Starting phenix.real_space_refine on Tue May 5 17:48:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9or5_70771/05_2026/9or5_70771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9or5_70771/05_2026/9or5_70771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9or5_70771/05_2026/9or5_70771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9or5_70771/05_2026/9or5_70771.map" model { file = "/net/cci-nas-00/data/ceres_data/9or5_70771/05_2026/9or5_70771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9or5_70771/05_2026/9or5_70771.cif" } resolution = 4.3 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 224 5.16 5 C 19660 2.51 5 N 5132 2.21 5 O 5420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30436 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 7609 Classifications: {'peptide': 946} Link IDs: {'PTRANS': 32, 'TRANS': 913} Chain breaks: 7 Chain: "B" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 7609 Classifications: {'peptide': 946} Link IDs: {'PTRANS': 32, 'TRANS': 913} Chain breaks: 7 Chain: "C" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 7609 Classifications: {'peptide': 946} Link IDs: {'PTRANS': 32, 'TRANS': 913} Chain breaks: 7 Chain: "D" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 7609 Classifications: {'peptide': 946} Link IDs: {'PTRANS': 32, 'TRANS': 913} Chain breaks: 7 Time building chain proxies: 7.08, per 1000 atoms: 0.23 Number of scatterers: 30436 At special positions: 0 Unit cell: (139.284, 140.238, 170.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 224 16.00 O 5420 8.00 N 5132 7.00 C 19660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 13 sheets defined 72.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.919A pdb=" N TYR A 112 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.698A pdb=" N LEU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 136 " --> pdb=" O HIS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.955A pdb=" N LEU A 209 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.524A pdb=" N GLN A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 315 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.770A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 383 " --> pdb=" O MET A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.702A pdb=" N ALA A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.732A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.688A pdb=" N GLN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 537 through 547 Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 596 through 603 removed outlier: 3.875A pdb=" N ARG A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 669 through 677 removed outlier: 3.760A pdb=" N PHE A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 Processing helix chain 'A' and resid 707 through 736 removed outlier: 3.829A pdb=" N SER A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 735 " --> pdb=" O GLN A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 746 removed outlier: 3.626A pdb=" N ALA A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 753 removed outlier: 3.550A pdb=" N ASN A 753 " --> pdb=" O LYS A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 749 through 753' Processing helix chain 'A' and resid 756 through 764 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 791 through 802 removed outlier: 4.104A pdb=" N LYS A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 798 " --> pdb=" O LEU A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 809 removed outlier: 4.280A pdb=" N ILE A 806 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 870 removed outlier: 3.821A pdb=" N PHE A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 870 " --> pdb=" O CYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 895 removed outlier: 3.779A pdb=" N PHE A 876 " --> pdb=" O PRO A 872 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 881 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 927 Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 942 through 965 Processing helix chain 'A' and resid 965 through 994 removed outlier: 4.294A pdb=" N TYR A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 972 " --> pdb=" O TYR A 968 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 981 " --> pdb=" O CYS A 977 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 985 " --> pdb=" O ILE A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1032 removed outlier: 4.078A pdb=" N MET A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A1017 " --> pdb=" O TYR A1013 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A1029 " --> pdb=" O PHE A1025 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1095 through 1149 removed outlier: 4.342A pdb=" N LEU A1100 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A1120 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A1126 " --> pdb=" O ASN A1122 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A1131 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1134 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A1140 " --> pdb=" O LYS A1136 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN A1141 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A1144 " --> pdb=" O TYR A1140 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR A1145 " --> pdb=" O GLN A1141 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A1147 " --> pdb=" O ILE A1143 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1149 " --> pdb=" O THR A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1170 removed outlier: 3.854A pdb=" N SER A1160 " --> pdb=" O MET A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1222 removed outlier: 3.719A pdb=" N GLU A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1215 " --> pdb=" O HIS A1211 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A1217 " --> pdb=" O ARG A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1270 removed outlier: 3.639A pdb=" N ARG A1228 " --> pdb=" O ASP A1224 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1238 " --> pdb=" O VAL A1234 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A1242 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A1253 " --> pdb=" O ASN A1249 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A1258 " --> pdb=" O SER A1254 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1260 " --> pdb=" O GLN A1256 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A1270 " --> pdb=" O GLU A1266 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 159 through 178 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 201 through 206 Processing helix chain 'B' and resid 268 through 283 Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.558A pdb=" N VAL B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.552A pdb=" N ILE B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 373 through 383 removed outlier: 3.669A pdb=" N ILE B 377 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.679A pdb=" N LEU B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.395A pdb=" N ALA B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 497 through 517 removed outlier: 3.525A pdb=" N ASN B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.875A pdb=" N GLU B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 537 through 547 Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 574 through 587 removed outlier: 3.565A pdb=" N LEU B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 604 Processing helix chain 'B' and resid 655 through 668 removed outlier: 3.801A pdb=" N GLU B 659 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 678 removed outlier: 3.962A pdb=" N GLN B 678 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 705 Processing helix chain 'B' and resid 707 through 736 removed outlier: 4.330A pdb=" N SER B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 746 Processing helix chain 'B' and resid 755 through 764 Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 771 through 783 Processing helix chain 'B' and resid 792 through 802 Processing helix chain 'B' and resid 804 through 809 removed outlier: 4.171A pdb=" N PHE B 808 " --> pdb=" O PRO B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 871 Processing helix chain 'B' and resid 871 through 896 Processing helix chain 'B' and resid 903 through 927 removed outlier: 3.562A pdb=" N VAL B 909 " --> pdb=" O GLN B 905 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 913 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 935 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.624A pdb=" N LEU B 940 " --> pdb=" O ILE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.573A pdb=" N ASP B 948 " --> pdb=" O TRP B 944 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 962 " --> pdb=" O GLY B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 994 removed outlier: 4.349A pdb=" N TYR B 971 " --> pdb=" O PRO B 967 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 974 " --> pdb=" O GLY B 970 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 981 " --> pdb=" O CYS B 977 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 988 " --> pdb=" O TYR B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1032 removed outlier: 3.607A pdb=" N ILE B1017 " --> pdb=" O TYR B1013 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1095 Processing helix chain 'B' and resid 1096 through 1149 removed outlier: 3.563A pdb=" N TYR B1104 " --> pdb=" O LEU B1100 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B1108 " --> pdb=" O TYR B1104 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B1127 " --> pdb=" O THR B1123 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B1130 " --> pdb=" O GLU B1126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B1131 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B1133 " --> pdb=" O SER B1129 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B1134 " --> pdb=" O ILE B1130 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B1140 " --> pdb=" O LYS B1136 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN B1141 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B1142 " --> pdb=" O GLN B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1156 Processing helix chain 'B' and resid 1157 through 1170 removed outlier: 4.121A pdb=" N TYR B1163 " --> pdb=" O LEU B1159 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B1165 " --> pdb=" O HIS B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1222 Processing helix chain 'B' and resid 1222 through 1248 removed outlier: 3.592A pdb=" N GLU B1232 " --> pdb=" O ARG B1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1270 removed outlier: 3.529A pdb=" N GLU B1266 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B1270 " --> pdb=" O GLU B1266 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.588A pdb=" N LEU C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 178 Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.685A pdb=" N LEU C 209 " --> pdb=" O ARG C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 268 through 283 Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 372 through 383 removed outlier: 4.333A pdb=" N ALA C 376 " --> pdb=" O HIS C 372 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 383 " --> pdb=" O MET C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 400 through 412 Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.526A pdb=" N TRP C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.536A pdb=" N PHE C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.675A pdb=" N LEU C 511 " --> pdb=" O GLU C 507 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.572A pdb=" N ASN C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 Processing helix chain 'C' and resid 537 through 547 Processing helix chain 'C' and resid 554 through 562 removed outlier: 4.172A pdb=" N ARG C 560 " --> pdb=" O HIS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 587 Processing helix chain 'C' and resid 596 through 604 Processing helix chain 'C' and resid 655 through 667 removed outlier: 3.511A pdb=" N LEU C 666 " --> pdb=" O VAL C 662 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 667 " --> pdb=" O TRP C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 Processing helix chain 'C' and resid 682 through 705 Processing helix chain 'C' and resid 707 through 736 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 749 through 753 Processing helix chain 'C' and resid 756 through 762 Processing helix chain 'C' and resid 765 through 770 removed outlier: 4.136A pdb=" N ILE C 769 " --> pdb=" O HIS C 765 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 770 " --> pdb=" O ARG C 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 765 through 770' Processing helix chain 'C' and resid 771 through 784 Processing helix chain 'C' and resid 793 through 802 removed outlier: 3.794A pdb=" N MET C 798 " --> pdb=" O LEU C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 809 removed outlier: 3.701A pdb=" N ILE C 806 " --> pdb=" O ILE C 802 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 807 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 808 " --> pdb=" O PRO C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 869 Processing helix chain 'C' and resid 871 through 896 removed outlier: 3.625A pdb=" N VAL C 896 " --> pdb=" O TYR C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 926 removed outlier: 3.557A pdb=" N GLU C 923 " --> pdb=" O GLU C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 4.119A pdb=" N LYS C 937 " --> pdb=" O SER C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.811A pdb=" N ILE C 946 " --> pdb=" O GLU C 942 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 958 " --> pdb=" O MET C 954 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 961 " --> pdb=" O VAL C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 971 removed outlier: 4.433A pdb=" N TYR C 971 " --> pdb=" O PRO C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 993 Processing helix chain 'C' and resid 997 through 1032 removed outlier: 3.627A pdb=" N VAL C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C1004 " --> pdb=" O TYR C1000 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C1017 " --> pdb=" O TYR C1013 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C1027 " --> pdb=" O MET C1023 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C1031 " --> pdb=" O VAL C1027 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C1032 " --> pdb=" O ALA C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1123 removed outlier: 3.952A pdb=" N CYS C1103 " --> pdb=" O ALA C1099 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1106 " --> pdb=" O ALA C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1148 removed outlier: 3.818A pdb=" N VAL C1134 " --> pdb=" O ILE C1130 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C1137 " --> pdb=" O GLN C1133 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C1138 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN C1141 " --> pdb=" O PHE C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1170 removed outlier: 3.532A pdb=" N ILE C1162 " --> pdb=" O ILE C1158 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C1167 " --> pdb=" O TYR C1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1222 removed outlier: 3.851A pdb=" N LEU C1197 " --> pdb=" O SER C1193 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN C1219 " --> pdb=" O LYS C1215 " (cutoff:3.500A) Processing helix chain 'C' and resid 1222 through 1269 removed outlier: 3.695A pdb=" N GLU C1232 " --> pdb=" O ARG C1228 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C1244 " --> pdb=" O ARG C1240 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C1246 " --> pdb=" O GLU C1242 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C1247 " --> pdb=" O GLU C1243 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C1266 " --> pdb=" O LEU C1262 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU C1267 " --> pdb=" O SER C1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 178 Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.649A pdb=" N MET D 219 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 220 " --> pdb=" O TRP D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 268 through 283 removed outlier: 3.654A pdb=" N GLN D 283 " --> pdb=" O HIS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 315 removed outlier: 3.531A pdb=" N VAL D 307 " --> pdb=" O GLY D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 370 through 382 removed outlier: 3.591A pdb=" N ILE D 377 " --> pdb=" O GLN D 373 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 411 Processing helix chain 'D' and resid 416 through 428 removed outlier: 4.423A pdb=" N SER D 422 " --> pdb=" O PRO D 418 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 441 removed outlier: 4.024A pdb=" N PHE D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY D 441 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 517 Processing helix chain 'D' and resid 518 through 529 Processing helix chain 'D' and resid 531 through 536 Processing helix chain 'D' and resid 537 through 547 Processing helix chain 'D' and resid 554 through 562 removed outlier: 3.533A pdb=" N ARG D 560 " --> pdb=" O HIS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 587 Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 596 through 604 Processing helix chain 'D' and resid 655 through 667 removed outlier: 4.073A pdb=" N VAL D 662 " --> pdb=" O HIS D 658 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET D 667 " --> pdb=" O TRP D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 removed outlier: 3.767A pdb=" N PHE D 675 " --> pdb=" O LYS D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 680 No H-bonds generated for 'chain 'D' and resid 678 through 680' Processing helix chain 'D' and resid 682 through 705 Processing helix chain 'D' and resid 707 through 736 removed outlier: 4.253A pdb=" N SER D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN D 712 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 746 Processing helix chain 'D' and resid 756 through 764 removed outlier: 3.667A pdb=" N ALA D 762 " --> pdb=" O LYS D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 771 Processing helix chain 'D' and resid 771 through 784 Processing helix chain 'D' and resid 792 through 802 removed outlier: 4.180A pdb=" N VAL D 796 " --> pdb=" O PRO D 792 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 802 " --> pdb=" O MET D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 810 removed outlier: 3.942A pdb=" N ILE D 806 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 807 " --> pdb=" O PRO D 803 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE D 808 " --> pdb=" O PRO D 804 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU D 810 " --> pdb=" O ILE D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 870 Processing helix chain 'D' and resid 871 through 896 removed outlier: 3.674A pdb=" N LYS D 875 " --> pdb=" O ALA D 871 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 887 " --> pdb=" O TYR D 883 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 888 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN D 891 " --> pdb=" O LEU D 887 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 892 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 893 " --> pdb=" O LEU D 889 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 927 removed outlier: 3.542A pdb=" N VAL D 909 " --> pdb=" O GLN D 905 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE D 913 " --> pdb=" O VAL D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 934 through 942 removed outlier: 4.412A pdb=" N LEU D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 964 removed outlier: 4.123A pdb=" N LEU D 949 " --> pdb=" O ASN D 945 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 963 " --> pdb=" O ALA D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 967 No H-bonds generated for 'chain 'D' and resid 965 through 967' Processing helix chain 'D' and resid 968 through 994 removed outlier: 4.177A pdb=" N VAL D 974 " --> pdb=" O GLY D 970 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 987 " --> pdb=" O TRP D 983 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 991 " --> pdb=" O VAL D 987 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 993 " --> pdb=" O ASP D 989 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN D 994 " --> pdb=" O ILE D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1032 removed outlier: 4.168A pdb=" N MET D1003 " --> pdb=" O PRO D 999 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS D1006 " --> pdb=" O MET D1002 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D1010 " --> pdb=" O LYS D1006 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D1026 " --> pdb=" O LEU D1022 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D1032 " --> pdb=" O ALA D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1148 removed outlier: 4.155A pdb=" N ALA D1099 " --> pdb=" O TRP D1095 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D1108 " --> pdb=" O TYR D1104 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D1129 " --> pdb=" O PHE D1125 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D1130 " --> pdb=" O GLU D1126 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D1134 " --> pdb=" O ILE D1130 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE D1137 " --> pdb=" O GLN D1133 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN D1138 " --> pdb=" O VAL D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1156 through 1170 Processing helix chain 'D' and resid 1193 through 1221 removed outlier: 3.506A pdb=" N SER D1221 " --> pdb=" O ASP D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1222 through 1271 removed outlier: 3.673A pdb=" N GLU D1232 " --> pdb=" O ARG D1228 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D1235 " --> pdb=" O SER D1231 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN D1245 " --> pdb=" O LEU D1241 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D1263 " --> pdb=" O ASP D1259 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D1268 " --> pdb=" O GLN D1264 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D1270 " --> pdb=" O GLU D1266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.760A pdb=" N LEU A 105 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 233 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.792A pdb=" N ALA A 211 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE A 256 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY A 213 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ALA A 258 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA A 215 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 146 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 298 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER A 148 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N VAL A 323 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY A 297 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N CYS A 325 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 299 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 322 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE A 391 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 324 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.694A pdb=" N GLN A 291 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 747 through 748 Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.001A pdb=" N ILE B 119 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 181 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE B 214 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 183 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 147 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 146 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 298 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 148 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 322 " --> pdb=" O THR B 389 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.765A pdb=" N GLN B 291 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 212 through 213 removed outlier: 3.577A pdb=" N ILE C 104 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 180 through 182 removed outlier: 6.697A pdb=" N LEU C 146 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU C 298 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER C 148 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL C 300 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS C 150 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL C 323 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY C 297 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AB1, first strand: chain 'C' and resid 747 through 748 Processing sheet with id=AB2, first strand: chain 'D' and resid 232 through 235 removed outlier: 6.839A pdb=" N LEU D 105 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR D 235 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE D 107 " --> pdb=" O TYR D 235 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET D 117 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU D 257 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 119 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS D 254 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 181 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE D 147 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU D 146 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 298 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER D 148 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL D 300 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS D 150 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 323 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY D 297 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AB4, first strand: chain 'D' and resid 747 through 748 1844 hydrogen bonds defined for protein. 5460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 3.64 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: 9677 1.34 - 1.46: 6963 1.46 - 1.58: 14020 1.58 - 1.70: 0 1.70 - 1.82: 396 Bond restraints: 31056 Sorted by residual: bond pdb=" N VAL D 90 " pdb=" CA VAL D 90 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N VAL C 90 " pdb=" CA VAL C 90 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N VAL A 90 " pdb=" CA VAL A 90 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" C GLY B 998 " pdb=" N PRO B 999 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.44e-02 4.82e+03 1.08e+00 ... (remaining 31051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 40925 1.35 - 2.70: 841 2.70 - 4.05: 144 4.05 - 5.40: 27 5.40 - 6.76: 11 Bond angle restraints: 41948 Sorted by residual: angle pdb=" N ASP D 317 " pdb=" CA ASP D 317 " pdb=" C ASP D 317 " ideal model delta sigma weight residual 113.25 108.41 4.84 1.30e+00 5.92e-01 1.39e+01 angle pdb=" N GLY B 329 " pdb=" CA GLY B 329 " pdb=" C GLY B 329 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.06e+00 angle pdb=" C ILE C 538 " pdb=" CA ILE C 538 " pdb=" CB ILE C 538 " ideal model delta sigma weight residual 113.70 111.23 2.47 9.50e-01 1.11e+00 6.75e+00 angle pdb=" C VAL D 165 " pdb=" N PHE D 166 " pdb=" CA PHE D 166 " ideal model delta sigma weight residual 120.68 116.34 4.34 1.70e+00 3.46e-01 6.51e+00 angle pdb=" CA TYR C1104 " pdb=" CB TYR C1104 " pdb=" CG TYR C1104 " ideal model delta sigma weight residual 113.90 109.39 4.51 1.80e+00 3.09e-01 6.28e+00 ... (remaining 41943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16952 17.95 - 35.90: 1448 35.90 - 53.85: 255 53.85 - 71.80: 35 71.80 - 89.75: 30 Dihedral angle restraints: 18720 sinusoidal: 7684 harmonic: 11036 Sorted by residual: dihedral pdb=" CA ASP D 317 " pdb=" C ASP D 317 " pdb=" N PRO D 318 " pdb=" CA PRO D 318 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU D1152 " pdb=" C LEU D1152 " pdb=" N PRO D1153 " pdb=" CA PRO D1153 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA TYR B 996 " pdb=" C TYR B 996 " pdb=" N LEU B 997 " pdb=" CA LEU B 997 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 18717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3287 0.028 - 0.057: 904 0.057 - 0.085: 378 0.085 - 0.113: 155 0.113 - 0.142: 40 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CA ILE D 104 " pdb=" N ILE D 104 " pdb=" C ILE D 104 " pdb=" CB ILE D 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL A 293 " pdb=" N VAL A 293 " pdb=" C VAL A 293 " pdb=" CB VAL A 293 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL D 90 " pdb=" N VAL D 90 " pdb=" C VAL D 90 " pdb=" CB VAL D 90 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 4761 not shown) Planarity restraints: 5224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 966 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 967 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 967 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 967 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 803 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D 804 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 804 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 804 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 803 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 804 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 804 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 804 " -0.028 5.00e-02 4.00e+02 ... (remaining 5221 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9231 2.82 - 3.34: 36904 3.34 - 3.86: 50922 3.86 - 4.38: 61761 4.38 - 4.90: 91101 Nonbonded interactions: 249919 Sorted by model distance: nonbonded pdb=" O ILE B 285 " pdb=" OD1 ASN B 286 " model vdw 2.297 3.040 nonbonded pdb=" O TYR C 123 " pdb=" OD1 ASP C 124 " model vdw 2.305 3.040 nonbonded pdb=" O GLN A 723 " pdb=" OE1 GLU A 727 " model vdw 2.327 3.040 nonbonded pdb=" O SER D1238 " pdb=" OE1 GLU D1242 " model vdw 2.341 3.040 nonbonded pdb=" OG SER C1193 " pdb=" OE1 GLU C1196 " model vdw 2.362 3.040 ... (remaining 249914 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.820 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31056 Z= 0.105 Angle : 0.499 6.756 41948 Z= 0.274 Chirality : 0.036 0.142 4764 Planarity : 0.004 0.059 5224 Dihedral : 13.816 89.754 11584 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % 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 are not related in a simple way. whole: -1.01 (0.14), residues: 3720 helix: -0.17 (0.10), residues: 2403 sheet: -1.44 (0.34), residues: 227 loop : -1.35 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 766 TYR 0.019 0.001 TYR B1163 PHE 0.024 0.001 PHE D1146 TRP 0.009 0.001 TRP C 427 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00214 (31056) covalent geometry : angle 0.49918 (41948) hydrogen bonds : bond 0.22302 ( 1844) hydrogen bonds : angle 8.87157 ( 5460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 MET cc_start: 0.9813 (tpp) cc_final: 0.9465 (tpp) REVERT: A 661 MET cc_start: 0.9134 (mmm) cc_final: 0.8618 (mmm) REVERT: A 666 LEU cc_start: 0.9832 (mt) cc_final: 0.9607 (mt) REVERT: A 667 MET cc_start: 0.9606 (mmp) cc_final: 0.9379 (mmp) REVERT: A 733 TYR cc_start: 0.9444 (t80) cc_final: 0.9191 (t80) REVERT: A 741 MET cc_start: 0.9561 (mmp) cc_final: 0.9183 (mmm) REVERT: A 765 HIS cc_start: 0.9499 (t70) cc_final: 0.9295 (t-90) REVERT: A 783 MET cc_start: 0.9536 (ttt) cc_final: 0.8776 (tmm) REVERT: A 788 MET cc_start: 0.7524 (tmm) cc_final: 0.7277 (tmm) REVERT: A 876 PHE cc_start: 0.9199 (m-10) cc_final: 0.8965 (m-10) REVERT: A 890 PHE cc_start: 0.9632 (t80) cc_final: 0.9432 (t80) REVERT: A 922 ARG cc_start: 0.9794 (tmt170) cc_final: 0.9540 (ttt-90) REVERT: A 969 MET cc_start: 0.8092 (tpt) cc_final: 0.7136 (tpt) REVERT: A 989 ASP cc_start: 0.9345 (m-30) cc_final: 0.9145 (m-30) REVERT: A 1003 MET cc_start: 0.9481 (mpp) cc_final: 0.9263 (mpp) REVERT: A 1135 TRP cc_start: 0.8551 (m-10) cc_final: 0.8283 (m-10) REVERT: A 1152 LEU cc_start: 0.9112 (mt) cc_final: 0.8678 (mt) REVERT: A 1158 ILE cc_start: 0.9704 (pt) cc_final: 0.9464 (pt) REVERT: A 1205 GLU cc_start: 0.9737 (tt0) cc_final: 0.9455 (tp30) REVERT: A 1210 GLU cc_start: 0.9605 (tp30) cc_final: 0.9285 (tp30) REVERT: A 1251 MET cc_start: 0.9573 (mmp) cc_final: 0.9265 (mmm) REVERT: B 112 TYR cc_start: 0.8082 (m-80) cc_final: 0.7880 (m-80) REVERT: B 117 MET cc_start: 0.9251 (tmm) cc_final: 0.8948 (tmm) REVERT: B 145 LEU cc_start: 0.9801 (pt) cc_final: 0.9337 (tt) REVERT: B 219 MET cc_start: 0.9181 (mmt) cc_final: 0.8669 (mmm) REVERT: B 272 LEU cc_start: 0.9847 (tp) cc_final: 0.9613 (mt) REVERT: B 382 MET cc_start: 0.9366 (tmm) cc_final: 0.9110 (tmm) REVERT: B 393 MET cc_start: 0.9213 (tmm) cc_final: 0.8925 (tmm) REVERT: B 510 MET cc_start: 0.9606 (tpp) cc_final: 0.9148 (tpp) REVERT: B 514 LEU cc_start: 0.9816 (mt) cc_final: 0.9469 (mt) REVERT: B 653 PHE cc_start: 0.8121 (m-10) cc_final: 0.7804 (m-80) REVERT: B 667 MET cc_start: 0.9281 (mmp) cc_final: 0.9035 (mmm) REVERT: B 677 TRP cc_start: 0.9557 (t60) cc_final: 0.9171 (t60) REVERT: B 697 MET cc_start: 0.9799 (pmm) cc_final: 0.9449 (pmm) REVERT: B 727 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9395 (mm-30) REVERT: B 758 LYS cc_start: 0.9823 (mmmm) cc_final: 0.9614 (mttt) REVERT: B 789 ARG cc_start: 0.9468 (mpp-170) cc_final: 0.9177 (mpt180) REVERT: B 898 MET cc_start: 0.6924 (tmm) cc_final: 0.6639 (tmm) REVERT: B 956 MET cc_start: 0.9335 (ppp) cc_final: 0.9129 (ppp) REVERT: B 983 TRP cc_start: 0.9434 (m-90) cc_final: 0.8924 (m100) REVERT: B 1008 MET cc_start: 0.9103 (mmt) cc_final: 0.8827 (mmp) REVERT: B 1011 MET cc_start: 0.9632 (mmp) cc_final: 0.9418 (mmp) REVERT: B 1013 TYR cc_start: 0.8886 (t80) cc_final: 0.8651 (t80) REVERT: B 1014 PHE cc_start: 0.8635 (m-10) cc_final: 0.7768 (m-10) REVERT: B 1144 MET cc_start: 0.9750 (mmt) cc_final: 0.9519 (mmm) REVERT: B 1189 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8587 (mtpp) REVERT: B 1204 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9461 (mt-10) REVERT: C 117 MET cc_start: 0.8161 (ppp) cc_final: 0.7730 (ppp) REVERT: C 175 MET cc_start: 0.9465 (ppp) cc_final: 0.9194 (ppp) REVERT: C 510 MET cc_start: 0.9449 (tpp) cc_final: 0.8904 (mmt) REVERT: C 661 MET cc_start: 0.9226 (mmm) cc_final: 0.8978 (mmm) REVERT: C 721 PHE cc_start: 0.9575 (m-10) cc_final: 0.9285 (m-10) REVERT: C 783 MET cc_start: 0.9072 (mtp) cc_final: 0.8816 (ptp) REVERT: C 878 PHE cc_start: 0.9134 (m-80) cc_final: 0.8699 (m-80) REVERT: C 890 PHE cc_start: 0.9031 (m-80) cc_final: 0.8625 (m-80) REVERT: C 898 MET cc_start: 0.8779 (tmm) cc_final: 0.8563 (tmm) REVERT: C 984 TYR cc_start: 0.9275 (m-80) cc_final: 0.9034 (m-80) REVERT: C 987 VAL cc_start: 0.9519 (t) cc_final: 0.9191 (t) REVERT: C 991 PHE cc_start: 0.9522 (t80) cc_final: 0.9321 (t80) REVERT: C 1152 LEU cc_start: 0.8751 (mt) cc_final: 0.8050 (mt) REVERT: C 1156 MET cc_start: 0.9635 (mmp) cc_final: 0.9256 (tpt) REVERT: C 1159 LEU cc_start: 0.9779 (tt) cc_final: 0.9397 (tt) REVERT: D 298 LEU cc_start: 0.9373 (tp) cc_final: 0.9134 (pp) REVERT: D 379 MET cc_start: 0.9276 (tmm) cc_final: 0.8665 (mmp) REVERT: D 672 MET cc_start: 0.9370 (mmt) cc_final: 0.8863 (mmt) REVERT: D 713 ASP cc_start: 0.9788 (t0) cc_final: 0.9478 (m-30) REVERT: D 721 PHE cc_start: 0.9686 (m-80) cc_final: 0.9126 (m-80) REVERT: D 781 MET cc_start: 0.9301 (mmt) cc_final: 0.9062 (mpp) REVERT: D 782 TRP cc_start: 0.9350 (t60) cc_final: 0.9075 (t60) REVERT: D 898 MET cc_start: 0.6444 (ttt) cc_final: 0.5956 (ttm) REVERT: D 983 TRP cc_start: 0.9199 (t-100) cc_final: 0.8772 (t-100) REVERT: D 1104 TYR cc_start: 0.9344 (t80) cc_final: 0.9128 (t80) REVERT: D 1112 LEU cc_start: 0.9693 (tt) cc_final: 0.9441 (mt) REVERT: D 1140 TYR cc_start: 0.8627 (m-80) cc_final: 0.8280 (m-80) REVERT: D 1144 MET cc_start: 0.9736 (tpp) cc_final: 0.9515 (tpp) REVERT: D 1146 PHE cc_start: 0.9493 (m-10) cc_final: 0.9146 (m-10) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1754 time to fit residues: 144.0006 Evaluate side-chains 406 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 40.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 765 HIS A 891 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 372 HIS C 398 GLN C 534 HIS C 716 ASN C 735 HIS C 753 ASN C1121 ASN C1201 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 HIS D 572 HIS D 753 ASN D1132 ASN D1201 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.076624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058720 restraints weight = 206546.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059918 restraints weight = 142820.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.060787 restraints weight = 110908.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061385 restraints weight = 92653.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.061826 restraints weight = 81807.899| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31056 Z= 0.188 Angle : 0.707 8.844 41948 Z= 0.381 Chirality : 0.043 0.203 4764 Planarity : 0.005 0.057 5224 Dihedral : 5.160 29.156 4084 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.21 % Allowed : 4.44 % Favored : 95.36 % 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 are not related in a simple way. whole: -0.48 (0.13), residues: 3720 helix: 0.27 (0.10), residues: 2468 sheet: -1.02 (0.33), residues: 234 loop : -1.35 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 208 TYR 0.030 0.002 TYR C1104 PHE 0.037 0.002 PHE D1137 TRP 0.018 0.002 TRP B1135 HIS 0.015 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00371 (31056) covalent geometry : angle 0.70666 (41948) hydrogen bonds : bond 0.06860 ( 1844) hydrogen bonds : angle 5.95797 ( 5460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 480 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 MET cc_start: 0.9116 (mmm) cc_final: 0.8848 (mmm) REVERT: A 666 LEU cc_start: 0.9757 (mt) cc_final: 0.9525 (mt) REVERT: A 697 MET cc_start: 0.9371 (mtp) cc_final: 0.9065 (mtp) REVERT: A 733 TYR cc_start: 0.9219 (t80) cc_final: 0.8981 (t80) REVERT: A 741 MET cc_start: 0.9504 (mmp) cc_final: 0.9201 (mtt) REVERT: A 783 MET cc_start: 0.9077 (ttt) cc_final: 0.8783 (tmm) REVERT: A 879 TYR cc_start: 0.9198 (m-10) cc_final: 0.8945 (m-10) REVERT: A 890 PHE cc_start: 0.9606 (t80) cc_final: 0.9356 (t80) REVERT: A 969 MET cc_start: 0.8422 (tpt) cc_final: 0.7470 (tpt) REVERT: A 989 ASP cc_start: 0.9331 (m-30) cc_final: 0.9119 (m-30) REVERT: A 1003 MET cc_start: 0.9357 (mpp) cc_final: 0.8944 (mpp) REVERT: A 1135 TRP cc_start: 0.8418 (m-10) cc_final: 0.8130 (m-10) REVERT: A 1137 PHE cc_start: 0.9571 (t80) cc_final: 0.9142 (t80) REVERT: A 1142 LEU cc_start: 0.9806 (mt) cc_final: 0.9555 (mt) REVERT: A 1152 LEU cc_start: 0.9025 (mt) cc_final: 0.8793 (tt) REVERT: A 1205 GLU cc_start: 0.9682 (tt0) cc_final: 0.9323 (tp30) REVERT: A 1210 GLU cc_start: 0.9481 (tp30) cc_final: 0.9095 (tp30) REVERT: A 1251 MET cc_start: 0.9619 (mmp) cc_final: 0.9311 (mmm) REVERT: B 112 TYR cc_start: 0.8181 (m-80) cc_final: 0.7923 (m-80) REVERT: B 117 MET cc_start: 0.9166 (tmm) cc_final: 0.8933 (tmm) REVERT: B 272 LEU cc_start: 0.9759 (tp) cc_final: 0.9544 (mt) REVERT: B 379 MET cc_start: 0.9318 (tpt) cc_final: 0.9113 (tpp) REVERT: B 382 MET cc_start: 0.9010 (tmm) cc_final: 0.8809 (tmm) REVERT: B 393 MET cc_start: 0.9175 (tmm) cc_final: 0.8815 (tpt) REVERT: B 510 MET cc_start: 0.9393 (tpp) cc_final: 0.8997 (tpp) REVERT: B 514 LEU cc_start: 0.9662 (mt) cc_final: 0.9191 (mt) REVERT: B 516 LEU cc_start: 0.9465 (tp) cc_final: 0.9224 (tp) REVERT: B 727 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9313 (mm-30) REVERT: B 956 MET cc_start: 0.9246 (ppp) cc_final: 0.9014 (ppp) REVERT: B 982 LEU cc_start: 0.9636 (mt) cc_final: 0.9331 (mt) REVERT: B 983 TRP cc_start: 0.9397 (m-90) cc_final: 0.8624 (m100) REVERT: B 984 TYR cc_start: 0.8868 (m-10) cc_final: 0.8511 (m-80) REVERT: B 1014 PHE cc_start: 0.8727 (m-10) cc_final: 0.7873 (m-10) REVERT: B 1132 ASN cc_start: 0.8845 (t0) cc_final: 0.8483 (t0) REVERT: B 1135 TRP cc_start: 0.8578 (m100) cc_final: 0.8255 (m100) REVERT: B 1144 MET cc_start: 0.9660 (mmt) cc_final: 0.9451 (mmm) REVERT: B 1189 LYS cc_start: 0.9373 (mtmt) cc_final: 0.8937 (mttm) REVERT: B 1204 GLU cc_start: 0.9619 (mt-10) cc_final: 0.9391 (mt-10) REVERT: B 1210 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9100 (tm-30) REVERT: C 298 LEU cc_start: 0.9540 (mp) cc_final: 0.9270 (tp) REVERT: C 510 MET cc_start: 0.9541 (tpp) cc_final: 0.8599 (tpp) REVERT: C 514 LEU cc_start: 0.9844 (mt) cc_final: 0.9385 (mt) REVERT: C 661 MET cc_start: 0.9198 (mmm) cc_final: 0.8928 (mmm) REVERT: C 667 MET cc_start: 0.9273 (mpp) cc_final: 0.8975 (mpp) REVERT: C 679 ARG cc_start: 0.9662 (mmm160) cc_final: 0.9386 (mmm-85) REVERT: C 766 ARG cc_start: 0.9588 (mpp-170) cc_final: 0.9272 (mpt-90) REVERT: C 878 PHE cc_start: 0.9080 (m-80) cc_final: 0.8584 (m-80) REVERT: C 883 TYR cc_start: 0.9288 (t80) cc_final: 0.8876 (t80) REVERT: C 984 TYR cc_start: 0.9328 (m-80) cc_final: 0.9009 (m-80) REVERT: C 991 PHE cc_start: 0.9427 (t80) cc_final: 0.9186 (t80) REVERT: C 1007 MET cc_start: 0.9456 (ptp) cc_final: 0.9155 (ptp) REVERT: C 1152 LEU cc_start: 0.8538 (mt) cc_final: 0.7807 (mt) REVERT: C 1156 MET cc_start: 0.9629 (mmp) cc_final: 0.9257 (tpt) REVERT: C 1159 LEU cc_start: 0.9759 (tt) cc_final: 0.9071 (tt) REVERT: C 1214 GLU cc_start: 0.9624 (OUTLIER) cc_final: 0.9398 (pp20) REVERT: D 298 LEU cc_start: 0.9362 (tp) cc_final: 0.9089 (pp) REVERT: D 684 MET cc_start: 0.9314 (mmm) cc_final: 0.9006 (tpp) REVERT: D 713 ASP cc_start: 0.9838 (t0) cc_final: 0.9595 (m-30) REVERT: D 721 PHE cc_start: 0.9543 (m-80) cc_final: 0.9061 (m-80) REVERT: D 898 MET cc_start: 0.5671 (ttt) cc_final: 0.4528 (ttt) REVERT: D 983 TRP cc_start: 0.9107 (t-100) cc_final: 0.8451 (t-100) REVERT: D 1101 MET cc_start: 0.9686 (mmp) cc_final: 0.9444 (mmm) REVERT: D 1104 TYR cc_start: 0.9396 (t80) cc_final: 0.9177 (t80) REVERT: D 1112 LEU cc_start: 0.9666 (tt) cc_final: 0.9408 (mt) REVERT: D 1144 MET cc_start: 0.9682 (tpp) cc_final: 0.9367 (tpp) REVERT: D 1251 MET cc_start: 0.9387 (tmm) cc_final: 0.9143 (tmm) outliers start: 7 outliers final: 1 residues processed: 484 average time/residue: 0.1680 time to fit residues: 134.7921 Evaluate side-chains 411 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 409 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 132 optimal weight: 0.4980 chunk 300 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 365 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 934 GLN A1209 GLN A1245 ASN A1249 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 HIS C 154 GLN C 735 HIS ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 ASN ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 ASN D 556 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047658 restraints weight = 136756.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048266 restraints weight = 119864.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048266 restraints weight = 108067.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048266 restraints weight = 108067.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048266 restraints weight = 108067.410| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31056 Z= 0.205 Angle : 0.680 8.221 41948 Z= 0.368 Chirality : 0.043 0.297 4764 Planarity : 0.005 0.060 5224 Dihedral : 5.245 30.655 4084 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.13), residues: 3720 helix: 0.27 (0.10), residues: 2470 sheet: -0.90 (0.34), residues: 234 loop : -1.34 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 518 TYR 0.047 0.002 TYR D 886 PHE 0.048 0.002 PHE D1025 TRP 0.022 0.002 TRP C 663 HIS 0.010 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00408 (31056) covalent geometry : angle 0.67978 (41948) hydrogen bonds : bond 0.05837 ( 1844) hydrogen bonds : angle 5.77366 ( 5460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 468 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 MET cc_start: 0.9147 (mmm) cc_final: 0.8836 (mmm) REVERT: A 697 MET cc_start: 0.9347 (mtp) cc_final: 0.9039 (mtp) REVERT: A 733 TYR cc_start: 0.9529 (t80) cc_final: 0.9269 (t80) REVERT: A 788 MET cc_start: 0.7718 (tmm) cc_final: 0.7434 (tmm) REVERT: A 798 MET cc_start: 0.9141 (tmm) cc_final: 0.8901 (tmm) REVERT: A 879 TYR cc_start: 0.9326 (m-10) cc_final: 0.8961 (m-10) REVERT: A 969 MET cc_start: 0.8660 (tpt) cc_final: 0.7920 (tpt) REVERT: A 983 TRP cc_start: 0.9361 (t-100) cc_final: 0.9128 (t-100) REVERT: A 989 ASP cc_start: 0.9321 (m-30) cc_final: 0.9086 (m-30) REVERT: A 1137 PHE cc_start: 0.9485 (t80) cc_final: 0.9212 (t80) REVERT: A 1138 GLN cc_start: 0.9714 (pt0) cc_final: 0.9511 (pp30) REVERT: A 1142 LEU cc_start: 0.9879 (mt) cc_final: 0.9633 (mt) REVERT: A 1152 LEU cc_start: 0.9020 (mt) cc_final: 0.8804 (mt) REVERT: A 1205 GLU cc_start: 0.9709 (tt0) cc_final: 0.9360 (tp30) REVERT: A 1210 GLU cc_start: 0.9567 (tp30) cc_final: 0.9341 (tp30) REVERT: A 1251 MET cc_start: 0.9652 (mmp) cc_final: 0.9305 (mmm) REVERT: B 112 TYR cc_start: 0.8180 (m-80) cc_final: 0.7958 (m-80) REVERT: B 219 MET cc_start: 0.9165 (mmt) cc_final: 0.8640 (mmt) REVERT: B 272 LEU cc_start: 0.9713 (tp) cc_final: 0.9397 (pp) REVERT: B 510 MET cc_start: 0.9481 (tpp) cc_final: 0.8943 (tpp) REVERT: B 514 LEU cc_start: 0.9594 (mt) cc_final: 0.9097 (mt) REVERT: B 516 LEU cc_start: 0.9411 (tp) cc_final: 0.9169 (tp) REVERT: B 727 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9356 (mm-30) REVERT: B 795 LYS cc_start: 0.8652 (tttt) cc_final: 0.8193 (tptt) REVERT: B 890 PHE cc_start: 0.9586 (t80) cc_final: 0.9369 (t80) REVERT: B 898 MET cc_start: 0.7829 (tmm) cc_final: 0.7376 (tmm) REVERT: B 982 LEU cc_start: 0.9612 (mt) cc_final: 0.9265 (mt) REVERT: B 983 TRP cc_start: 0.9395 (m-90) cc_final: 0.8546 (m100) REVERT: B 1013 TYR cc_start: 0.8711 (t80) cc_final: 0.8486 (t80) REVERT: B 1014 PHE cc_start: 0.8765 (m-10) cc_final: 0.7865 (m-10) REVERT: B 1189 LYS cc_start: 0.9402 (mtmt) cc_final: 0.9001 (mtpp) REVERT: B 1204 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9434 (mt-10) REVERT: B 1210 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9283 (tm-30) REVERT: C 510 MET cc_start: 0.9433 (tpp) cc_final: 0.8698 (tpp) REVERT: C 514 LEU cc_start: 0.9762 (mt) cc_final: 0.9431 (mt) REVERT: C 661 MET cc_start: 0.9135 (mmm) cc_final: 0.8783 (mmm) REVERT: C 667 MET cc_start: 0.8960 (mpp) cc_final: 0.8686 (mpp) REVERT: C 748 LEU cc_start: 0.9837 (mm) cc_final: 0.9583 (mm) REVERT: C 766 ARG cc_start: 0.9582 (mpp-170) cc_final: 0.9259 (mpt-90) REVERT: C 878 PHE cc_start: 0.9123 (m-80) cc_final: 0.8629 (m-80) REVERT: C 883 TYR cc_start: 0.9105 (t80) cc_final: 0.8453 (t80) REVERT: C 926 MET cc_start: 0.9433 (mmp) cc_final: 0.9073 (mpp) REVERT: C 948 ASP cc_start: 0.9527 (t0) cc_final: 0.9243 (t0) REVERT: C 980 ILE cc_start: 0.9913 (mp) cc_final: 0.9653 (mp) REVERT: C 984 TYR cc_start: 0.9258 (m-80) cc_final: 0.8771 (m-80) REVERT: C 1152 LEU cc_start: 0.8733 (mt) cc_final: 0.8088 (mt) REVERT: C 1156 MET cc_start: 0.9673 (mmp) cc_final: 0.9317 (tpt) REVERT: C 1237 MET cc_start: 0.9534 (mmp) cc_final: 0.9312 (mmm) REVERT: D 298 LEU cc_start: 0.9398 (tp) cc_final: 0.9057 (pp) REVERT: D 672 MET cc_start: 0.9410 (mmt) cc_final: 0.9025 (mmt) REVERT: D 684 MET cc_start: 0.9516 (mmm) cc_final: 0.9163 (tpp) REVERT: D 713 ASP cc_start: 0.9659 (t0) cc_final: 0.9407 (m-30) REVERT: D 721 PHE cc_start: 0.9434 (m-80) cc_final: 0.8866 (m-80) REVERT: D 898 MET cc_start: 0.6702 (ttt) cc_final: 0.6199 (ttt) REVERT: D 983 TRP cc_start: 0.9032 (t-100) cc_final: 0.8723 (t-100) REVERT: D 984 TYR cc_start: 0.9270 (t80) cc_final: 0.9027 (t80) REVERT: D 1023 MET cc_start: 0.9345 (mmp) cc_final: 0.9020 (ttt) REVERT: D 1112 LEU cc_start: 0.9604 (tt) cc_final: 0.9373 (mt) REVERT: D 1251 MET cc_start: 0.9355 (tmm) cc_final: 0.9072 (tmm) outliers start: 3 outliers final: 0 residues processed: 470 average time/residue: 0.1632 time to fit residues: 127.5642 Evaluate side-chains 391 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 92 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 GLN A1245 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN B1211 HIS C 154 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN D1121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045542 restraints weight = 153815.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046136 restraints weight = 129983.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046439 restraints weight = 116030.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046847 restraints weight = 107891.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046847 restraints weight = 101446.145| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31056 Z= 0.255 Angle : 0.729 9.339 41948 Z= 0.394 Chirality : 0.044 0.258 4764 Planarity : 0.005 0.064 5224 Dihedral : 5.405 30.537 4084 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.03 % Allowed : 4.64 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.13), residues: 3720 helix: 0.10 (0.10), residues: 2475 sheet: -0.91 (0.34), residues: 228 loop : -1.45 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 434 TYR 0.056 0.002 TYR B 984 PHE 0.041 0.002 PHE A1124 TRP 0.036 0.002 TRP C 427 HIS 0.008 0.002 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00498 (31056) covalent geometry : angle 0.72939 (41948) hydrogen bonds : bond 0.05330 ( 1844) hydrogen bonds : angle 5.77992 ( 5460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 MET cc_start: 0.9160 (mmm) cc_final: 0.8928 (mmm) REVERT: A 697 MET cc_start: 0.9361 (mtp) cc_final: 0.9067 (mtp) REVERT: A 733 TYR cc_start: 0.9441 (t80) cc_final: 0.9154 (t80) REVERT: A 741 MET cc_start: 0.9328 (mtm) cc_final: 0.9039 (mmp) REVERT: A 798 MET cc_start: 0.9151 (tmm) cc_final: 0.8872 (tmm) REVERT: A 876 PHE cc_start: 0.8866 (m-80) cc_final: 0.8544 (m-80) REVERT: A 883 TYR cc_start: 0.9094 (m-10) cc_final: 0.8869 (m-10) REVERT: A 969 MET cc_start: 0.8783 (tpt) cc_final: 0.8045 (tpt) REVERT: A 989 ASP cc_start: 0.9359 (m-30) cc_final: 0.9138 (m-30) REVERT: A 1135 TRP cc_start: 0.8511 (m-10) cc_final: 0.8184 (m-10) REVERT: A 1137 PHE cc_start: 0.9532 (t80) cc_final: 0.9202 (t80) REVERT: A 1251 MET cc_start: 0.9611 (mmp) cc_final: 0.9246 (mmm) REVERT: B 112 TYR cc_start: 0.8195 (m-80) cc_final: 0.7977 (m-80) REVERT: B 117 MET cc_start: 0.9414 (tmm) cc_final: 0.9024 (tmm) REVERT: B 219 MET cc_start: 0.9219 (mmt) cc_final: 0.8793 (mmt) REVERT: B 272 LEU cc_start: 0.9694 (tp) cc_final: 0.9372 (pp) REVERT: B 382 MET cc_start: 0.9184 (tmm) cc_final: 0.8801 (tmm) REVERT: B 510 MET cc_start: 0.9386 (tpp) cc_final: 0.8892 (tpp) REVERT: B 516 LEU cc_start: 0.9433 (tp) cc_final: 0.9208 (tp) REVERT: B 727 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9316 (mm-30) REVERT: B 898 MET cc_start: 0.7962 (tmm) cc_final: 0.7641 (tmm) REVERT: B 982 LEU cc_start: 0.9574 (mt) cc_final: 0.9134 (mt) REVERT: B 983 TRP cc_start: 0.9246 (m-90) cc_final: 0.8523 (m100) REVERT: B 1013 TYR cc_start: 0.8710 (t80) cc_final: 0.8446 (t80) REVERT: B 1014 PHE cc_start: 0.8686 (m-10) cc_final: 0.7992 (m-10) REVERT: B 1021 VAL cc_start: 0.9390 (m) cc_final: 0.9120 (m) REVERT: B 1025 PHE cc_start: 0.8520 (m-80) cc_final: 0.8293 (m-80) REVERT: B 1135 TRP cc_start: 0.8568 (m100) cc_final: 0.8164 (m100) REVERT: B 1144 MET cc_start: 0.9710 (mmp) cc_final: 0.9436 (mmm) REVERT: B 1189 LYS cc_start: 0.9288 (mtmt) cc_final: 0.8956 (mttm) REVERT: B 1210 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9229 (tm-30) REVERT: C 510 MET cc_start: 0.9341 (tpp) cc_final: 0.8937 (tpp) REVERT: C 661 MET cc_start: 0.9109 (mmm) cc_final: 0.8749 (mmm) REVERT: C 741 MET cc_start: 0.9507 (ptp) cc_final: 0.9228 (ptp) REVERT: C 766 ARG cc_start: 0.9577 (mpp-170) cc_final: 0.9291 (mpt-90) REVERT: C 878 PHE cc_start: 0.9091 (m-80) cc_final: 0.8577 (m-80) REVERT: C 879 TYR cc_start: 0.9525 (t80) cc_final: 0.9296 (t80) REVERT: C 883 TYR cc_start: 0.9259 (t80) cc_final: 0.8622 (t80) REVERT: C 887 LEU cc_start: 0.9656 (mt) cc_final: 0.9444 (mt) REVERT: C 926 MET cc_start: 0.9426 (mmp) cc_final: 0.9163 (mmm) REVERT: C 1152 LEU cc_start: 0.8603 (mt) cc_final: 0.7926 (mt) REVERT: C 1156 MET cc_start: 0.9693 (mmp) cc_final: 0.9335 (tpt) REVERT: D 298 LEU cc_start: 0.9353 (tp) cc_final: 0.8961 (pp) REVERT: D 672 MET cc_start: 0.9433 (tpp) cc_final: 0.9229 (tpp) REVERT: D 684 MET cc_start: 0.9376 (mmm) cc_final: 0.9156 (mmm) REVERT: D 713 ASP cc_start: 0.9663 (t0) cc_final: 0.9367 (m-30) REVERT: D 721 PHE cc_start: 0.9429 (m-80) cc_final: 0.8826 (m-80) REVERT: D 898 MET cc_start: 0.6598 (ttt) cc_final: 0.5710 (ttt) REVERT: D 983 TRP cc_start: 0.9033 (t-100) cc_final: 0.8666 (t-100) REVERT: D 1112 LEU cc_start: 0.9644 (tt) cc_final: 0.9412 (mt) REVERT: D 1251 MET cc_start: 0.9263 (tmm) cc_final: 0.9032 (tmm) outliers start: 1 outliers final: 1 residues processed: 446 average time/residue: 0.1635 time to fit residues: 121.8351 Evaluate side-chains 376 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 345 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1121 ASN A1211 HIS A1245 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 945 ASN D1121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059146 restraints weight = 198841.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060296 restraints weight = 140207.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.061159 restraints weight = 109479.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061768 restraints weight = 91828.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062074 restraints weight = 80921.619| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31056 Z= 0.157 Angle : 0.659 8.296 41948 Z= 0.349 Chirality : 0.042 0.250 4764 Planarity : 0.005 0.077 5224 Dihedral : 5.291 30.493 4084 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3720 helix: 0.34 (0.10), residues: 2474 sheet: -0.85 (0.34), residues: 244 loop : -1.36 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 330 TYR 0.032 0.002 TYR C1104 PHE 0.033 0.002 PHE D1025 TRP 0.016 0.001 TRP B1135 HIS 0.008 0.001 HIS A1161 Details of bonding type rmsd covalent geometry : bond 0.00322 (31056) covalent geometry : angle 0.65937 (41948) hydrogen bonds : bond 0.04899 ( 1844) hydrogen bonds : angle 5.39852 ( 5460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 478 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 LEU cc_start: 0.9906 (mt) cc_final: 0.9633 (pp) REVERT: A 661 MET cc_start: 0.9196 (mmm) cc_final: 0.8668 (mmm) REVERT: A 666 LEU cc_start: 0.9689 (mt) cc_final: 0.9474 (mt) REVERT: A 697 MET cc_start: 0.9297 (mtp) cc_final: 0.8984 (mtp) REVERT: A 733 TYR cc_start: 0.9101 (t80) cc_final: 0.8821 (t80) REVERT: A 798 MET cc_start: 0.9073 (tmm) cc_final: 0.8870 (tmm) REVERT: A 879 TYR cc_start: 0.9128 (m-10) cc_final: 0.8553 (m-10) REVERT: A 890 PHE cc_start: 0.9642 (t80) cc_final: 0.8985 (t80) REVERT: A 969 MET cc_start: 0.8766 (tpt) cc_final: 0.8129 (tpt) REVERT: A 1135 TRP cc_start: 0.8472 (m-10) cc_final: 0.8110 (m-10) REVERT: A 1137 PHE cc_start: 0.9497 (t80) cc_final: 0.9073 (t80) REVERT: A 1142 LEU cc_start: 0.9793 (mt) cc_final: 0.9509 (mt) REVERT: A 1152 LEU cc_start: 0.8894 (mt) cc_final: 0.8660 (tp) REVERT: A 1205 GLU cc_start: 0.9655 (tt0) cc_final: 0.9231 (tp30) REVERT: A 1210 GLU cc_start: 0.9570 (tp30) cc_final: 0.9110 (tp30) REVERT: A 1251 MET cc_start: 0.9608 (mmp) cc_final: 0.9265 (mmm) REVERT: B 112 TYR cc_start: 0.8097 (m-80) cc_final: 0.7820 (m-80) REVERT: B 117 MET cc_start: 0.9357 (tmm) cc_final: 0.9031 (tmm) REVERT: B 219 MET cc_start: 0.9271 (mmt) cc_final: 0.8881 (mmt) REVERT: B 272 LEU cc_start: 0.9756 (tp) cc_final: 0.9528 (mt) REVERT: B 379 MET cc_start: 0.9188 (tpt) cc_final: 0.8935 (tmm) REVERT: B 510 MET cc_start: 0.9414 (tpp) cc_final: 0.8788 (tpp) REVERT: B 514 LEU cc_start: 0.9722 (mt) cc_final: 0.9292 (mt) REVERT: B 516 LEU cc_start: 0.9466 (tp) cc_final: 0.9226 (tp) REVERT: B 684 MET cc_start: 0.9538 (mmp) cc_final: 0.9234 (mmp) REVERT: B 727 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9266 (mm-30) REVERT: B 898 MET cc_start: 0.6813 (tmm) cc_final: 0.6368 (tmm) REVERT: B 956 MET cc_start: 0.9105 (ppp) cc_final: 0.8871 (ppp) REVERT: B 982 LEU cc_start: 0.9682 (mt) cc_final: 0.9435 (mt) REVERT: B 983 TRP cc_start: 0.9185 (m-90) cc_final: 0.8568 (m100) REVERT: B 1013 TYR cc_start: 0.8604 (t80) cc_final: 0.8365 (t80) REVERT: B 1014 PHE cc_start: 0.8671 (m-10) cc_final: 0.7884 (m-10) REVERT: B 1021 VAL cc_start: 0.9315 (m) cc_final: 0.9024 (m) REVERT: B 1025 PHE cc_start: 0.8527 (m-80) cc_final: 0.8322 (m-80) REVERT: B 1135 TRP cc_start: 0.8594 (m100) cc_final: 0.8184 (m100) REVERT: B 1144 MET cc_start: 0.9714 (mmp) cc_final: 0.9416 (mmm) REVERT: B 1189 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8844 (mtpp) REVERT: B 1210 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9010 (tm-30) REVERT: C 158 MET cc_start: 0.8223 (pmm) cc_final: 0.8010 (pmm) REVERT: C 510 MET cc_start: 0.9301 (tpp) cc_final: 0.8655 (tpp) REVERT: C 514 LEU cc_start: 0.9711 (mt) cc_final: 0.9351 (mt) REVERT: C 661 MET cc_start: 0.9247 (mmm) cc_final: 0.8916 (mmm) REVERT: C 667 MET cc_start: 0.8732 (mpp) cc_final: 0.8455 (mpp) REVERT: C 748 LEU cc_start: 0.9748 (mm) cc_final: 0.9454 (mm) REVERT: C 783 MET cc_start: 0.8865 (mmp) cc_final: 0.8634 (ptp) REVERT: C 878 PHE cc_start: 0.9022 (m-80) cc_final: 0.8524 (m-80) REVERT: C 879 TYR cc_start: 0.9543 (t80) cc_final: 0.9336 (t80) REVERT: C 883 TYR cc_start: 0.9308 (t80) cc_final: 0.8557 (t80) REVERT: C 926 MET cc_start: 0.9383 (mmp) cc_final: 0.9120 (mmm) REVERT: C 987 VAL cc_start: 0.9559 (t) cc_final: 0.9250 (t) REVERT: C 991 PHE cc_start: 0.9409 (t80) cc_final: 0.9203 (t80) REVERT: C 1152 LEU cc_start: 0.8502 (mt) cc_final: 0.8129 (mt) REVERT: C 1156 MET cc_start: 0.9621 (mmp) cc_final: 0.9326 (tpt) REVERT: C 1214 GLU cc_start: 0.9572 (OUTLIER) cc_final: 0.9369 (pp20) REVERT: D 298 LEU cc_start: 0.9376 (tp) cc_final: 0.9067 (pp) REVERT: D 684 MET cc_start: 0.9145 (mmm) cc_final: 0.8840 (tpp) REVERT: D 694 TYR cc_start: 0.8835 (m-10) cc_final: 0.8550 (m-80) REVERT: D 898 MET cc_start: 0.6162 (ttt) cc_final: 0.4606 (ttt) REVERT: D 983 TRP cc_start: 0.9004 (t-100) cc_final: 0.8712 (t-100) REVERT: D 1023 MET cc_start: 0.9358 (mmp) cc_final: 0.8908 (ttt) REVERT: D 1112 LEU cc_start: 0.9644 (tt) cc_final: 0.9387 (mt) REVERT: D 1144 MET cc_start: 0.9645 (tpt) cc_final: 0.9426 (tpp) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.1554 time to fit residues: 124.7318 Evaluate side-chains 393 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 298 optimal weight: 30.0000 chunk 217 optimal weight: 0.0870 chunk 299 optimal weight: 40.0000 chunk 297 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 190 optimal weight: 40.0000 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 891 ASN D 716 ASN ** D 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048024 restraints weight = 140114.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048496 restraints weight = 118941.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048504 restraints weight = 108118.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048504 restraints weight = 107989.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048504 restraints weight = 107989.238| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31056 Z= 0.143 Angle : 0.656 8.136 41948 Z= 0.345 Chirality : 0.042 0.224 4764 Planarity : 0.004 0.063 5224 Dihedral : 5.167 29.057 4084 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % 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 are not related in a simple way. whole: -0.22 (0.14), residues: 3720 helix: 0.45 (0.10), residues: 2474 sheet: -0.69 (0.35), residues: 242 loop : -1.27 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 962 TYR 0.034 0.002 TYR D 984 PHE 0.038 0.002 PHE A1124 TRP 0.022 0.002 TRP B 751 HIS 0.008 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00292 (31056) covalent geometry : angle 0.65604 (41948) hydrogen bonds : bond 0.04616 ( 1844) hydrogen bonds : angle 5.22511 ( 5460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 474 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.9513 (tpp) cc_final: 0.9309 (tpt) REVERT: A 660 LEU cc_start: 0.9863 (mt) cc_final: 0.9661 (pp) REVERT: A 661 MET cc_start: 0.9159 (mmm) cc_final: 0.8614 (mmm) REVERT: A 697 MET cc_start: 0.9305 (mtp) cc_final: 0.8961 (mtp) REVERT: A 733 TYR cc_start: 0.9500 (t80) cc_final: 0.9249 (t80) REVERT: A 741 MET cc_start: 0.9489 (ptp) cc_final: 0.9063 (ppp) REVERT: A 798 MET cc_start: 0.9115 (tmm) cc_final: 0.8879 (tmm) REVERT: A 869 TYR cc_start: 0.8854 (m-10) cc_final: 0.8543 (m-10) REVERT: A 879 TYR cc_start: 0.9229 (m-10) cc_final: 0.8874 (m-10) REVERT: A 883 TYR cc_start: 0.9029 (m-10) cc_final: 0.8793 (m-10) REVERT: A 890 PHE cc_start: 0.9665 (t80) cc_final: 0.9050 (t80) REVERT: A 926 MET cc_start: 0.9024 (mmp) cc_final: 0.8688 (mmp) REVERT: A 969 MET cc_start: 0.8882 (tpt) cc_final: 0.8646 (tpp) REVERT: A 1103 CYS cc_start: 0.9763 (t) cc_final: 0.9540 (t) REVERT: A 1135 TRP cc_start: 0.8592 (m-10) cc_final: 0.8286 (m-10) REVERT: A 1137 PHE cc_start: 0.9409 (t80) cc_final: 0.9048 (t80) REVERT: A 1152 LEU cc_start: 0.8985 (mt) cc_final: 0.8648 (mt) REVERT: A 1205 GLU cc_start: 0.9695 (tt0) cc_final: 0.9302 (tp30) REVERT: A 1250 PHE cc_start: 0.9763 (t80) cc_final: 0.9525 (t80) REVERT: A 1251 MET cc_start: 0.9619 (mmp) cc_final: 0.9120 (mmm) REVERT: B 112 TYR cc_start: 0.8159 (m-80) cc_final: 0.7939 (m-80) REVERT: B 117 MET cc_start: 0.9339 (tmm) cc_final: 0.9083 (tmm) REVERT: B 219 MET cc_start: 0.9230 (mmt) cc_final: 0.8852 (mmt) REVERT: B 272 LEU cc_start: 0.9706 (tp) cc_final: 0.9380 (pp) REVERT: B 510 MET cc_start: 0.9549 (tpp) cc_final: 0.8861 (tpp) REVERT: B 514 LEU cc_start: 0.9706 (mt) cc_final: 0.9284 (mt) REVERT: B 516 LEU cc_start: 0.9443 (tp) cc_final: 0.9216 (tp) REVERT: B 672 MET cc_start: 0.8940 (mmp) cc_final: 0.8475 (mmm) REVERT: B 684 MET cc_start: 0.9417 (mmp) cc_final: 0.9111 (mmp) REVERT: B 727 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9341 (mm-30) REVERT: B 758 LYS cc_start: 0.9809 (mmtm) cc_final: 0.9536 (mttt) REVERT: B 898 MET cc_start: 0.8100 (tmm) cc_final: 0.7647 (tmm) REVERT: B 1011 MET cc_start: 0.9580 (mmp) cc_final: 0.9372 (mmp) REVERT: B 1013 TYR cc_start: 0.8591 (t80) cc_final: 0.8305 (t80) REVERT: B 1014 PHE cc_start: 0.8640 (m-10) cc_final: 0.7960 (m-10) REVERT: B 1021 VAL cc_start: 0.9401 (m) cc_final: 0.9149 (m) REVERT: B 1025 PHE cc_start: 0.8599 (m-80) cc_final: 0.8286 (m-80) REVERT: B 1135 TRP cc_start: 0.8574 (m100) cc_final: 0.8114 (m100) REVERT: B 1144 MET cc_start: 0.9730 (mmp) cc_final: 0.9442 (mmm) REVERT: B 1210 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9133 (tm-30) REVERT: C 298 LEU cc_start: 0.9592 (mp) cc_final: 0.9330 (tp) REVERT: C 510 MET cc_start: 0.9643 (tpt) cc_final: 0.9119 (tpp) REVERT: C 514 LEU cc_start: 0.9796 (mt) cc_final: 0.9528 (mt) REVERT: C 661 MET cc_start: 0.9178 (mmm) cc_final: 0.8745 (mmm) REVERT: C 667 MET cc_start: 0.8807 (mpp) cc_final: 0.8504 (mpp) REVERT: C 708 ASP cc_start: 0.9283 (t0) cc_final: 0.8898 (p0) REVERT: C 721 PHE cc_start: 0.9280 (m-80) cc_final: 0.8901 (m-10) REVERT: C 783 MET cc_start: 0.8651 (mmp) cc_final: 0.8246 (ptp) REVERT: C 878 PHE cc_start: 0.9024 (m-80) cc_final: 0.8520 (m-80) REVERT: C 883 TYR cc_start: 0.9287 (t80) cc_final: 0.8413 (t80) REVERT: C 926 MET cc_start: 0.9414 (mmp) cc_final: 0.9119 (mmm) REVERT: C 969 MET cc_start: 0.8927 (mmp) cc_final: 0.8650 (mmp) REVERT: C 987 VAL cc_start: 0.9551 (t) cc_final: 0.9256 (t) REVERT: C 1007 MET cc_start: 0.9617 (mtt) cc_final: 0.9235 (mmm) REVERT: C 1114 ASN cc_start: 0.9485 (m110) cc_final: 0.9175 (m110) REVERT: C 1152 LEU cc_start: 0.8695 (mt) cc_final: 0.8300 (mt) REVERT: C 1156 MET cc_start: 0.9644 (mmp) cc_final: 0.9349 (tpt) REVERT: D 298 LEU cc_start: 0.9397 (tp) cc_final: 0.9040 (pp) REVERT: D 672 MET cc_start: 0.9527 (tpp) cc_final: 0.9316 (mmt) REVERT: D 684 MET cc_start: 0.9418 (mmm) cc_final: 0.9171 (tpp) REVERT: D 721 PHE cc_start: 0.9135 (m-80) cc_final: 0.8462 (m-80) REVERT: D 898 MET cc_start: 0.7233 (ttt) cc_final: 0.6579 (ttt) REVERT: D 984 TYR cc_start: 0.9326 (t80) cc_final: 0.8922 (t80) REVERT: D 1112 LEU cc_start: 0.9645 (tt) cc_final: 0.9381 (mt) REVERT: D 1251 MET cc_start: 0.9398 (tmm) cc_final: 0.9068 (tmm) outliers start: 3 outliers final: 3 residues processed: 477 average time/residue: 0.1604 time to fit residues: 128.4317 Evaluate side-chains 408 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 405 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 151 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 891 ASN A1245 ASN ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.058341 restraints weight = 204891.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059481 restraints weight = 144824.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060291 restraints weight = 113684.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060807 restraints weight = 95682.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.061245 restraints weight = 85457.593| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31056 Z= 0.212 Angle : 0.699 9.545 41948 Z= 0.373 Chirality : 0.043 0.201 4764 Planarity : 0.005 0.066 5224 Dihedral : 5.234 28.858 4084 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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 are not related in a simple way. whole: -0.35 (0.14), residues: 3720 helix: 0.36 (0.10), residues: 2476 sheet: -0.79 (0.35), residues: 242 loop : -1.35 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 789 TYR 0.031 0.002 TYR C1104 PHE 0.035 0.002 PHE D1025 TRP 0.016 0.002 TRP B 751 HIS 0.008 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00422 (31056) covalent geometry : angle 0.69921 (41948) hydrogen bonds : bond 0.04575 ( 1844) hydrogen bonds : angle 5.42174 ( 5460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.9629 (pp) cc_final: 0.9368 (pp) REVERT: A 666 LEU cc_start: 0.9691 (mt) cc_final: 0.9471 (mt) REVERT: A 667 MET cc_start: 0.9342 (mmp) cc_final: 0.9124 (mmm) REVERT: A 697 MET cc_start: 0.9332 (mtp) cc_final: 0.9030 (mtp) REVERT: A 733 TYR cc_start: 0.9118 (t80) cc_final: 0.8857 (t80) REVERT: A 741 MET cc_start: 0.9404 (ptp) cc_final: 0.9114 (ptp) REVERT: A 781 MET cc_start: 0.9567 (mtt) cc_final: 0.9321 (mmt) REVERT: A 798 MET cc_start: 0.9024 (tmm) cc_final: 0.8820 (tmm) REVERT: A 890 PHE cc_start: 0.9687 (t80) cc_final: 0.9075 (t80) REVERT: A 926 MET cc_start: 0.8800 (mmp) cc_final: 0.8538 (mmp) REVERT: A 969 MET cc_start: 0.8847 (tpt) cc_final: 0.8229 (tpt) REVERT: A 1003 MET cc_start: 0.9568 (mpp) cc_final: 0.9221 (mpp) REVERT: A 1137 PHE cc_start: 0.9536 (t80) cc_final: 0.9195 (t80) REVERT: A 1152 LEU cc_start: 0.8831 (mt) cc_final: 0.8601 (mp) REVERT: A 1205 GLU cc_start: 0.9658 (tt0) cc_final: 0.9243 (tp30) REVERT: A 1250 PHE cc_start: 0.9738 (t80) cc_final: 0.9500 (t80) REVERT: A 1251 MET cc_start: 0.9621 (mmp) cc_final: 0.9060 (mmm) REVERT: B 112 TYR cc_start: 0.8174 (m-80) cc_final: 0.7868 (m-80) REVERT: B 219 MET cc_start: 0.9288 (mmt) cc_final: 0.8908 (mmt) REVERT: B 272 LEU cc_start: 0.9760 (tp) cc_final: 0.9424 (pp) REVERT: B 510 MET cc_start: 0.9398 (tpp) cc_final: 0.8782 (tpp) REVERT: B 514 LEU cc_start: 0.9688 (mt) cc_final: 0.9222 (mt) REVERT: B 516 LEU cc_start: 0.9507 (tp) cc_final: 0.9281 (tp) REVERT: B 672 MET cc_start: 0.9346 (mmp) cc_final: 0.8744 (mmm) REVERT: B 684 MET cc_start: 0.9526 (mmp) cc_final: 0.9150 (mmp) REVERT: B 727 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9272 (mm-30) REVERT: B 883 TYR cc_start: 0.9389 (t80) cc_final: 0.9065 (t80) REVERT: B 898 MET cc_start: 0.6851 (tmm) cc_final: 0.6406 (tmm) REVERT: B 956 MET cc_start: 0.9123 (ppp) cc_final: 0.8891 (ppp) REVERT: B 989 ASP cc_start: 0.8496 (t70) cc_final: 0.8191 (t70) REVERT: B 1011 MET cc_start: 0.9674 (mmp) cc_final: 0.9472 (mmp) REVERT: B 1013 TYR cc_start: 0.8599 (t80) cc_final: 0.8372 (t80) REVERT: B 1014 PHE cc_start: 0.8725 (m-10) cc_final: 0.7937 (m-10) REVERT: B 1021 VAL cc_start: 0.9300 (m) cc_final: 0.9005 (m) REVERT: B 1025 PHE cc_start: 0.8512 (m-80) cc_final: 0.8283 (m-80) REVERT: B 1144 MET cc_start: 0.9704 (mmp) cc_final: 0.9413 (mmm) REVERT: B 1189 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8925 (mttm) REVERT: B 1210 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9090 (tm-30) REVERT: C 158 MET cc_start: 0.8029 (pmm) cc_final: 0.7740 (pmm) REVERT: C 510 MET cc_start: 0.9680 (tpt) cc_final: 0.9172 (tpp) REVERT: C 514 LEU cc_start: 0.9795 (mt) cc_final: 0.9483 (mt) REVERT: C 661 MET cc_start: 0.9271 (mmm) cc_final: 0.8925 (mmm) REVERT: C 667 MET cc_start: 0.8625 (mpp) cc_final: 0.8412 (mpp) REVERT: C 721 PHE cc_start: 0.9438 (m-80) cc_final: 0.9064 (m-10) REVERT: C 878 PHE cc_start: 0.9038 (m-80) cc_final: 0.8557 (m-80) REVERT: C 883 TYR cc_start: 0.9313 (t80) cc_final: 0.8294 (t80) REVERT: C 926 MET cc_start: 0.9384 (mmp) cc_final: 0.9115 (mmm) REVERT: C 987 VAL cc_start: 0.9608 (t) cc_final: 0.9196 (t) REVERT: C 1007 MET cc_start: 0.9601 (mtt) cc_final: 0.9231 (mmm) REVERT: C 1114 ASN cc_start: 0.9523 (m110) cc_final: 0.9218 (m110) REVERT: C 1152 LEU cc_start: 0.8375 (mt) cc_final: 0.7948 (mt) REVERT: C 1156 MET cc_start: 0.9607 (mmp) cc_final: 0.9358 (tpt) REVERT: D 298 LEU cc_start: 0.9364 (tp) cc_final: 0.9042 (pp) REVERT: D 684 MET cc_start: 0.9151 (mmm) cc_final: 0.8906 (tpp) REVERT: D 721 PHE cc_start: 0.9458 (m-80) cc_final: 0.8788 (m-80) REVERT: D 898 MET cc_start: 0.6374 (ttt) cc_final: 0.5130 (ttm) REVERT: D 984 TYR cc_start: 0.9428 (t80) cc_final: 0.9112 (t80) REVERT: D 986 ARG cc_start: 0.9059 (tpt90) cc_final: 0.8545 (tpt-90) REVERT: D 1007 MET cc_start: 0.4634 (mmp) cc_final: 0.2675 (ptt) REVERT: D 1112 LEU cc_start: 0.9690 (tt) cc_final: 0.9420 (mt) REVERT: D 1144 MET cc_start: 0.9658 (tpt) cc_final: 0.9450 (tpp) REVERT: D 1251 MET cc_start: 0.9317 (tmm) cc_final: 0.9016 (tmm) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1603 time to fit residues: 122.9752 Evaluate side-chains 389 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 49 optimal weight: 2.9990 chunk 199 optimal weight: 40.0000 chunk 246 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 267 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.046741 restraints weight = 151563.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047622 restraints weight = 122431.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048252 restraints weight = 106075.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048507 restraints weight = 95602.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048847 restraints weight = 90487.819| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31056 Z= 0.134 Angle : 0.677 7.887 41948 Z= 0.349 Chirality : 0.042 0.194 4764 Planarity : 0.004 0.066 5224 Dihedral : 5.147 29.206 4084 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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 are not related in a simple way. whole: -0.08 (0.14), residues: 3720 helix: 0.56 (0.10), residues: 2463 sheet: -0.57 (0.35), residues: 246 loop : -1.25 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 789 TYR 0.036 0.002 TYR C 976 PHE 0.036 0.002 PHE D1025 TRP 0.030 0.002 TRP A 751 HIS 0.011 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00278 (31056) covalent geometry : angle 0.67737 (41948) hydrogen bonds : bond 0.04334 ( 1844) hydrogen bonds : angle 5.09864 ( 5460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.9486 (tpp) cc_final: 0.9187 (tpt) REVERT: A 661 MET cc_start: 0.9151 (mmm) cc_final: 0.8717 (mmm) REVERT: A 666 LEU cc_start: 0.9596 (mt) cc_final: 0.9353 (mt) REVERT: A 697 MET cc_start: 0.9300 (mtp) cc_final: 0.8996 (mtp) REVERT: A 733 TYR cc_start: 0.9453 (t80) cc_final: 0.9207 (t80) REVERT: A 741 MET cc_start: 0.9461 (ptp) cc_final: 0.9021 (ppp) REVERT: A 781 MET cc_start: 0.9632 (mtp) cc_final: 0.9369 (mmt) REVERT: A 798 MET cc_start: 0.9027 (tmm) cc_final: 0.8744 (tmm) REVERT: A 869 TYR cc_start: 0.8839 (m-10) cc_final: 0.8535 (m-10) REVERT: A 879 TYR cc_start: 0.9149 (m-10) cc_final: 0.8675 (m-10) REVERT: A 883 TYR cc_start: 0.8889 (m-10) cc_final: 0.8684 (m-10) REVERT: A 890 PHE cc_start: 0.9672 (t80) cc_final: 0.9070 (t80) REVERT: A 926 MET cc_start: 0.8889 (mmp) cc_final: 0.8560 (mmp) REVERT: A 989 ASP cc_start: 0.9223 (m-30) cc_final: 0.9021 (m-30) REVERT: A 1103 CYS cc_start: 0.9785 (t) cc_final: 0.9561 (t) REVERT: A 1137 PHE cc_start: 0.9456 (t80) cc_final: 0.9081 (t80) REVERT: A 1152 LEU cc_start: 0.8708 (mt) cc_final: 0.8479 (tt) REVERT: A 1205 GLU cc_start: 0.9687 (tt0) cc_final: 0.9260 (tp30) REVERT: A 1251 MET cc_start: 0.9623 (mmp) cc_final: 0.9211 (mmm) REVERT: B 112 TYR cc_start: 0.8188 (m-80) cc_final: 0.7918 (m-80) REVERT: B 117 MET cc_start: 0.9232 (tmm) cc_final: 0.8816 (tmm) REVERT: B 118 TYR cc_start: 0.8844 (t80) cc_final: 0.8581 (t80) REVERT: B 219 MET cc_start: 0.9245 (mmt) cc_final: 0.8918 (mmt) REVERT: B 238 MET cc_start: 0.6274 (mmt) cc_final: 0.6001 (mmt) REVERT: B 272 LEU cc_start: 0.9673 (tp) cc_final: 0.9360 (pp) REVERT: B 510 MET cc_start: 0.9481 (tpp) cc_final: 0.8758 (tpp) REVERT: B 514 LEU cc_start: 0.9694 (mt) cc_final: 0.9200 (mt) REVERT: B 516 LEU cc_start: 0.9343 (tp) cc_final: 0.9081 (tp) REVERT: B 672 MET cc_start: 0.8761 (mmp) cc_final: 0.8280 (mmm) REVERT: B 684 MET cc_start: 0.9378 (mmp) cc_final: 0.9044 (mmp) REVERT: B 883 TYR cc_start: 0.9545 (t80) cc_final: 0.9179 (t80) REVERT: B 982 LEU cc_start: 0.9652 (mt) cc_final: 0.9284 (mp) REVERT: B 983 TRP cc_start: 0.9256 (m-90) cc_final: 0.8386 (m100) REVERT: B 1011 MET cc_start: 0.9619 (mmp) cc_final: 0.9403 (mmp) REVERT: B 1013 TYR cc_start: 0.8675 (t80) cc_final: 0.8435 (t80) REVERT: B 1014 PHE cc_start: 0.8650 (m-10) cc_final: 0.7917 (m-10) REVERT: B 1021 VAL cc_start: 0.9366 (m) cc_final: 0.9072 (m) REVERT: B 1025 PHE cc_start: 0.8468 (m-80) cc_final: 0.8203 (m-80) REVERT: B 1144 MET cc_start: 0.9707 (mmp) cc_final: 0.9416 (mmm) REVERT: B 1189 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8852 (mtpp) REVERT: B 1210 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9125 (tm-30) REVERT: B 1219 GLN cc_start: 0.9840 (tm-30) cc_final: 0.9612 (pp30) REVERT: C 298 LEU cc_start: 0.9548 (mp) cc_final: 0.9328 (tp) REVERT: C 510 MET cc_start: 0.9650 (tpt) cc_final: 0.9128 (tpp) REVERT: C 514 LEU cc_start: 0.9790 (mt) cc_final: 0.9513 (mt) REVERT: C 661 MET cc_start: 0.9240 (mmm) cc_final: 0.8859 (mmm) REVERT: C 667 MET cc_start: 0.8765 (mpp) cc_final: 0.8472 (mpp) REVERT: C 703 GLU cc_start: 0.8653 (pt0) cc_final: 0.8438 (pt0) REVERT: C 708 ASP cc_start: 0.9295 (t70) cc_final: 0.8905 (p0) REVERT: C 721 PHE cc_start: 0.9330 (m-80) cc_final: 0.9124 (m-80) REVERT: C 878 PHE cc_start: 0.9011 (m-80) cc_final: 0.8531 (m-80) REVERT: C 883 TYR cc_start: 0.9246 (t80) cc_final: 0.8328 (t80) REVERT: C 926 MET cc_start: 0.9431 (mmp) cc_final: 0.9131 (mmm) REVERT: C 987 VAL cc_start: 0.9513 (t) cc_final: 0.9219 (t) REVERT: C 1007 MET cc_start: 0.9623 (mtt) cc_final: 0.9243 (mmm) REVERT: C 1114 ASN cc_start: 0.9521 (m110) cc_final: 0.9207 (m110) REVERT: C 1152 LEU cc_start: 0.8616 (mt) cc_final: 0.8212 (mt) REVERT: C 1156 MET cc_start: 0.9616 (mmp) cc_final: 0.9351 (tpt) REVERT: D 298 LEU cc_start: 0.9378 (tp) cc_final: 0.9026 (pp) REVERT: D 672 MET cc_start: 0.9488 (tpp) cc_final: 0.9227 (tpp) REVERT: D 684 MET cc_start: 0.9393 (mmm) cc_final: 0.9142 (tpp) REVERT: D 721 PHE cc_start: 0.9348 (m-80) cc_final: 0.8658 (m-80) REVERT: D 898 MET cc_start: 0.6836 (ttt) cc_final: 0.6077 (ttm) REVERT: D 984 TYR cc_start: 0.9348 (t80) cc_final: 0.8940 (t80) REVERT: D 986 ARG cc_start: 0.9082 (tpt90) cc_final: 0.8817 (tpt-90) REVERT: D 1007 MET cc_start: 0.4944 (mmp) cc_final: 0.2704 (ptt) REVERT: D 1023 MET cc_start: 0.9297 (mmp) cc_final: 0.8870 (ttt) REVERT: D 1251 MET cc_start: 0.9317 (tmm) cc_final: 0.8979 (tmm) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.1645 time to fit residues: 133.6634 Evaluate side-chains 404 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 225 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 335 optimal weight: 0.0070 chunk 309 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 367 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN ** D 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048272 restraints weight = 138485.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048935 restraints weight = 118486.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049039 restraints weight = 106598.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049039 restraints weight = 104169.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049039 restraints weight = 104169.498| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31056 Z= 0.146 Angle : 0.691 15.246 41948 Z= 0.357 Chirality : 0.043 0.231 4764 Planarity : 0.005 0.065 5224 Dihedral : 5.131 27.751 4084 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 are not related in a simple way. whole: -0.12 (0.14), residues: 3720 helix: 0.51 (0.10), residues: 2471 sheet: -0.50 (0.35), residues: 244 loop : -1.23 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 962 TYR 0.041 0.002 TYR B 984 PHE 0.036 0.002 PHE A1124 TRP 0.043 0.002 TRP B1135 HIS 0.013 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00303 (31056) covalent geometry : angle 0.69086 (41948) hydrogen bonds : bond 0.04271 ( 1844) hydrogen bonds : angle 5.11068 ( 5460) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8864 (mmt) cc_final: 0.8663 (mmt) REVERT: A 382 MET cc_start: 0.9536 (tpp) cc_final: 0.9318 (tpt) REVERT: A 661 MET cc_start: 0.9152 (mmm) cc_final: 0.8826 (mmm) REVERT: A 697 MET cc_start: 0.9312 (mtp) cc_final: 0.9009 (mtp) REVERT: A 733 TYR cc_start: 0.9512 (t80) cc_final: 0.9267 (t80) REVERT: A 741 MET cc_start: 0.9455 (ptp) cc_final: 0.9206 (ptp) REVERT: A 781 MET cc_start: 0.9640 (mtp) cc_final: 0.9388 (mmt) REVERT: A 798 MET cc_start: 0.9013 (tmm) cc_final: 0.8768 (tmm) REVERT: A 869 TYR cc_start: 0.8820 (m-10) cc_final: 0.8528 (m-10) REVERT: A 879 TYR cc_start: 0.9240 (m-10) cc_final: 0.8826 (m-10) REVERT: A 890 PHE cc_start: 0.9699 (t80) cc_final: 0.9124 (t80) REVERT: A 1103 CYS cc_start: 0.9797 (t) cc_final: 0.9584 (t) REVERT: A 1135 TRP cc_start: 0.8492 (m-10) cc_final: 0.8274 (m-10) REVERT: A 1137 PHE cc_start: 0.9457 (t80) cc_final: 0.9104 (t80) REVERT: A 1152 LEU cc_start: 0.8876 (mt) cc_final: 0.8455 (tt) REVERT: A 1205 GLU cc_start: 0.9692 (tt0) cc_final: 0.9301 (tp30) REVERT: A 1250 PHE cc_start: 0.9775 (t80) cc_final: 0.9547 (t80) REVERT: A 1251 MET cc_start: 0.9618 (mmp) cc_final: 0.9103 (mmm) REVERT: B 117 MET cc_start: 0.9307 (tmm) cc_final: 0.9095 (tmm) REVERT: B 219 MET cc_start: 0.9255 (mmt) cc_final: 0.8922 (mmt) REVERT: B 238 MET cc_start: 0.6266 (mmt) cc_final: 0.6021 (mmt) REVERT: B 272 LEU cc_start: 0.9707 (tp) cc_final: 0.9389 (pp) REVERT: B 510 MET cc_start: 0.9527 (tpp) cc_final: 0.8789 (tpp) REVERT: B 514 LEU cc_start: 0.9698 (mt) cc_final: 0.9220 (mt) REVERT: B 516 LEU cc_start: 0.9420 (tp) cc_final: 0.9152 (tp) REVERT: B 684 MET cc_start: 0.9390 (mmp) cc_final: 0.8818 (mmp) REVERT: B 733 TYR cc_start: 0.9462 (t80) cc_final: 0.9241 (t80) REVERT: B 883 TYR cc_start: 0.9593 (t80) cc_final: 0.9240 (t80) REVERT: B 890 PHE cc_start: 0.9604 (t80) cc_final: 0.9235 (t80) REVERT: B 898 MET cc_start: 0.7847 (tmm) cc_final: 0.7364 (tmm) REVERT: B 982 LEU cc_start: 0.9581 (mt) cc_final: 0.9364 (mt) REVERT: B 983 TRP cc_start: 0.9178 (m-90) cc_final: 0.8485 (m-90) REVERT: B 984 TYR cc_start: 0.9116 (m-80) cc_final: 0.8050 (m-80) REVERT: B 1011 MET cc_start: 0.9598 (mmp) cc_final: 0.9383 (mmp) REVERT: B 1013 TYR cc_start: 0.8671 (t80) cc_final: 0.8412 (t80) REVERT: B 1014 PHE cc_start: 0.8620 (m-10) cc_final: 0.7903 (m-10) REVERT: B 1021 VAL cc_start: 0.9351 (m) cc_final: 0.9054 (m) REVERT: B 1025 PHE cc_start: 0.8450 (m-80) cc_final: 0.8188 (m-80) REVERT: B 1144 MET cc_start: 0.9711 (mmp) cc_final: 0.9438 (mmm) REVERT: B 1210 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9182 (tm-30) REVERT: B 1219 GLN cc_start: 0.9825 (tm-30) cc_final: 0.9617 (pp30) REVERT: C 298 LEU cc_start: 0.9569 (mp) cc_final: 0.9350 (tp) REVERT: C 510 MET cc_start: 0.9621 (tpt) cc_final: 0.9135 (tpp) REVERT: C 514 LEU cc_start: 0.9785 (mt) cc_final: 0.9507 (mt) REVERT: C 661 MET cc_start: 0.9214 (mmm) cc_final: 0.8837 (mmm) REVERT: C 667 MET cc_start: 0.8667 (mpp) cc_final: 0.8430 (mpp) REVERT: C 703 GLU cc_start: 0.8666 (pt0) cc_final: 0.8452 (pt0) REVERT: C 708 ASP cc_start: 0.9315 (t70) cc_final: 0.8932 (p0) REVERT: C 721 PHE cc_start: 0.9354 (m-80) cc_final: 0.9144 (m-80) REVERT: C 748 LEU cc_start: 0.9829 (mm) cc_final: 0.9588 (mm) REVERT: C 878 PHE cc_start: 0.9043 (m-80) cc_final: 0.8563 (m-80) REVERT: C 883 TYR cc_start: 0.9284 (t80) cc_final: 0.8372 (t80) REVERT: C 926 MET cc_start: 0.9421 (mmp) cc_final: 0.9121 (mmm) REVERT: C 987 VAL cc_start: 0.9551 (t) cc_final: 0.9262 (t) REVERT: C 988 LEU cc_start: 0.9600 (tp) cc_final: 0.9357 (tp) REVERT: C 1007 MET cc_start: 0.9639 (mtt) cc_final: 0.9283 (mmm) REVERT: C 1114 ASN cc_start: 0.9513 (m110) cc_final: 0.9201 (m110) REVERT: C 1152 LEU cc_start: 0.8611 (mt) cc_final: 0.8165 (mt) REVERT: C 1156 MET cc_start: 0.9641 (mmp) cc_final: 0.9365 (tpt) REVERT: D 238 MET cc_start: 0.5985 (tpt) cc_final: 0.5620 (tpt) REVERT: D 298 LEU cc_start: 0.9403 (tp) cc_final: 0.9054 (pp) REVERT: D 672 MET cc_start: 0.9479 (tpp) cc_final: 0.9238 (mmt) REVERT: D 684 MET cc_start: 0.9423 (mmm) cc_final: 0.9189 (tpp) REVERT: D 721 PHE cc_start: 0.9387 (m-80) cc_final: 0.8823 (m-80) REVERT: D 898 MET cc_start: 0.7052 (ttt) cc_final: 0.6495 (ttm) REVERT: D 984 TYR cc_start: 0.9326 (t80) cc_final: 0.8912 (t80) REVERT: D 986 ARG cc_start: 0.9092 (tpt90) cc_final: 0.8610 (tpt-90) REVERT: D 1007 MET cc_start: 0.5021 (mmp) cc_final: 0.2827 (ptt) REVERT: D 1023 MET cc_start: 0.9354 (mmp) cc_final: 0.8931 (ttt) REVERT: D 1251 MET cc_start: 0.9313 (tmm) cc_final: 0.8857 (tmm) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.1578 time to fit residues: 125.6877 Evaluate side-chains 399 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 149 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 318 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 188 optimal weight: 30.0000 chunk 330 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.059293 restraints weight = 199096.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060521 restraints weight = 139332.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061386 restraints weight = 108634.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062029 restraints weight = 90968.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062473 restraints weight = 79916.034| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31056 Z= 0.138 Angle : 0.692 14.157 41948 Z= 0.356 Chirality : 0.043 0.254 4764 Planarity : 0.005 0.065 5224 Dihedral : 5.090 26.109 4084 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 are not related in a simple way. whole: -0.09 (0.14), residues: 3720 helix: 0.53 (0.10), residues: 2462 sheet: -0.43 (0.35), residues: 244 loop : -1.21 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 897 TYR 0.082 0.002 TYR C1104 PHE 0.036 0.002 PHE D1025 TRP 0.032 0.002 TRP A 983 HIS 0.009 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00286 (31056) covalent geometry : angle 0.69160 (41948) hydrogen bonds : bond 0.04225 ( 1844) hydrogen bonds : angle 5.07713 ( 5460) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8901 (mmt) cc_final: 0.8689 (mmt) REVERT: A 382 MET cc_start: 0.9316 (tpp) cc_final: 0.8932 (tpt) REVERT: A 661 MET cc_start: 0.9120 (mmm) cc_final: 0.8809 (mmm) REVERT: A 666 LEU cc_start: 0.9661 (mt) cc_final: 0.9438 (mt) REVERT: A 667 MET cc_start: 0.9293 (mmp) cc_final: 0.9059 (mmm) REVERT: A 697 MET cc_start: 0.9277 (mtp) cc_final: 0.8979 (mtp) REVERT: A 733 TYR cc_start: 0.9208 (t80) cc_final: 0.8958 (t80) REVERT: A 741 MET cc_start: 0.9439 (ptp) cc_final: 0.9111 (ptp) REVERT: A 781 MET cc_start: 0.9502 (mtp) cc_final: 0.9298 (mmt) REVERT: A 798 MET cc_start: 0.8953 (tmm) cc_final: 0.8710 (tmm) REVERT: A 869 TYR cc_start: 0.8807 (m-10) cc_final: 0.8539 (m-10) REVERT: A 879 TYR cc_start: 0.9113 (m-10) cc_final: 0.8615 (m-10) REVERT: A 890 PHE cc_start: 0.9631 (t80) cc_final: 0.8995 (t80) REVERT: A 1137 PHE cc_start: 0.9475 (t80) cc_final: 0.9097 (t80) REVERT: A 1152 LEU cc_start: 0.8812 (mt) cc_final: 0.8393 (tt) REVERT: A 1205 GLU cc_start: 0.9662 (tt0) cc_final: 0.9227 (tp30) REVERT: A 1251 MET cc_start: 0.9613 (mmp) cc_final: 0.9251 (mmm) REVERT: B 219 MET cc_start: 0.9286 (mmt) cc_final: 0.8966 (mmt) REVERT: B 238 MET cc_start: 0.6197 (mmt) cc_final: 0.5963 (mmt) REVERT: B 272 LEU cc_start: 0.9752 (tp) cc_final: 0.9427 (pp) REVERT: B 510 MET cc_start: 0.9397 (tpp) cc_final: 0.8708 (tpp) REVERT: B 514 LEU cc_start: 0.9728 (mt) cc_final: 0.9223 (mt) REVERT: B 518 ARG cc_start: 0.8508 (mmt-90) cc_final: 0.7929 (mmt-90) REVERT: B 586 MET cc_start: 0.9424 (ptp) cc_final: 0.8894 (ppp) REVERT: B 684 MET cc_start: 0.9520 (mmp) cc_final: 0.9240 (mmp) REVERT: B 724 LEU cc_start: 0.9796 (mt) cc_final: 0.9574 (mt) REVERT: B 733 TYR cc_start: 0.9365 (t80) cc_final: 0.9144 (t80) REVERT: B 883 TYR cc_start: 0.9451 (t80) cc_final: 0.9094 (t80) REVERT: B 898 MET cc_start: 0.6521 (tmm) cc_final: 0.6178 (tmm) REVERT: B 956 MET cc_start: 0.9062 (ppp) cc_final: 0.8828 (ppp) REVERT: B 957 VAL cc_start: 0.9462 (t) cc_final: 0.9160 (t) REVERT: B 1014 PHE cc_start: 0.8703 (m-10) cc_final: 0.7870 (m-10) REVERT: B 1021 VAL cc_start: 0.9291 (m) cc_final: 0.8975 (m) REVERT: B 1025 PHE cc_start: 0.8486 (m-80) cc_final: 0.8222 (m-80) REVERT: B 1135 TRP cc_start: 0.8599 (m100) cc_final: 0.8240 (m100) REVERT: B 1144 MET cc_start: 0.9673 (mmp) cc_final: 0.9402 (mmm) REVERT: B 1210 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9028 (tm-30) REVERT: B 1219 GLN cc_start: 0.9837 (tm-30) cc_final: 0.9596 (pp30) REVERT: C 158 MET cc_start: 0.8081 (pmm) cc_final: 0.7733 (pmm) REVERT: C 510 MET cc_start: 0.9661 (tpt) cc_final: 0.9111 (tpp) REVERT: C 514 LEU cc_start: 0.9801 (mt) cc_final: 0.9497 (mt) REVERT: C 661 MET cc_start: 0.9282 (mmm) cc_final: 0.8944 (mmm) REVERT: C 708 ASP cc_start: 0.9269 (t70) cc_final: 0.8871 (p0) REVERT: C 721 PHE cc_start: 0.9477 (m-80) cc_final: 0.9253 (m-80) REVERT: C 786 LEU cc_start: 0.9740 (tp) cc_final: 0.9469 (tp) REVERT: C 789 ARG cc_start: 0.8746 (mpp-170) cc_final: 0.8215 (ptp90) REVERT: C 878 PHE cc_start: 0.8983 (m-80) cc_final: 0.8494 (m-80) REVERT: C 883 TYR cc_start: 0.9187 (t80) cc_final: 0.8253 (t80) REVERT: C 890 PHE cc_start: 0.8421 (m-10) cc_final: 0.8182 (m-80) REVERT: C 926 MET cc_start: 0.9391 (mmp) cc_final: 0.9073 (mmm) REVERT: C 987 VAL cc_start: 0.9566 (t) cc_final: 0.9178 (t) REVERT: C 991 PHE cc_start: 0.9367 (t80) cc_final: 0.9135 (t80) REVERT: C 1152 LEU cc_start: 0.8464 (mt) cc_final: 0.8138 (mt) REVERT: C 1156 MET cc_start: 0.9556 (mmp) cc_final: 0.9319 (tpt) REVERT: D 238 MET cc_start: 0.5899 (tpt) cc_final: 0.5560 (tpt) REVERT: D 298 LEU cc_start: 0.9366 (tp) cc_final: 0.9054 (pp) REVERT: D 684 MET cc_start: 0.9193 (mmm) cc_final: 0.8942 (tpp) REVERT: D 721 PHE cc_start: 0.9515 (m-80) cc_final: 0.9035 (m-80) REVERT: D 898 MET cc_start: 0.6067 (ttt) cc_final: 0.4906 (ttm) REVERT: D 983 TRP cc_start: 0.9324 (t-100) cc_final: 0.8987 (t-100) REVERT: D 986 ARG cc_start: 0.8973 (tpt90) cc_final: 0.8559 (tpt-90) REVERT: D 987 VAL cc_start: 0.9451 (t) cc_final: 0.9141 (t) REVERT: D 1007 MET cc_start: 0.4582 (mmp) cc_final: 0.2714 (ptt) REVERT: D 1023 MET cc_start: 0.9320 (mmp) cc_final: 0.8824 (ttt) REVERT: D 1144 MET cc_start: 0.9612 (tpt) cc_final: 0.9364 (tpp) REVERT: D 1251 MET cc_start: 0.9272 (tmm) cc_final: 0.8920 (tmm) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.1600 time to fit residues: 126.9114 Evaluate side-chains 407 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 252 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 301 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1109 ASN ** 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 = 0.3338 r_free = 0.3338 target = 0.075596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057626 restraints weight = 206495.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058797 restraints weight = 144495.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059612 restraints weight = 113005.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.060168 restraints weight = 94668.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060601 restraints weight = 83843.293| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31056 Z= 0.220 Angle : 0.735 11.572 41948 Z= 0.389 Chirality : 0.044 0.234 4764 Planarity : 0.005 0.070 5224 Dihedral : 5.237 26.950 4084 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 are not related in a simple way. whole: -0.31 (0.14), residues: 3720 helix: 0.35 (0.10), residues: 2456 sheet: -0.60 (0.35), residues: 244 loop : -1.21 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 789 TYR 0.050 0.002 TYR C1104 PHE 0.034 0.002 PHE A 991 TRP 0.030 0.002 TRP A 751 HIS 0.010 0.002 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00440 (31056) covalent geometry : angle 0.73512 (41948) hydrogen bonds : bond 0.04400 ( 1844) hydrogen bonds : angle 5.37844 ( 5460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5232.67 seconds wall clock time: 91 minutes 31.10 seconds (5491.10 seconds total)