbonded interactions: 178612 Sorted by model distance: nonbonded pdb=" OG SER C1686 " pdb=" OD2 ASP C1689 " model vdw 2.210 3.040 nonbonded pdb=" O SER D1855 " pdb=" OG SER D1855 " model vdw 2.248 3.040 nonbonded pdb=" O THR C1355 " pdb=" OG SER C1359 " model vdw 2.251 3.040 nonbonded pdb=" O ASN D2138 " pdb=" OG SER D2141 " model vdw 2.260 3.040 nonbonded pdb=" NZ LYS D2073 " pdb=" O ARG D2153 " model vdw 2.266 3.120 ... (remaining 178607 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 : 0.003 0.053 24147 Z= 0.139 Angle : 0.670 10.267 32674 Z= 0.358 Chirality : 0.045 0.327 3658 Planarity : 0.004 0.062 4152 Dihedral : 14.269 87.925 8975 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 0.38 % Allowed : 1.03 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 2853 helix: -0.63 (0.14), residues: 1271 sheet: 0.62 (0.37), residues: 189 loop : -0.66 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 209 TYR 0.033 0.001 TYR C1278 PHE 0.017 0.001 PHE D1242 TRP 0.025 0.001 TRP C1426 HIS 0.005 0.001 HIS C 520 Details of bonding type rmsd covalent geometry : bond 0.00276 (24137) covalent geometry : angle 0.66690 (32663) SS BOND : bond 0.00088 ( 2) SS BOND : angle 1.85031 ( 4) hydrogen bonds : bond 0.26374 ( 933) hydrogen bonds : angle 7.50546 ( 2677) metal coordination : bond 0.00484 ( 8) metal coordination : angle 4.31124 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 248 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7368 (mm) REVERT: C 243 MET cc_start: 0.7044 (mtm) cc_final: 0.6703 (mtm) REVERT: C 403 ASN cc_start: 0.8544 (p0) cc_final: 0.8193 (p0) REVERT: C 523 MET cc_start: -0.0738 (mmm) cc_final: -0.2332 (ptm) REVERT: C 1059 MET cc_start: 0.1961 (tpt) cc_final: 0.1705 (ptt) REVERT: C 1360 SER cc_start: 0.5655 (p) cc_final: 0.5354 (t) REVERT: C 1372 ASN cc_start: 0.5333 (t0) cc_final: 0.4976 (t0) REVERT: C 1375 MET cc_start: 0.4266 (mmp) cc_final: 0.3407 (tpt) REVERT: C 1540 VAL cc_start: 0.7849 (m) cc_final: 0.7636 (t) REVERT: D 1316 MET cc_start: 0.7337 (ptp) cc_final: 0.7066 (ptp) REVERT: A 1 MET cc_start: 0.5655 (mmm) cc_final: 0.4990 (tpt) outliers start: 10 outliers final: 0 residues processed: 256 average time/residue: 0.1547 time to fit residues: 61.3997 Evaluate side-chains 133 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN C 577 GLN C 595 ASN C 783 ASN ** C1575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1615 ASN ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN D1383 ASN D1852 GLN D1970 GLN B 13 GLN B 54 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.150665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.122796 restraints weight = 90231.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116199 restraints weight = 105934.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.114159 restraints weight = 60015.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113307 restraints weight = 63947.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113823 restraints weight = 47145.870| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24147 Z= 0.160 Angle : 0.648 13.208 32674 Z= 0.322 Chirality : 0.043 0.144 3658 Planarity : 0.005 0.059 4152 Dihedral : 4.264 21.245 3156 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 0.72 % Allowed : 8.35 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 2853 helix: -0.12 (0.14), residues: 1364 sheet: 0.64 (0.34), residues: 201 loop : -0.71 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1267 TYR 0.022 0.001 TYR C1613 PHE 0.017 0.001 PHE D1163 TRP 0.015 0.001 TRP C 257 HIS 0.008 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00370 (24137) covalent geometry : angle 0.64451 (32663) SS BOND : bond 0.00024 ( 2) SS BOND : angle 1.66021 ( 4) hydrogen bonds : bond 0.05122 ( 933) hydrogen bonds : angle 4.88409 ( 2677) metal coordination : bond 0.00867 ( 8) metal coordination : angle 4.54661 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: C 428 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 523 MET cc_start: -0.1456 (mmm) cc_final: -0.2686 (ptm) REVERT: C 613 MET cc_start: 0.1028 (mtp) cc_final: -0.0314 (tpt) REVERT: C 1059 MET cc_start: 0.2429 (tpt) cc_final: 0.1614 (ptt) REVERT: C 1375 MET cc_start: 0.3843 (mmp) cc_final: 0.2663 (tpt) REVERT: C 1486 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8633 (mt) REVERT: D 1917 MET cc_start: 0.7721 (ttm) cc_final: 0.7348 (ttm) REVERT: A 61 MET cc_start: 0.8053 (mmm) cc_final: 0.7848 (mmt) REVERT: B 22 LEU cc_start: 0.8807 (mt) cc_final: 0.8361 (tp) REVERT: B 257 MET cc_start: 0.6586 (mtp) cc_final: 0.6270 (ttm) outliers start: 19 outliers final: 10 residues processed: 156 average time/residue: 0.1222 time to fit residues: 32.4281 Evaluate side-chains 132 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 1376 ASN Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1243 MET Chi-restraints excluded: chain D residue 1356 GLU Chi-restraints excluded: chain D residue 1895 MET Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 1 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 82 optimal weight: 40.0000 chunk 63 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 ASN ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.149202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.119717 restraints weight = 81215.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116337 restraints weight = 112044.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113497 restraints weight = 67634.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112624 restraints weight = 62490.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113316 restraints weight = 51233.520| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24147 Z= 0.155 Angle : 0.589 12.799 32674 Z= 0.290 Chirality : 0.042 0.149 3658 Planarity : 0.004 0.061 4152 Dihedral : 4.117 18.727 3154 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.21 % Rotamer: Outliers : 1.03 % Allowed : 10.97 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2853 helix: 0.16 (0.14), residues: 1377 sheet: 0.12 (0.33), residues: 223 loop : -0.70 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 119 TYR 0.012 0.001 TYR C 235 PHE 0.019 0.001 PHE D1163 TRP 0.016 0.001 TRP D 345 HIS 0.006 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00362 (24137) covalent geometry : angle 0.58557 (32663) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.89184 ( 4) hydrogen bonds : bond 0.04445 ( 933) hydrogen bonds : angle 4.49284 ( 2677) metal coordination : bond 0.00934 ( 8) metal coordination : angle 4.16948 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: C 523 MET cc_start: -0.1548 (mmm) cc_final: -0.2343 (ptm) REVERT: C 613 MET cc_start: 0.0584 (mtp) cc_final: -0.0813 (tpt) REVERT: C 1059 MET cc_start: 0.2439 (tpt) cc_final: 0.1576 (ptp) REVERT: C 1346 ARG cc_start: 0.6578 (pmt-80) cc_final: 0.6229 (tpp80) REVERT: C 1367 ILE cc_start: 0.2948 (mm) cc_final: 0.2529 (pt) REVERT: C 1375 MET cc_start: 0.3540 (mmp) cc_final: 0.2687 (tpt) REVERT: C 1486 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8608 (mt) REVERT: A 1 MET cc_start: 0.5791 (mmm) cc_final: 0.5583 (tpt) REVERT: B 22 LEU cc_start: 0.8822 (mt) cc_final: 0.8356 (tp) outliers start: 26 outliers final: 14 residues processed: 150 average time/residue: 0.1390 time to fit residues: 34.7738 Evaluate side-chains 135 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1243 MET Chi-restraints excluded: chain D residue 1356 GLU Chi-restraints excluded: chain D residue 1808 THR Chi-restraints excluded: chain D residue 1814 LEU Chi-restraints excluded: chain D residue 1951 THR Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 139 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 189 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 80 optimal weight: 0.0070 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.150657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.123205 restraints weight = 74592.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113647 restraints weight = 93520.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112835 restraints weight = 65501.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.110667 restraints weight = 54837.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111020 restraints weight = 55178.019| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24147 Z= 0.101 Angle : 0.533 10.265 32674 Z= 0.260 Chirality : 0.040 0.147 3658 Planarity : 0.004 0.067 4152 Dihedral : 3.847 18.444 3154 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 0.99 % Allowed : 12.45 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2853 helix: 0.49 (0.14), residues: 1365 sheet: 0.25 (0.34), residues: 216 loop : -0.58 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1400 TYR 0.011 0.001 TYR C 235 PHE 0.020 0.001 PHE D1163 TRP 0.011 0.001 TRP C 103 HIS 0.005 0.001 HIS D2103 Details of bonding type rmsd covalent geometry : bond 0.00220 (24137) covalent geometry : angle 0.53066 (32663) SS BOND : bond 0.00095 ( 2) SS BOND : angle 1.51386 ( 4) hydrogen bonds : bond 0.03459 ( 933) hydrogen bonds : angle 4.16239 ( 2677) metal coordination : bond 0.00345 ( 8) metal coordination : angle 3.35289 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: C 523 MET cc_start: -0.1003 (mmm) cc_final: -0.1908 (ptm) REVERT: C 613 MET cc_start: 0.0894 (mtp) cc_final: -0.0373 (tpt) REVERT: C 1059 MET cc_start: 0.2163 (tpt) cc_final: 0.1358 (ptp) REVERT: C 1346 ARG cc_start: 0.6847 (pmt-80) cc_final: 0.6392 (tpp80) REVERT: C 1367 ILE cc_start: 0.3303 (mm) cc_final: 0.2800 (pt) REVERT: C 1375 MET cc_start: 0.3797 (mmp) cc_final: 0.2804 (tpt) REVERT: C 1486 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 1671 LEU cc_start: 0.8107 (mm) cc_final: 0.7466 (mt) REVERT: A 1 MET cc_start: 0.5891 (mmm) cc_final: 0.5691 (tpt) REVERT: A 61 MET cc_start: 0.8010 (mmm) cc_final: 0.7766 (mmt) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.1257 time to fit residues: 33.8684 Evaluate side-chains 143 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1570 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1243 MET Chi-restraints excluded: chain D residue 1356 GLU Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1955 THR Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 252 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 121 optimal weight: 9.9990 chunk 98 optimal weight: 0.0170 chunk 18 optimal weight: 10.0000 chunk 198 optimal weight: 0.0870 chunk 146 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 129 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.123117 restraints weight = 84854.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115629 restraints weight = 103474.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113506 restraints weight = 63061.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113241 restraints weight = 58050.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113636 restraints weight = 44868.058| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24147 Z= 0.099 Angle : 0.529 9.583 32674 Z= 0.257 Chirality : 0.040 0.175 3658 Planarity : 0.004 0.067 4152 Dihedral : 3.720 17.793 3154 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 1.40 % Allowed : 13.14 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 2853 helix: 0.64 (0.14), residues: 1368 sheet: 0.28 (0.34), residues: 216 loop : -0.52 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1400 TYR 0.008 0.001 TYR C1613 PHE 0.021 0.001 PHE D1163 TRP 0.010 0.001 TRP C 103 HIS 0.004 0.001 HIS D2103 Details of bonding type rmsd covalent geometry : bond 0.00223 (24137) covalent geometry : angle 0.52661 (32663) SS BOND : bond 0.00078 ( 2) SS BOND : angle 1.48035 ( 4) hydrogen bonds : bond 0.03287 ( 933) hydrogen bonds : angle 4.02749 ( 2677) metal coordination : bond 0.00348 ( 8) metal coordination : angle 3.19737 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: C 523 MET cc_start: -0.1254 (mmm) cc_final: -0.1954 (ptm) REVERT: C 613 MET cc_start: 0.0764 (mtp) cc_final: -0.0638 (tpt) REVERT: C 870 VAL cc_start: -0.0212 (OUTLIER) cc_final: -0.0607 (p) REVERT: C 1059 MET cc_start: 0.2186 (tpt) cc_final: 0.1382 (ptp) REVERT: C 1346 ARG cc_start: 0.6860 (pmt-80) cc_final: 0.6359 (tpp80) REVERT: C 1367 ILE cc_start: 0.3184 (mm) cc_final: 0.2683 (pt) REVERT: C 1375 MET cc_start: 0.3604 (mmp) cc_final: 0.2788 (tpt) REVERT: C 1486 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8602 (mt) REVERT: D 1671 LEU cc_start: 0.8101 (mm) cc_final: 0.7467 (mt) REVERT: A 1 MET cc_start: 0.5867 (mmm) cc_final: 0.5627 (tpt) REVERT: A 61 MET cc_start: 0.7974 (mmm) cc_final: 0.7718 (mmt) outliers start: 36 outliers final: 24 residues processed: 162 average time/residue: 0.1369 time to fit residues: 37.3098 Evaluate side-chains 154 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1109 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1238 HIS Chi-restraints excluded: chain D residue 1243 MET Chi-restraints excluded: chain D residue 1356 GLU Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 252 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 194 optimal weight: 0.1980 chunk 120 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.149060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.118453 restraints weight = 70151.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111553 restraints weight = 93462.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109117 restraints weight = 61862.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107157 restraints weight = 63409.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107889 restraints weight = 54202.046| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24147 Z= 0.136 Angle : 0.556 9.965 32674 Z= 0.270 Chirality : 0.041 0.148 3658 Planarity : 0.004 0.066 4152 Dihedral : 3.822 18.777 3154 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 1.56 % Allowed : 13.97 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2853 helix: 0.60 (0.14), residues: 1381 sheet: 0.19 (0.34), residues: 218 loop : -0.54 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1536 TYR 0.014 0.001 TYR C 235 PHE 0.021 0.001 PHE D1163 TRP 0.018 0.001 TRP D 345 HIS 0.004 0.001 HIS D2103 Details of bonding type rmsd covalent geometry : bond 0.00325 (24137) covalent geometry : angle 0.55280 (32663) SS BOND : bond 0.00192 ( 2) SS BOND : angle 1.78624 ( 4) hydrogen bonds : bond 0.03433 ( 933) hydrogen bonds : angle 4.06981 ( 2677) metal coordination : bond 0.00645 ( 8) metal coordination : angle 3.68591 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7835 (mttt) cc_final: 0.7553 (mmtt) REVERT: C 523 MET cc_start: -0.1142 (mmm) cc_final: -0.1919 (ptm) REVERT: C 613 MET cc_start: 0.0669 (mtp) cc_final: -0.0620 (tpt) REVERT: C 870 VAL cc_start: 0.0381 (OUTLIER) cc_final: -0.0060 (p) REVERT: C 1059 MET cc_start: 0.2056 (tpt) cc_final: 0.1158 (ptp) REVERT: C 1346 ARG cc_start: 0.6676 (pmt-80) cc_final: 0.6219 (tpp80) REVERT: C 1367 ILE cc_start: 0.3098 (mm) cc_final: 0.2512 (pt) REVERT: C 1375 MET cc_start: 0.3519 (mmp) cc_final: 0.2768 (tpt) REVERT: C 1486 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 224 MET cc_start: 0.6298 (pmm) cc_final: 0.4538 (ptt) REVERT: D 1281 MET cc_start: 0.7922 (tpp) cc_final: 0.7714 (tpp) outliers start: 40 outliers final: 30 residues processed: 163 average time/residue: 0.1322 time to fit residues: 36.7408 Evaluate side-chains 157 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain C residue 1570 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1109 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1238 HIS Chi-restraints excluded: chain D residue 1243 MET Chi-restraints excluded: chain D residue 1356 GLU Chi-restraints excluded: chain D residue 1681 ILE Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1814 LEU Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1955 THR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2099 SER Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 252 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 55 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.148000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117585 restraints weight = 74415.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.109341 restraints weight = 96750.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108011 restraints weight = 66145.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105827 restraints weight = 62554.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106305 restraints weight = 51618.848| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24147 Z= 0.157 Angle : 0.582 10.881 32674 Z= 0.285 Chirality : 0.042 0.183 3658 Planarity : 0.004 0.065 4152 Dihedral : 3.994 19.055 3154 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 1.71 % Allowed : 14.65 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2853 helix: 0.59 (0.14), residues: 1381 sheet: 0.06 (0.34), residues: 223 loop : -0.64 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1400 TYR 0.013 0.001 TYR B 184 PHE 0.021 0.001 PHE D1163 TRP 0.023 0.001 TRP D 345 HIS 0.004 0.001 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00374 (24137) covalent geometry : angle 0.57816 (32663) SS BOND : bond 0.00203 ( 2) SS BOND : angle 1.95993 ( 4) hydrogen bonds : bond 0.03597 ( 933) hydrogen bonds : angle 4.13434 ( 2677) metal coordination : bond 0.00822 ( 8) metal coordination : angle 4.22895 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7898 (mttt) cc_final: 0.7652 (mmtt) REVERT: C 523 MET cc_start: -0.1018 (mmm) cc_final: -0.1654 (ptm) REVERT: C 613 MET cc_start: 0.0687 (mtp) cc_final: -0.0591 (tpt) REVERT: C 870 VAL cc_start: 0.0482 (OUTLIER) cc_final: 0.0039 (p) REVERT: C 942 ASP cc_start: 0.3385 (p0) cc_final: 0.2513 (t0) REVERT: C 1059 MET cc_start: 0.2060 (tpt) cc_final: 0.1303 (ptp) REVERT: C 1346 ARG cc_start: 0.6707 (pmt-80) cc_final: 0.6227 (tpp80) REVERT: C 1367 ILE cc_start: 0.3096 (mm) cc_final: 0.2428 (pt) REVERT: C 1375 MET cc_start: 0.3679 (mmp) cc_final: 0.2987 (tpt) REVERT: C 1486 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8634 (mt) REVERT: D 224 MET cc_start: 0.6213 (pmm) cc_final: 0.5062 (ptt) REVERT: A 1 MET cc_start: 0.6058 (mmm) cc_final: 0.5856 (tpt) outliers start: 44 outliers final: 33 residues processed: 160 average time/residue: 0.1226 time to fit residues: 33.5513 Evaluate side-chains 158 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain C residue 1570 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1109 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1356 GLU Chi-restraints excluded: chain D residue 1681 ILE Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1814 LEU Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1951 THR Chi-restraints excluded: chain D residue 1955 THR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2099 SER Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 252 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 172 optimal weight: 0.0770 chunk 119 optimal weight: 0.0570 chunk 251 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109243 restraints weight = 62387.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105723 restraints weight = 46424.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105728 restraints weight = 45053.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106199 restraints weight = 43035.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106324 restraints weight = 36867.213| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24147 Z= 0.113 Angle : 0.541 9.953 32674 Z= 0.263 Chirality : 0.040 0.173 3658 Planarity : 0.004 0.063 4152 Dihedral : 3.831 17.734 3154 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.56 % Allowed : 15.00 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2853 helix: 0.66 (0.14), residues: 1395 sheet: 0.17 (0.34), residues: 216 loop : -0.62 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1400 TYR 0.013 0.001 TYR D 240 PHE 0.023 0.001 PHE D1163 TRP 0.020 0.001 TRP D 345 HIS 0.005 0.001 HIS D2103 Details of bonding type rmsd covalent geometry : bond 0.00267 (24137) covalent geometry : angle 0.53841 (32663) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.72955 ( 4) hydrogen bonds : bond 0.03233 ( 933) hydrogen bonds : angle 3.97791 ( 2677) metal coordination : bond 0.00548 ( 8) metal coordination : angle 3.68014 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7901 (mttt) cc_final: 0.7661 (mmtt) REVERT: C 523 MET cc_start: -0.1095 (mmm) cc_final: -0.1608 (ptm) REVERT: C 613 MET cc_start: 0.0514 (mtp) cc_final: -0.0709 (tpt) REVERT: C 870 VAL cc_start: 0.0668 (OUTLIER) cc_final: 0.0291 (p) REVERT: C 942 ASP cc_start: 0.3362 (p0) cc_final: 0.2469 (t0) REVERT: C 1059 MET cc_start: 0.1939 (tpt) cc_final: 0.1224 (ptp) REVERT: C 1346 ARG cc_start: 0.6725 (pmt-80) cc_final: 0.6222 (tpp80) REVERT: C 1367 ILE cc_start: 0.3037 (mm) cc_final: 0.2421 (pt) REVERT: C 1375 MET cc_start: 0.3722 (mmp) cc_final: 0.2994 (tpt) REVERT: C 1486 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 1499 LEU cc_start: 0.7657 (pt) cc_final: 0.7411 (mp) REVERT: D 224 MET cc_start: 0.6274 (pmm) cc_final: 0.5227 (ptt) REVERT: B 257 MET cc_start: 0.7170 (mtp) cc_final: 0.6630 (ttp) outliers start: 40 outliers final: 32 residues processed: 155 average time/residue: 0.1250 time to fit residues: 32.5039 Evaluate side-chains 157 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1528 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain C residue 1570 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1109 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1238 HIS Chi-restraints excluded: chain D residue 1671 LEU Chi-restraints excluded: chain D residue 1681 ILE Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1814 LEU Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1951 THR Chi-restraints excluded: chain D residue 1955 THR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2099 SER Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 252 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 152 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1538 ASN ** C1644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.153074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126293 restraints weight = 84292.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.117306 restraints weight = 98246.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.117323 restraints weight = 61112.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115466 restraints weight = 53365.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115798 restraints weight = 44477.136| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24147 Z= 0.103 Angle : 0.540 11.582 32674 Z= 0.262 Chirality : 0.040 0.303 3658 Planarity : 0.004 0.061 4152 Dihedral : 3.759 17.321 3154 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 1.44 % Allowed : 15.26 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.16), residues: 2853 helix: 0.73 (0.14), residues: 1389 sheet: 0.21 (0.34), residues: 216 loop : -0.58 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1400 TYR 0.013 0.001 TYR C 235 PHE 0.024 0.001 PHE D1163 TRP 0.019 0.001 TRP D 345 HIS 0.008 0.001 HIS D1238 Details of bonding type rmsd covalent geometry : bond 0.00239 (24137) covalent geometry : angle 0.53696 (32663) SS BOND : bond 0.00160 ( 2) SS BOND : angle 1.76063 ( 4) hydrogen bonds : bond 0.03150 ( 933) hydrogen bonds : angle 3.92855 ( 2677) metal coordination : bond 0.00437 ( 8) metal coordination : angle 3.57480 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.697 Fit side-chains REVERT: C 523 MET cc_start: -0.1188 (mmm) cc_final: -0.1625 (ptm) REVERT: C 613 MET cc_start: 0.0437 (mtp) cc_final: -0.0806 (tpt) REVERT: C 870 VAL cc_start: 0.0277 (OUTLIER) cc_final: -0.0108 (p) REVERT: C 942 ASP cc_start: 0.3444 (p0) cc_final: 0.2541 (t0) REVERT: C 1059 MET cc_start: 0.2005 (tpt) cc_final: 0.1264 (ptp) REVERT: C 1346 ARG cc_start: 0.6655 (pmt-80) cc_final: 0.6218 (tpp80) REVERT: C 1367 ILE cc_start: 0.3038 (mm) cc_final: 0.2420 (pt) REVERT: C 1375 MET cc_start: 0.3512 (mmp) cc_final: 0.2809 (tpt) REVERT: C 1486 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8642 (mt) REVERT: C 1499 LEU cc_start: 0.7492 (pt) cc_final: 0.7288 (mp) REVERT: D 224 MET cc_start: 0.6240 (pmm) cc_final: 0.5292 (ptt) REVERT: D 2095 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7282 (m-80) outliers start: 37 outliers final: 31 residues processed: 154 average time/residue: 0.1257 time to fit residues: 32.9794 Evaluate side-chains 156 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1366 MET Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain C residue 1570 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1109 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1232 CYS Chi-restraints excluded: chain D residue 1671 LEU Chi-restraints excluded: chain D residue 1681 ILE Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1814 LEU Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1951 THR Chi-restraints excluded: chain D residue 1955 THR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2095 PHE Chi-restraints excluded: chain D residue 2099 SER Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 79 optimal weight: 0.1980 chunk 128 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 222 optimal weight: 0.5980 chunk 174 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 254 optimal weight: 0.0060 chunk 270 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1621 GLN ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.153290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.126439 restraints weight = 96738.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119247 restraints weight = 107471.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.119525 restraints weight = 60266.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.117867 restraints weight = 55507.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.118417 restraints weight = 38995.805| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 24147 Z= 0.100 Angle : 0.532 10.403 32674 Z= 0.257 Chirality : 0.040 0.293 3658 Planarity : 0.004 0.060 4152 Dihedral : 3.668 17.720 3154 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 1.33 % Allowed : 15.38 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.16), residues: 2853 helix: 0.82 (0.14), residues: 1389 sheet: 0.23 (0.34), residues: 216 loop : -0.55 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1400 TYR 0.013 0.001 TYR C 235 PHE 0.025 0.001 PHE D1163 TRP 0.021 0.001 TRP D 345 HIS 0.005 0.001 HIS D2103 Details of bonding type rmsd covalent geometry : bond 0.00230 (24137) covalent geometry : angle 0.52929 (32663) SS BOND : bond 0.00169 ( 2) SS BOND : angle 1.72161 ( 4) hydrogen bonds : bond 0.02973 ( 933) hydrogen bonds : angle 3.84466 ( 2677) metal coordination : bond 0.00395 ( 8) metal coordination : angle 3.49743 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.842 Fit side-chains REVERT: C 523 MET cc_start: -0.1039 (mmm) cc_final: -0.1507 (ptm) REVERT: C 613 MET cc_start: 0.0388 (mtp) cc_final: -0.0859 (tpt) REVERT: C 870 VAL cc_start: 0.0177 (OUTLIER) cc_final: -0.0194 (p) REVERT: C 942 ASP cc_start: 0.3660 (p0) cc_final: 0.2658 (t0) REVERT: C 1059 MET cc_start: 0.1715 (tpt) cc_final: 0.1132 (ptp) REVERT: C 1139 GLN cc_start: 0.4172 (OUTLIER) cc_final: 0.3894 (pm20) REVERT: C 1346 ARG cc_start: 0.6751 (pmt-80) cc_final: 0.6203 (tpp80) REVERT: C 1367 ILE cc_start: 0.2971 (mm) cc_final: 0.2163 (pt) REVERT: C 1375 MET cc_start: 0.3706 (mmp) cc_final: 0.2952 (tpt) REVERT: C 1486 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8622 (mt) REVERT: D 224 MET cc_start: 0.6250 (pmm) cc_final: 0.5500 (ptt) REVERT: D 2095 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: A 297 MET cc_start: 0.6485 (ppp) cc_final: 0.6104 (ppp) outliers start: 34 outliers final: 28 residues processed: 151 average time/residue: 0.1295 time to fit residues: 33.7184 Evaluate side-chains 158 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 863 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 1139 GLN Chi-restraints excluded: chain C residue 1366 MET Chi-restraints excluded: chain C residue 1431 LEU Chi-restraints excluded: chain C residue 1486 LEU Chi-restraints excluded: chain C residue 1540 VAL Chi-restraints excluded: chain C residue 1570 VAL Chi-restraints excluded: chain C residue 1679 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 1109 VAL Chi-restraints excluded: chain D residue 1200 PHE Chi-restraints excluded: chain D residue 1671 LEU Chi-restraints excluded: chain D residue 1681 ILE Chi-restraints excluded: chain D residue 1684 THR Chi-restraints excluded: chain D residue 1814 LEU Chi-restraints excluded: chain D residue 1926 MET Chi-restraints excluded: chain D residue 1955 THR Chi-restraints excluded: chain D residue 1969 VAL Chi-restraints excluded: chain D residue 2079 ASP Chi-restraints excluded: chain D residue 2095 PHE Chi-restraints excluded: chain D residue 2130 LEU Chi-restraints excluded: chain D residue 2149 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 72 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN C 520 HIS ** C1353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.151747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.124813 restraints weight = 80053.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117598 restraints weight = 98319.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114531 restraints weight = 61450.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113907 restraints weight = 62147.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114895 restraints weight = 43047.469| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24147 Z= 0.137 Angle : 0.564 10.999 32674 Z= 0.274 Chirality : 0.041 0.284 3658 Planarity : 0.004 0.060 4152 Dihedral : 3.796 18.470 3154 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 1.56 % Allowed : 15.26 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2853 helix: 0.76 (0.14), residues: 1390 sheet: 0.31 (0.34), residues: 211 loop : -0.62 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1400 TYR 0.013 0.001 TYR C 235 PHE 0.023 0.001 PHE D1163 TRP 0.020 0.001 TRP D 345 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00330 (24137) covalent geometry : angle 0.56068 (32663) SS BOND : bond 0.00244 ( 2) SS BOND : angle 1.86421 ( 4) hydrogen bonds : bond 0.03269 ( 933) hydrogen bonds : angle 3.93930 ( 2677) metal coordination : bond 0.00713 ( 8) metal coordination : angle 3.81949 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.76 seconds wall clock time: 62 minutes 31.90 seconds (3751.90 seconds total)