Starting phenix.real_space_refine on Fri Sep 19 07:29:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mrw_23959/09_2025/7mrw_23959.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mrw_23959/09_2025/7mrw_23959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mrw_23959/09_2025/7mrw_23959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mrw_23959/09_2025/7mrw_23959.map" model { file = "/net/cci-nas-00/data/ceres_data/7mrw_23959/09_2025/7mrw_23959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mrw_23959/09_2025/7mrw_23959.cif" } resolution = 3.72 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= 0.004 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 119 5.16 5 C 15709 2.51 5 N 3882 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24152 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1209, 10149 Classifications: {'peptide': 1209} Link IDs: {'PTRANS': 26, 'TRANS': 1182} Chain breaks: 6 Chain: "B" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8123 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 3 Chain: "C" Number of atoms: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5880 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 677} Chain breaks: 2 Time building chain proxies: 4.92, per 1000 atoms: 0.20 Number of scatterers: 24152 At special positions: 0 Unit cell: (97.76, 137.28, 173.68, 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 119 16.00 O 4442 8.00 N 3882 7.00 C 15709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 413 " distance=2.02 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 791 " - pdb=" SG CYS B 851 " distance=2.02 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 947 " - pdb=" SG CYS B1034 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 620 " distance=2.02 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 536 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 863.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 9 sheets defined 65.5% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.572A pdb=" N GLN A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.592A pdb=" N GLU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 143 removed outlier: 3.717A pdb=" N LEU A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 160 through 181 removed outlier: 4.053A pdb=" N THR A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Proline residue: A 173 - end of helix removed outlier: 3.515A pdb=" N LYS A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.755A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 224 removed outlier: 4.195A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.761A pdb=" N LYS A 242 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.851A pdb=" N PHE A 252 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.546A pdb=" N ASN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.650A pdb=" N LYS A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 313 through 320 Processing helix chain 'A' and resid 321 through 333 removed outlier: 4.546A pdb=" N PHE A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.516A pdb=" N THR A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.747A pdb=" N ASP A 353 " --> pdb=" O LEU A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.715A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.630A pdb=" N PHE A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.749A pdb=" N HIS A 417 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 removed outlier: 3.670A pdb=" N TYR A 451 " --> pdb=" O TYR A 447 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.688A pdb=" N VAL A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.907A pdb=" N TYR A 479 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.713A pdb=" N VAL A 497 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 499 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 501 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.699A pdb=" N SER A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 Processing helix chain 'A' and resid 561 through 572 removed outlier: 4.044A pdb=" N VAL A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 585 through 596 removed outlier: 4.090A pdb=" N ASP A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 611 removed outlier: 4.147A pdb=" N TYR A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.637A pdb=" N TYR A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.654A pdb=" N VAL A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 641' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 691 through 700 removed outlier: 3.758A pdb=" N GLN A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 732 removed outlier: 3.835A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.605A pdb=" N TYR A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.968A pdb=" N ASP A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 784 removed outlier: 3.544A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 770 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.823A pdb=" N ASN A 790 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 791 " --> pdb=" O HIS A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 817 removed outlier: 4.231A pdb=" N ILE A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 816 " --> pdb=" O ASP A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 891 removed outlier: 4.252A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 914 removed outlier: 3.651A pdb=" N TYR A 905 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.930A pdb=" N ASN A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 976 removed outlier: 3.811A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 973 " --> pdb=" O MET A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 988 removed outlier: 4.229A pdb=" N ALA A 985 " --> pdb=" O ASN A 981 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 removed outlier: 3.808A pdb=" N VAL A 994 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 removed outlier: 3.557A pdb=" N THR A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.599A pdb=" N LEU A1032 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1054 removed outlier: 3.813A pdb=" N MET A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A1047 " --> pdb=" O TYR A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.926A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1083 removed outlier: 4.009A pdb=" N LYS A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A1081 " --> pdb=" O LYS A1077 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A1082 " --> pdb=" O LYS A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1101 removed outlier: 3.804A pdb=" N TRP A1101 " --> pdb=" O MET A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 3.519A pdb=" N GLY A1108 " --> pdb=" O PHE A1105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN A1109 " --> pdb=" O THR A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1141 through 1167 removed outlier: 3.693A pdb=" N ALA A1145 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A1162 " --> pdb=" O ASN A1158 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1218 removed outlier: 3.522A pdb=" N GLY A1207 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A1212 " --> pdb=" O PHE A1208 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A1214 " --> pdb=" O TYR A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 removed outlier: 3.503A pdb=" N TYR A1223 " --> pdb=" O MET A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1256 removed outlier: 3.624A pdb=" N ARG A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A1242 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A1244 " --> pdb=" O ARG A1240 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A1255 " --> pdb=" O ASN A1251 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A1256 " --> pdb=" O TYR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1281 removed outlier: 3.606A pdb=" N ILE A1266 " --> pdb=" O SER A1262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1287 Processing helix chain 'A' and resid 1288 through 1290 No H-bonds generated for 'chain 'A' and resid 1288 through 1290' Processing helix chain 'A' and resid 1296 through 1301 removed outlier: 3.667A pdb=" N HIS A1301 " --> pdb=" O MET A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1318 removed outlier: 3.830A pdb=" N ASN A1310 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A1314 " --> pdb=" O ASN A1310 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A1316 " --> pdb=" O ARG A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1346 removed outlier: 3.600A pdb=" N LEU A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A1345 " --> pdb=" O GLN A1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.559A pdb=" N SER B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 82 removed outlier: 3.626A pdb=" N ALA B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 105 removed outlier: 3.566A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.642A pdb=" N SER B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.627A pdb=" N LEU B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.985A pdb=" N ILE B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.559A pdb=" N PHE B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.890A pdb=" N TYR B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 230 through 236 removed outlier: 4.217A pdb=" N SER B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 258 removed outlier: 3.525A pdb=" N SER B 248 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.855A pdb=" N ASP B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 357 through 376 Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 390 through 408 removed outlier: 3.504A pdb=" N ARG B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.811A pdb=" N TYR B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.663A pdb=" N LEU B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.589A pdb=" N PHE B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 462 " --> pdb=" O HIS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.729A pdb=" N LYS B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.564A pdb=" N GLU B 497 " --> pdb=" O LYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 513 through 528 removed outlier: 3.530A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 540 through 556 removed outlier: 3.817A pdb=" N PHE B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 3.969A pdb=" N ILE B 566 " --> pdb=" O PRO B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 removed outlier: 3.503A pdb=" N LEU B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 611 removed outlier: 3.921A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 601 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 602 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 657 removed outlier: 3.960A pdb=" N TYR B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.726A pdb=" N GLN B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 removed outlier: 3.960A pdb=" N THR B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 735 Processing helix chain 'B' and resid 740 through 755 removed outlier: 4.004A pdb=" N LEU B 748 " --> pdb=" O TYR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 780 through 798 removed outlier: 3.519A pdb=" N LEU B 784 " --> pdb=" O TYR B 780 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 785 " --> pdb=" O HIS B 781 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 829 Processing helix chain 'B' and resid 842 through 854 removed outlier: 3.507A pdb=" N LYS B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 850 " --> pdb=" O LYS B 846 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 853 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 871 removed outlier: 3.540A pdb=" N ALA B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 Processing helix chain 'B' and resid 882 through 892 Processing helix chain 'B' and resid 897 through 919 removed outlier: 3.670A pdb=" N LYS B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 914 " --> pdb=" O LEU B 910 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 917 " --> pdb=" O LYS B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 937 removed outlier: 3.905A pdb=" N LEU B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 966 removed outlier: 3.599A pdb=" N THR B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 949 " --> pdb=" O TYR B 945 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 962 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 985 removed outlier: 3.643A pdb=" N ALA B 975 " --> pdb=" O ARG B 971 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR B 979 " --> pdb=" O ALA B 975 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 984 " --> pdb=" O ASP B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1002 through 1018 removed outlier: 3.538A pdb=" N LEU B1011 " --> pdb=" O GLU B1007 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B1013 " --> pdb=" O LYS B1009 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B1016 " --> pdb=" O GLU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1032 removed outlier: 3.539A pdb=" N TYR B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1039 removed outlier: 4.263A pdb=" N THR B1038 " --> pdb=" O CYS B1034 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER B1039 " --> pdb=" O HIS B1035 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1034 through 1039' Processing helix chain 'B' and resid 1039 through 1054 removed outlier: 4.927A pdb=" N LEU B1046 " --> pdb=" O ASN B1042 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP B1047 " --> pdb=" O PHE B1043 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1079 removed outlier: 3.506A pdb=" N PHE B1063 " --> pdb=" O TYR B1059 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B1064 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP B1068 " --> pdb=" O PHE B1064 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B1073 " --> pdb=" O GLN B1069 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B1074 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B1075 " --> pdb=" O ILE B1071 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B1076 " --> pdb=" O ARG B1072 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.615A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.597A pdb=" N SER C 59 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 60 " --> pdb=" O ALA C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.818A pdb=" N PHE C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.792A pdb=" N ASP C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 4.146A pdb=" N LEU C 100 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.758A pdb=" N GLU C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 137 removed outlier: 4.006A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 191 removed outlier: 3.515A pdb=" N LYS C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 removed outlier: 4.106A pdb=" N SER C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR C 205 " --> pdb=" O ASN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.771A pdb=" N LEU C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 249 through 264 removed outlier: 4.116A pdb=" N ASP C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 removed outlier: 3.985A pdb=" N CYS C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 298 removed outlier: 3.649A pdb=" N ASP C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET C 298 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 369 through 376 removed outlier: 3.669A pdb=" N THR C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 399 through 407 removed outlier: 3.611A pdb=" N HIS C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.009A pdb=" N ASN C 423 " --> pdb=" O GLN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 455 removed outlier: 3.534A pdb=" N GLY C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 492 removed outlier: 3.520A pdb=" N ILE C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 479 " --> pdb=" O CYS C 475 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 514 removed outlier: 3.904A pdb=" N TYR C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 514 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.532A pdb=" N ALA C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 removed outlier: 4.029A pdb=" N SER C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 570 removed outlier: 4.164A pdb=" N LEU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 592 removed outlier: 3.645A pdb=" N ILE C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 589 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 622 removed outlier: 4.295A pdb=" N LEU C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 615 " --> pdb=" O ASN C 611 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 619 " --> pdb=" O TYR C 615 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.843A pdb=" N GLU C 627 " --> pdb=" O PRO C 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU C 628 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 651 removed outlier: 3.512A pdb=" N ILE C 642 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 648 " --> pdb=" O LYS C 644 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 651 " --> pdb=" O ASP C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 666 removed outlier: 3.569A pdb=" N ARG C 659 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 665 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 690 removed outlier: 3.793A pdb=" N VAL C 676 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS C 688 " --> pdb=" O ASP C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 728 removed outlier: 3.612A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 726 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 removed outlier: 3.626A pdb=" N ALA C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA2, first strand: chain 'A' and resid 828 through 831 removed outlier: 3.577A pdb=" N SER A 858 " --> pdb=" O ARG A 831 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 482 removed outlier: 4.013A pdb=" N THR B 481 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 234 through 238 removed outlier: 3.546A pdb=" N LYS C 339 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'C' and resid 175 through 179 removed outlier: 5.146A pdb=" N LEU C 176 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 165 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 178 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AA9, first strand: chain 'C' and resid 310 through 311 removed outlier: 4.407A pdb=" N VAL C 706 " --> pdb=" O VAL C 311 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 2.43 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: 7354 1.34 - 1.46: 6345 1.46 - 1.59: 10830 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 24727 Sorted by residual: bond pdb=" CA PHE B 739 " pdb=" CB PHE B 739 " ideal model delta sigma weight residual 1.530 1.455 0.076 1.50e-02 4.44e+03 2.54e+01 bond pdb=" CB THR A 163 " pdb=" CG2 THR A 163 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CG1 ILE A 285 " pdb=" CD1 ILE A 285 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.74e+00 bond pdb=" CB ASN B 588 " pdb=" CG ASN B 588 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.37e+00 bond pdb=" CG LEU B 826 " pdb=" CD1 LEU B 826 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 24722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 31891 2.18 - 4.35: 1225 4.35 - 6.53: 150 6.53 - 8.71: 39 8.71 - 10.88: 9 Bond angle restraints: 33314 Sorted by residual: angle pdb=" N VAL A 934 " pdb=" CA VAL A 934 " pdb=" C VAL A 934 " ideal model delta sigma weight residual 109.46 101.80 7.66 1.38e+00 5.25e-01 3.08e+01 angle pdb=" C PHE C 471 " pdb=" N ARG C 472 " pdb=" CA ARG C 472 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C ILE C 93 " pdb=" N HIS C 94 " pdb=" CA HIS C 94 " ideal model delta sigma weight residual 121.31 128.10 -6.79 1.49e+00 4.50e-01 2.08e+01 angle pdb=" C ILE A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 120.38 126.69 -6.31 1.46e+00 4.69e-01 1.87e+01 angle pdb=" C LYS B 966 " pdb=" N PHE B 967 " pdb=" CA PHE B 967 " ideal model delta sigma weight residual 124.31 131.51 -7.20 1.67e+00 3.59e-01 1.86e+01 ... (remaining 33309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 14053 15.71 - 31.43: 743 31.43 - 47.14: 83 47.14 - 62.85: 12 62.85 - 78.56: 5 Dihedral angle restraints: 14896 sinusoidal: 6197 harmonic: 8699 Sorted by residual: dihedral pdb=" CA SER A1011 " pdb=" C SER A1011 " pdb=" N ILE A1012 " pdb=" CA ILE A1012 " ideal model delta harmonic sigma weight residual -180.00 -132.49 -47.51 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -164.56 78.56 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CA LEU C 286 " pdb=" C LEU C 286 " pdb=" N LYS C 287 " pdb=" CA LYS C 287 " ideal model delta harmonic sigma weight residual -180.00 -147.16 -32.84 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 14893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2493 0.054 - 0.108: 942 0.108 - 0.162: 128 0.162 - 0.215: 24 0.215 - 0.269: 7 Chirality restraints: 3594 Sorted by residual: chirality pdb=" CB ILE B 349 " pdb=" CA ILE B 349 " pdb=" CG1 ILE B 349 " pdb=" CG2 ILE B 349 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE C 93 " pdb=" CA ILE C 93 " pdb=" CG1 ILE C 93 " pdb=" CG2 ILE C 93 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3591 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 253 " -0.013 2.00e-02 2.50e+03 2.37e-02 9.82e+00 pdb=" CG PHE A 253 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 253 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 253 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 253 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 253 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 583 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" CG ASN B 583 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B 583 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 583 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 705 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO B 706 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 706 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 706 " 0.038 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4723 2.75 - 3.29: 22870 3.29 - 3.83: 38978 3.83 - 4.36: 49364 4.36 - 4.90: 81513 Nonbonded interactions: 197448 Sorted by model distance: nonbonded pdb=" O PRO A 838 " pdb=" OH TYR B 441 " model vdw 2.217 3.040 nonbonded pdb=" O LEU A 704 " pdb=" OH TYR B 689 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR A1024 " pdb=" OD2 ASP A1315 " model vdw 2.249 3.040 nonbonded pdb=" O ASP C 433 " pdb=" OG1 THR C 436 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR A1326 " pdb=" O ILE C 498 " model vdw 2.260 3.040 ... (remaining 197443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.660 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.009 0.085 24740 Z= 0.384 Angle : 1.003 10.885 33340 Z= 0.559 Chirality : 0.054 0.269 3594 Planarity : 0.006 0.068 4182 Dihedral : 9.641 77.618 9235 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 0.22 % Allowed : 0.96 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.11), residues: 2859 helix: -3.74 (0.07), residues: 1661 sheet: -0.93 (0.76), residues: 53 loop : -1.66 (0.15), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 549 TYR 0.033 0.003 TYR A 467 PHE 0.052 0.004 PHE A 253 TRP 0.039 0.005 TRP B 557 HIS 0.013 0.003 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00891 (24727) covalent geometry : angle 1.00113 (33314) SS BOND : bond 0.00731 ( 13) SS BOND : angle 2.21192 ( 26) hydrogen bonds : bond 0.29589 ( 1057) hydrogen bonds : angle 10.01286 ( 3087) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 565 time to evaluate : 0.893 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: A 814 TYR cc_start: 0.9041 (t80) cc_final: 0.8714 (t80) REVERT: A 970 LEU cc_start: 0.9097 (mt) cc_final: 0.8523 (mt) REVERT: A 1220 MET cc_start: 0.6902 (ptm) cc_final: 0.6478 (ptm) REVERT: B 96 MET cc_start: 0.7815 (tpt) cc_final: 0.7512 (tpp) REVERT: B 152 ASN cc_start: 0.8575 (m-40) cc_final: 0.7865 (m110) REVERT: B 349 ILE cc_start: 0.7117 (mm) cc_final: 0.5686 (mm) REVERT: B 359 LYS cc_start: 0.8868 (tttt) cc_final: 0.8239 (tppt) REVERT: B 393 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6801 (mt-10) REVERT: B 522 LEU cc_start: 0.8648 (tp) cc_final: 0.8362 (tt) REVERT: B 575 VAL cc_start: 0.8887 (t) cc_final: 0.8635 (p) REVERT: B 652 ASP cc_start: 0.8228 (t70) cc_final: 0.7929 (t0) REVERT: B 743 SER cc_start: 0.8766 (m) cc_final: 0.8505 (t) REVERT: B 787 LEU cc_start: 0.9069 (tp) cc_final: 0.8706 (tp) REVERT: B 839 ASP cc_start: 0.7629 (m-30) cc_final: 0.7429 (m-30) REVERT: B 861 GLU cc_start: 0.8367 (tp30) cc_final: 0.8034 (tp30) REVERT: B 943 LYS cc_start: 0.9001 (mttt) cc_final: 0.8752 (mtpp) REVERT: B 980 ASP cc_start: 0.8572 (m-30) cc_final: 0.8183 (m-30) REVERT: B 1001 GLN cc_start: 0.8452 (mt0) cc_final: 0.7658 (mp10) REVERT: C 59 SER cc_start: 0.9598 (m) cc_final: 0.9097 (t) REVERT: C 104 TRP cc_start: 0.9021 (t60) cc_final: 0.8576 (t60) REVERT: C 164 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8576 (mmtt) REVERT: C 506 LEU cc_start: 0.9305 (tp) cc_final: 0.7886 (tp) REVERT: C 534 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7419 (mtm110) REVERT: C 640 ASP cc_start: 0.7991 (m-30) cc_final: 0.7627 (m-30) outliers start: 6 outliers final: 0 residues processed: 568 average time/residue: 0.1487 time to fit residues: 135.1463 Evaluate side-chains 273 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 247 ASN A 279 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 478 ASN A 525 GLN A 621 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 785 GLN A 801 ASN A 933 ASN A 937 ASN A 978 ASN A1042 ASN B 73 ASN B 157 ASN B 223 ASN B 286 HIS B 450 ASN B 521 GLN B 588 ASN B 666 ASN B 729 ASN B 875 GLN ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 ASN C 128 GLN C 225 ASN C 468 HIS C 486 ASN C 572 ASN C 617 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084567 restraints weight = 59260.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087240 restraints weight = 29921.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089010 restraints weight = 18703.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090203 restraints weight = 13478.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091006 restraints weight = 10731.784| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24740 Z= 0.152 Angle : 0.619 10.293 33340 Z= 0.329 Chirality : 0.041 0.164 3594 Planarity : 0.004 0.064 4182 Dihedral : 5.565 41.053 3158 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.17 % Allowed : 7.33 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.13), residues: 2859 helix: -1.63 (0.10), residues: 1696 sheet: -0.36 (0.73), residues: 53 loop : -1.18 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 957 TYR 0.027 0.002 TYR A1242 PHE 0.031 0.002 PHE A 614 TRP 0.018 0.002 TRP A 645 HIS 0.009 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00341 (24727) covalent geometry : angle 0.61778 (33314) SS BOND : bond 0.00283 ( 13) SS BOND : angle 1.68894 ( 26) hydrogen bonds : bond 0.05268 ( 1057) hydrogen bonds : angle 5.22147 ( 3087) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 363 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.7856 (m-80) cc_final: 0.7622 (m-80) REVERT: A 377 GLU cc_start: 0.8144 (tp30) cc_final: 0.7872 (tp30) REVERT: A 463 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8035 (mppt) REVERT: A 595 TYR cc_start: 0.9291 (t80) cc_final: 0.8808 (t80) REVERT: A 626 MET cc_start: 0.7984 (tpp) cc_final: 0.7768 (tpt) REVERT: A 781 MET cc_start: 0.8598 (mmp) cc_final: 0.8136 (mtp) REVERT: A 788 VAL cc_start: 0.9469 (t) cc_final: 0.9219 (p) REVERT: A 807 MET cc_start: 0.8905 (mmm) cc_final: 0.7316 (mmm) REVERT: A 814 TYR cc_start: 0.9006 (t80) cc_final: 0.8678 (t80) REVERT: A 970 LEU cc_start: 0.9014 (mt) cc_final: 0.8474 (mt) REVERT: A 974 MET cc_start: 0.7720 (mtm) cc_final: 0.6878 (mtm) REVERT: A 1146 GLU cc_start: 0.8638 (tp30) cc_final: 0.8347 (mm-30) REVERT: A 1220 MET cc_start: 0.6970 (ptm) cc_final: 0.6621 (ptm) REVERT: A 1308 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7540 (mmt) REVERT: A 1329 ASP cc_start: 0.8222 (t0) cc_final: 0.7948 (t0) REVERT: B 152 ASN cc_start: 0.8729 (m-40) cc_final: 0.8514 (m110) REVERT: B 246 SER cc_start: 0.9392 (m) cc_final: 0.9039 (t) REVERT: B 349 ILE cc_start: 0.7118 (mm) cc_final: 0.5787 (mm) REVERT: B 359 LYS cc_start: 0.8801 (tttt) cc_final: 0.8196 (tppt) REVERT: B 365 MET cc_start: 0.8518 (mmm) cc_final: 0.8226 (mmp) REVERT: B 384 TYR cc_start: 0.7985 (t80) cc_final: 0.7530 (t80) REVERT: B 396 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7512 (tpt170) REVERT: B 522 LEU cc_start: 0.8463 (tp) cc_final: 0.8261 (tt) REVERT: B 980 ASP cc_start: 0.8619 (m-30) cc_final: 0.8269 (m-30) REVERT: C 59 SER cc_start: 0.9636 (m) cc_final: 0.9134 (t) REVERT: C 75 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 164 LYS cc_start: 0.9221 (mmtp) cc_final: 0.8919 (mmtt) REVERT: C 534 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7364 (mtm110) REVERT: C 650 MET cc_start: 0.8117 (mmm) cc_final: 0.7567 (mmm) outliers start: 59 outliers final: 23 residues processed: 403 average time/residue: 0.1749 time to fit residues: 113.3507 Evaluate side-chains 287 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 552 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 68 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 564 GLN A 629 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN B 450 ASN B 704 ASN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.100993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085782 restraints weight = 58315.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088400 restraints weight = 28929.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090150 restraints weight = 17862.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091337 restraints weight = 12718.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092061 restraints weight = 10015.136| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24740 Z= 0.129 Angle : 0.552 9.059 33340 Z= 0.289 Chirality : 0.040 0.178 3594 Planarity : 0.003 0.060 4182 Dihedral : 5.019 38.494 3158 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.39 % Allowed : 9.35 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.14), residues: 2859 helix: -0.63 (0.12), residues: 1698 sheet: -0.39 (0.71), residues: 53 loop : -0.96 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 957 TYR 0.022 0.001 TYR A1242 PHE 0.030 0.001 PHE A 402 TRP 0.017 0.002 TRP B 896 HIS 0.009 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00288 (24727) covalent geometry : angle 0.55127 (33314) SS BOND : bond 0.00222 ( 13) SS BOND : angle 1.21704 ( 26) hydrogen bonds : bond 0.04260 ( 1057) hydrogen bonds : angle 4.74163 ( 3087) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 1.031 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: A 140 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7012 (tt0) REVERT: A 312 PHE cc_start: 0.7607 (m-80) cc_final: 0.7353 (m-80) REVERT: A 392 MET cc_start: 0.7565 (mmt) cc_final: 0.7321 (tpp) REVERT: A 393 MET cc_start: 0.8367 (mtp) cc_final: 0.7817 (mtt) REVERT: A 595 TYR cc_start: 0.9274 (t80) cc_final: 0.8643 (t80) REVERT: A 628 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 781 MET cc_start: 0.8577 (mmp) cc_final: 0.8129 (mtp) REVERT: A 788 VAL cc_start: 0.9414 (t) cc_final: 0.9188 (p) REVERT: A 807 MET cc_start: 0.8757 (mmm) cc_final: 0.7733 (mmm) REVERT: A 814 TYR cc_start: 0.9039 (t80) cc_final: 0.8802 (t80) REVERT: A 1030 THR cc_start: 0.8954 (p) cc_final: 0.8752 (t) REVERT: A 1045 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8248 (tpp) REVERT: A 1146 GLU cc_start: 0.8600 (tp30) cc_final: 0.8311 (mm-30) REVERT: A 1220 MET cc_start: 0.7073 (ptm) cc_final: 0.6784 (ptm) REVERT: A 1308 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7296 (mmt) REVERT: A 1316 MET cc_start: 0.8956 (mmm) cc_final: 0.8531 (tpp) REVERT: A 1329 ASP cc_start: 0.8060 (t0) cc_final: 0.7719 (t0) REVERT: B 246 SER cc_start: 0.9199 (m) cc_final: 0.8741 (t) REVERT: B 278 LYS cc_start: 0.8434 (tttp) cc_final: 0.8152 (pttt) REVERT: B 359 LYS cc_start: 0.8798 (tttt) cc_final: 0.8186 (tppt) REVERT: B 365 MET cc_start: 0.8490 (mmm) cc_final: 0.8212 (mmp) REVERT: B 384 TYR cc_start: 0.7928 (t80) cc_final: 0.7555 (t80) REVERT: B 396 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7509 (tpt-90) REVERT: B 741 TYR cc_start: 0.8551 (m-80) cc_final: 0.8302 (m-10) REVERT: B 843 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8490 (tp) REVERT: B 847 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 886 MET cc_start: 0.8717 (ttp) cc_final: 0.8499 (ttp) REVERT: B 906 TYR cc_start: 0.9079 (t80) cc_final: 0.8839 (t80) REVERT: B 918 MET cc_start: 0.7847 (ptt) cc_final: 0.7466 (ptm) REVERT: B 941 MET cc_start: 0.8674 (ttm) cc_final: 0.8315 (tpp) REVERT: B 977 ASP cc_start: 0.8956 (m-30) cc_final: 0.8717 (m-30) REVERT: B 980 ASP cc_start: 0.8605 (m-30) cc_final: 0.8267 (m-30) REVERT: B 1054 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6640 (tt) REVERT: C 59 SER cc_start: 0.9629 (m) cc_final: 0.9129 (t) REVERT: C 75 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 164 LYS cc_start: 0.9165 (mmtp) cc_final: 0.8892 (mmtt) REVERT: C 450 GLU cc_start: 0.8384 (tp30) cc_final: 0.8114 (mm-30) REVERT: C 534 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7385 (mtm110) REVERT: C 629 ILE cc_start: 0.8898 (mt) cc_final: 0.8619 (mt) REVERT: C 650 MET cc_start: 0.8145 (mmm) cc_final: 0.7683 (mmm) outliers start: 65 outliers final: 33 residues processed: 362 average time/residue: 0.1385 time to fit residues: 83.9870 Evaluate side-chains 300 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 842 SER Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 150 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 165 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 937 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083958 restraints weight = 58784.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086490 restraints weight = 29389.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088218 restraints weight = 18179.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089307 restraints weight = 12975.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090121 restraints weight = 10317.350| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24740 Z= 0.163 Angle : 0.558 9.300 33340 Z= 0.290 Chirality : 0.041 0.180 3594 Planarity : 0.003 0.061 4182 Dihedral : 4.835 37.521 3158 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.21 % Allowed : 10.42 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 2859 helix: -0.08 (0.12), residues: 1692 sheet: -0.48 (0.70), residues: 53 loop : -0.86 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 946 TYR 0.027 0.001 TYR A1242 PHE 0.021 0.001 PHE A 607 TRP 0.011 0.001 TRP B 545 HIS 0.008 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00374 (24727) covalent geometry : angle 0.55670 (33314) SS BOND : bond 0.00529 ( 13) SS BOND : angle 1.21899 ( 26) hydrogen bonds : bond 0.03934 ( 1057) hydrogen bonds : angle 4.59167 ( 3087) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.875 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: A 140 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7220 (tt0) REVERT: A 262 MET cc_start: 0.7736 (mtm) cc_final: 0.7453 (mtp) REVERT: A 377 GLU cc_start: 0.8239 (tp30) cc_final: 0.7953 (tp30) REVERT: A 392 MET cc_start: 0.7612 (mmt) cc_final: 0.7298 (tpp) REVERT: A 393 MET cc_start: 0.8437 (mtp) cc_final: 0.7865 (mtt) REVERT: A 624 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 781 MET cc_start: 0.8519 (mmp) cc_final: 0.8118 (mtp) REVERT: A 788 VAL cc_start: 0.9510 (t) cc_final: 0.9280 (p) REVERT: A 807 MET cc_start: 0.8801 (mmm) cc_final: 0.7681 (mmm) REVERT: A 814 TYR cc_start: 0.9124 (t80) cc_final: 0.8730 (t80) REVERT: A 968 GLN cc_start: 0.6990 (tp-100) cc_final: 0.6779 (tp-100) REVERT: A 1012 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.5018 (mt) REVERT: A 1020 LEU cc_start: 0.8803 (mm) cc_final: 0.8498 (mm) REVERT: A 1030 THR cc_start: 0.8966 (p) cc_final: 0.8749 (t) REVERT: A 1045 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: A 1146 GLU cc_start: 0.8624 (tp30) cc_final: 0.8313 (mm-30) REVERT: A 1221 TYR cc_start: 0.8342 (m-10) cc_final: 0.8061 (m-10) REVERT: A 1308 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7370 (mpp) REVERT: A 1316 MET cc_start: 0.8899 (mmm) cc_final: 0.8189 (tpt) REVERT: A 1329 ASP cc_start: 0.8173 (t0) cc_final: 0.7877 (t0) REVERT: B 278 LYS cc_start: 0.8424 (tttp) cc_final: 0.8061 (ptmt) REVERT: B 359 LYS cc_start: 0.8797 (tttt) cc_final: 0.8188 (tppt) REVERT: B 379 ASP cc_start: 0.6060 (t0) cc_final: 0.5374 (t0) REVERT: B 384 TYR cc_start: 0.8014 (t80) cc_final: 0.7657 (t80) REVERT: B 396 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7536 (tpt-90) REVERT: B 437 ILE cc_start: 0.8801 (mm) cc_final: 0.8518 (mm) REVERT: B 509 ASN cc_start: 0.8288 (m-40) cc_final: 0.8003 (m-40) REVERT: B 769 MET cc_start: 0.6627 (mtt) cc_final: 0.5793 (mtt) REVERT: B 843 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 847 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (tt) REVERT: B 892 SER cc_start: 0.8963 (p) cc_final: 0.8689 (t) REVERT: B 914 MET cc_start: 0.7803 (mmm) cc_final: 0.7145 (tpt) REVERT: B 918 MET cc_start: 0.7879 (ptt) cc_final: 0.7540 (ptm) REVERT: B 977 ASP cc_start: 0.8961 (m-30) cc_final: 0.8742 (m-30) REVERT: B 980 ASP cc_start: 0.8578 (m-30) cc_final: 0.8290 (m-30) REVERT: B 1054 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6684 (tt) REVERT: C 59 SER cc_start: 0.9627 (m) cc_final: 0.9128 (t) REVERT: C 75 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8805 (tm-30) REVERT: C 114 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: C 121 MET cc_start: 0.8919 (mmm) cc_final: 0.8494 (mmm) REVERT: C 534 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7416 (mtm110) REVERT: C 629 ILE cc_start: 0.8963 (mt) cc_final: 0.8242 (mt) REVERT: C 633 MET cc_start: 0.7919 (mtm) cc_final: 0.7462 (mtm) REVERT: C 650 MET cc_start: 0.8176 (mmm) cc_final: 0.7673 (mmm) outliers start: 60 outliers final: 39 residues processed: 314 average time/residue: 0.1446 time to fit residues: 75.6937 Evaluate side-chains 288 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 180 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 402 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN B 730 HIS B 755 HIS ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 GLN B1035 HIS C 481 HIS ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080945 restraints weight = 60229.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083464 restraints weight = 31099.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085154 restraints weight = 19875.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086304 restraints weight = 14596.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087075 restraints weight = 11750.081| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24740 Z= 0.205 Angle : 0.587 9.556 33340 Z= 0.303 Chirality : 0.042 0.196 3594 Planarity : 0.003 0.064 4182 Dihedral : 4.831 36.597 3158 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.98 % Allowed : 10.94 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 2859 helix: 0.23 (0.12), residues: 1697 sheet: -0.62 (0.71), residues: 53 loop : -0.77 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 946 TYR 0.021 0.002 TYR A1242 PHE 0.029 0.002 PHE A 261 TRP 0.010 0.002 TRP B 896 HIS 0.007 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00470 (24727) covalent geometry : angle 0.58600 (33314) SS BOND : bond 0.00303 ( 13) SS BOND : angle 1.22859 ( 26) hydrogen bonds : bond 0.03878 ( 1057) hydrogen bonds : angle 4.55380 ( 3087) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7337 (tt0) REVERT: A 262 MET cc_start: 0.7992 (mtm) cc_final: 0.7693 (mtp) REVERT: A 377 GLU cc_start: 0.8328 (tp30) cc_final: 0.8071 (tp30) REVERT: A 392 MET cc_start: 0.7601 (mmt) cc_final: 0.7359 (tpp) REVERT: A 393 MET cc_start: 0.8449 (mtp) cc_final: 0.7884 (mtt) REVERT: A 781 MET cc_start: 0.8480 (mmp) cc_final: 0.8134 (mtp) REVERT: A 807 MET cc_start: 0.8973 (mmm) cc_final: 0.7775 (mmm) REVERT: A 814 TYR cc_start: 0.9187 (t80) cc_final: 0.8754 (t80) REVERT: A 1012 ILE cc_start: 0.5635 (OUTLIER) cc_final: 0.5161 (mt) REVERT: A 1030 THR cc_start: 0.8958 (p) cc_final: 0.8741 (t) REVERT: A 1146 GLU cc_start: 0.8627 (tp30) cc_final: 0.8237 (mm-30) REVERT: A 1221 TYR cc_start: 0.8252 (m-10) cc_final: 0.8031 (m-10) REVERT: A 1242 TYR cc_start: 0.8509 (t80) cc_final: 0.8270 (t80) REVERT: A 1308 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7427 (mpp) REVERT: A 1316 MET cc_start: 0.8778 (mmm) cc_final: 0.8141 (tpt) REVERT: A 1329 ASP cc_start: 0.8265 (t0) cc_final: 0.8047 (t0) REVERT: B 278 LYS cc_start: 0.8435 (tttp) cc_final: 0.8075 (ptmt) REVERT: B 359 LYS cc_start: 0.8781 (tttt) cc_final: 0.8176 (tppt) REVERT: B 379 ASP cc_start: 0.6079 (t0) cc_final: 0.5342 (t0) REVERT: B 384 TYR cc_start: 0.8065 (t80) cc_final: 0.7734 (t80) REVERT: B 396 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7430 (tpt-90) REVERT: B 437 ILE cc_start: 0.8804 (mm) cc_final: 0.8432 (mm) REVERT: B 509 ASN cc_start: 0.8243 (m-40) cc_final: 0.7965 (m-40) REVERT: B 741 TYR cc_start: 0.8644 (m-80) cc_final: 0.8415 (m-10) REVERT: B 769 MET cc_start: 0.6916 (mtt) cc_final: 0.6127 (mtt) REVERT: B 843 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8545 (tp) REVERT: B 847 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8085 (tt) REVERT: B 892 SER cc_start: 0.8936 (p) cc_final: 0.8619 (t) REVERT: B 914 MET cc_start: 0.7847 (mmm) cc_final: 0.7181 (tpt) REVERT: B 918 MET cc_start: 0.7986 (ptt) cc_final: 0.7618 (ptm) REVERT: B 922 MET cc_start: 0.7830 (ppp) cc_final: 0.7557 (ppp) REVERT: B 980 ASP cc_start: 0.8598 (m-30) cc_final: 0.8328 (m-30) REVERT: B 1001 GLN cc_start: 0.8516 (mt0) cc_final: 0.7693 (mt0) REVERT: B 1041 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7797 (tp30) REVERT: B 1054 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6784 (tt) REVERT: C 59 SER cc_start: 0.9641 (m) cc_final: 0.9104 (t) REVERT: C 75 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8765 (tm-30) REVERT: C 114 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: C 121 MET cc_start: 0.8929 (mmm) cc_final: 0.8552 (mmm) REVERT: C 534 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7468 (mtm110) REVERT: C 629 ILE cc_start: 0.9010 (mt) cc_final: 0.8245 (mt) REVERT: C 633 MET cc_start: 0.8007 (mtm) cc_final: 0.7500 (mtm) REVERT: C 650 MET cc_start: 0.8170 (mmm) cc_final: 0.7768 (mmm) outliers start: 81 outliers final: 48 residues processed: 314 average time/residue: 0.1374 time to fit residues: 72.7425 Evaluate side-chains 281 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 723 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 54 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 254 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083841 restraints weight = 58923.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.086453 restraints weight = 29860.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088195 restraints weight = 18711.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089365 restraints weight = 13475.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090073 restraints weight = 10716.407| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24740 Z= 0.116 Angle : 0.516 8.809 33340 Z= 0.265 Chirality : 0.039 0.214 3594 Planarity : 0.003 0.057 4182 Dihedral : 4.579 35.289 3158 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.06 % Allowed : 12.63 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 2859 helix: 0.56 (0.13), residues: 1703 sheet: -0.65 (0.71), residues: 53 loop : -0.74 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 946 TYR 0.017 0.001 TYR A1242 PHE 0.020 0.001 PHE A 607 TRP 0.009 0.001 TRP A 767 HIS 0.008 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00265 (24727) covalent geometry : angle 0.51566 (33314) SS BOND : bond 0.00226 ( 13) SS BOND : angle 1.17030 ( 26) hydrogen bonds : bond 0.03485 ( 1057) hydrogen bonds : angle 4.31033 ( 3087) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7348 (tt0) REVERT: A 262 MET cc_start: 0.8044 (mtm) cc_final: 0.7707 (mtp) REVERT: A 377 GLU cc_start: 0.8196 (tp30) cc_final: 0.7974 (tp30) REVERT: A 392 MET cc_start: 0.7628 (mmt) cc_final: 0.7413 (tpp) REVERT: A 393 MET cc_start: 0.8470 (mtp) cc_final: 0.7961 (mtt) REVERT: A 781 MET cc_start: 0.8434 (mmp) cc_final: 0.8129 (mtp) REVERT: A 807 MET cc_start: 0.8785 (mmm) cc_final: 0.7424 (mmm) REVERT: A 814 TYR cc_start: 0.9080 (t80) cc_final: 0.8795 (t80) REVERT: A 1012 ILE cc_start: 0.5610 (OUTLIER) cc_final: 0.5221 (mt) REVERT: A 1030 THR cc_start: 0.9010 (p) cc_final: 0.8786 (t) REVERT: A 1146 GLU cc_start: 0.8571 (tp30) cc_final: 0.8250 (mm-30) REVERT: A 1221 TYR cc_start: 0.8275 (m-10) cc_final: 0.8036 (m-10) REVERT: A 1242 TYR cc_start: 0.8386 (t80) cc_final: 0.8156 (t80) REVERT: A 1308 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7162 (mmm) REVERT: A 1316 MET cc_start: 0.8766 (mmm) cc_final: 0.8149 (tpt) REVERT: A 1329 ASP cc_start: 0.8050 (t0) cc_final: 0.7836 (t0) REVERT: B 121 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8634 (mt) REVERT: B 125 TYR cc_start: 0.8695 (t80) cc_final: 0.8411 (t80) REVERT: B 278 LYS cc_start: 0.8438 (tttp) cc_final: 0.8129 (pttt) REVERT: B 359 LYS cc_start: 0.8753 (tttt) cc_final: 0.8158 (tppt) REVERT: B 379 ASP cc_start: 0.5820 (t0) cc_final: 0.5248 (t0) REVERT: B 384 TYR cc_start: 0.8125 (t80) cc_final: 0.7789 (t80) REVERT: B 396 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7435 (tpt-90) REVERT: B 509 ASN cc_start: 0.8216 (m-40) cc_final: 0.7923 (m-40) REVERT: B 769 MET cc_start: 0.6877 (mtt) cc_final: 0.6175 (mtt) REVERT: B 843 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 847 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 892 SER cc_start: 0.8924 (p) cc_final: 0.8620 (t) REVERT: B 914 MET cc_start: 0.7832 (mmm) cc_final: 0.7552 (tpp) REVERT: B 918 MET cc_start: 0.7788 (ptt) cc_final: 0.7503 (ptm) REVERT: B 980 ASP cc_start: 0.8534 (m-30) cc_final: 0.8231 (m-30) REVERT: B 1001 GLN cc_start: 0.8516 (mt0) cc_final: 0.8280 (mt0) REVERT: B 1054 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6700 (tt) REVERT: C 59 SER cc_start: 0.9608 (m) cc_final: 0.9122 (t) REVERT: C 75 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8811 (tm-30) REVERT: C 114 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8805 (mp0) REVERT: C 121 MET cc_start: 0.8955 (mmm) cc_final: 0.8566 (mmm) REVERT: C 320 TYR cc_start: 0.8339 (m-80) cc_final: 0.8127 (m-10) REVERT: C 534 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7452 (mtm110) REVERT: C 629 ILE cc_start: 0.9018 (mt) cc_final: 0.8132 (mt) REVERT: C 633 MET cc_start: 0.7948 (mtm) cc_final: 0.7555 (mtm) REVERT: C 650 MET cc_start: 0.8183 (mmm) cc_final: 0.7758 (mmm) outliers start: 56 outliers final: 33 residues processed: 317 average time/residue: 0.1394 time to fit residues: 73.7602 Evaluate side-chains 273 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 723 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 53 optimal weight: 0.3980 chunk 260 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 193 optimal weight: 0.4980 chunk 42 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 272 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1158 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085716 restraints weight = 58124.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088302 restraints weight = 29092.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090042 restraints weight = 17928.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091212 restraints weight = 12745.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091866 restraints weight = 10011.535| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24740 Z= 0.106 Angle : 0.506 10.017 33340 Z= 0.258 Chirality : 0.039 0.229 3594 Planarity : 0.003 0.052 4182 Dihedral : 4.383 33.942 3158 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.10 % Allowed : 12.78 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.16), residues: 2859 helix: 0.84 (0.13), residues: 1697 sheet: -0.57 (0.71), residues: 53 loop : -0.60 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 946 TYR 0.020 0.001 TYR A 450 PHE 0.020 0.001 PHE A 607 TRP 0.008 0.001 TRP A 602 HIS 0.008 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00243 (24727) covalent geometry : angle 0.50516 (33314) SS BOND : bond 0.00195 ( 13) SS BOND : angle 1.06305 ( 26) hydrogen bonds : bond 0.03323 ( 1057) hydrogen bonds : angle 4.19495 ( 3087) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: A 140 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7357 (tt0) REVERT: A 377 GLU cc_start: 0.8165 (tp30) cc_final: 0.7957 (tp30) REVERT: A 587 ASP cc_start: 0.8007 (m-30) cc_final: 0.7316 (m-30) REVERT: A 626 MET cc_start: 0.8213 (tpp) cc_final: 0.7209 (tpp) REVERT: A 678 THR cc_start: 0.8371 (p) cc_final: 0.8121 (m) REVERT: A 747 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8753 (tmm-80) REVERT: A 781 MET cc_start: 0.8361 (mmp) cc_final: 0.8117 (mtp) REVERT: A 807 MET cc_start: 0.8822 (mmm) cc_final: 0.7374 (mmm) REVERT: A 814 TYR cc_start: 0.9074 (t80) cc_final: 0.8710 (t80) REVERT: A 1012 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.5132 (mt) REVERT: A 1030 THR cc_start: 0.8986 (p) cc_final: 0.8738 (t) REVERT: A 1146 GLU cc_start: 0.8549 (tp30) cc_final: 0.8255 (mm-30) REVERT: A 1242 TYR cc_start: 0.8376 (t80) cc_final: 0.8168 (t80) REVERT: A 1308 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7190 (mmm) REVERT: A 1316 MET cc_start: 0.8755 (mmm) cc_final: 0.8540 (tpt) REVERT: A 1329 ASP cc_start: 0.7975 (t0) cc_final: 0.7752 (t0) REVERT: B 121 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8611 (mt) REVERT: B 125 TYR cc_start: 0.8664 (t80) cc_final: 0.8388 (t80) REVERT: B 278 LYS cc_start: 0.8379 (tttp) cc_final: 0.8013 (pttt) REVERT: B 359 LYS cc_start: 0.8728 (tttt) cc_final: 0.8170 (tppt) REVERT: B 379 ASP cc_start: 0.5572 (t0) cc_final: 0.5100 (t0) REVERT: B 384 TYR cc_start: 0.8120 (t80) cc_final: 0.7792 (t80) REVERT: B 396 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7370 (tpt-90) REVERT: B 509 ASN cc_start: 0.8243 (m-40) cc_final: 0.7953 (m-40) REVERT: B 769 MET cc_start: 0.6811 (mtt) cc_final: 0.6147 (mtt) REVERT: B 847 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7975 (tt) REVERT: B 892 SER cc_start: 0.9028 (p) cc_final: 0.8690 (t) REVERT: B 914 MET cc_start: 0.7837 (mmm) cc_final: 0.7078 (tpt) REVERT: B 918 MET cc_start: 0.7780 (ptt) cc_final: 0.7558 (ptm) REVERT: B 980 ASP cc_start: 0.8464 (m-30) cc_final: 0.8173 (m-30) REVERT: B 1054 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6645 (tt) REVERT: C 59 SER cc_start: 0.9613 (m) cc_final: 0.9140 (t) REVERT: C 75 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8850 (tm-30) REVERT: C 114 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8801 (mp0) REVERT: C 121 MET cc_start: 0.8926 (mmm) cc_final: 0.8564 (mmm) REVERT: C 320 TYR cc_start: 0.8300 (m-80) cc_final: 0.8084 (m-10) REVERT: C 534 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7449 (mtm110) REVERT: C 629 ILE cc_start: 0.9003 (mt) cc_final: 0.8053 (mt) REVERT: C 633 MET cc_start: 0.7926 (mtm) cc_final: 0.7502 (mtm) REVERT: C 650 MET cc_start: 0.8117 (mmm) cc_final: 0.7816 (mmm) outliers start: 57 outliers final: 35 residues processed: 305 average time/residue: 0.1369 time to fit residues: 69.9731 Evaluate side-chains 292 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 174 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 144 optimal weight: 0.0040 chunk 175 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 236 optimal weight: 0.7980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A 891 ASN A 902 GLN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 = 0.3543 r_free = 0.3543 target = 0.100987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085589 restraints weight = 58981.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088216 restraints weight = 29683.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089963 restraints weight = 18473.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091043 restraints weight = 13240.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091884 restraints weight = 10581.472| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24740 Z= 0.118 Angle : 0.525 10.394 33340 Z= 0.265 Chirality : 0.040 0.239 3594 Planarity : 0.003 0.049 4182 Dihedral : 4.340 33.437 3158 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 13.29 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.16), residues: 2859 helix: 0.97 (0.13), residues: 1687 sheet: -0.47 (0.81), residues: 43 loop : -0.62 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 946 TYR 0.016 0.001 TYR A1350 PHE 0.019 0.001 PHE A 607 TRP 0.021 0.001 TRP A 602 HIS 0.007 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00272 (24727) covalent geometry : angle 0.52441 (33314) SS BOND : bond 0.00213 ( 13) SS BOND : angle 1.00863 ( 26) hydrogen bonds : bond 0.03327 ( 1057) hydrogen bonds : angle 4.18984 ( 3087) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 376 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8692 (mm) REVERT: A 626 MET cc_start: 0.8204 (tpp) cc_final: 0.7133 (tpp) REVERT: A 678 THR cc_start: 0.8401 (p) cc_final: 0.8054 (m) REVERT: A 781 MET cc_start: 0.8366 (mmp) cc_final: 0.8092 (mtp) REVERT: A 807 MET cc_start: 0.8880 (mmm) cc_final: 0.7511 (mmm) REVERT: A 814 TYR cc_start: 0.9091 (t80) cc_final: 0.8615 (t80) REVERT: A 902 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: A 1012 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.4995 (mt) REVERT: A 1030 THR cc_start: 0.8983 (p) cc_final: 0.8731 (t) REVERT: A 1050 MET cc_start: 0.7538 (mmp) cc_final: 0.7308 (mmm) REVERT: A 1097 MET cc_start: 0.7925 (tpp) cc_final: 0.7453 (tpp) REVERT: A 1146 GLU cc_start: 0.8592 (tp30) cc_final: 0.8285 (mm-30) REVERT: A 1221 TYR cc_start: 0.8287 (m-10) cc_final: 0.7969 (m-10) REVERT: A 1297 MET cc_start: 0.9029 (mmm) cc_final: 0.8635 (mmm) REVERT: A 1308 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7155 (mmm) REVERT: A 1316 MET cc_start: 0.8728 (mmm) cc_final: 0.8104 (tpt) REVERT: A 1329 ASP cc_start: 0.8040 (t0) cc_final: 0.7733 (t0) REVERT: B 121 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 125 TYR cc_start: 0.8733 (t80) cc_final: 0.8456 (t80) REVERT: B 278 LYS cc_start: 0.8416 (tttp) cc_final: 0.8071 (pttt) REVERT: B 359 LYS cc_start: 0.8695 (tttt) cc_final: 0.8123 (tppt) REVERT: B 379 ASP cc_start: 0.5736 (t0) cc_final: 0.5243 (t0) REVERT: B 384 TYR cc_start: 0.8153 (t80) cc_final: 0.7830 (t80) REVERT: B 396 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7323 (tpt-90) REVERT: B 509 ASN cc_start: 0.8276 (m-40) cc_final: 0.7982 (m-40) REVERT: B 769 MET cc_start: 0.6702 (mtt) cc_final: 0.6043 (mtt) REVERT: B 847 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 892 SER cc_start: 0.9094 (p) cc_final: 0.8824 (t) REVERT: B 914 MET cc_start: 0.7894 (mmm) cc_final: 0.7126 (tpt) REVERT: B 918 MET cc_start: 0.7858 (ptt) cc_final: 0.7617 (ptm) REVERT: B 980 ASP cc_start: 0.8511 (m-30) cc_final: 0.8209 (m-30) REVERT: B 1054 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6590 (tt) REVERT: C 59 SER cc_start: 0.9634 (m) cc_final: 0.9140 (t) REVERT: C 75 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8865 (tm-30) REVERT: C 114 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8814 (mp0) REVERT: C 121 MET cc_start: 0.8963 (mmm) cc_final: 0.8593 (mmm) REVERT: C 320 TYR cc_start: 0.8318 (m-80) cc_final: 0.8057 (m-10) REVERT: C 534 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7430 (mtm110) REVERT: C 629 ILE cc_start: 0.9003 (mt) cc_final: 0.8018 (mt) REVERT: C 633 MET cc_start: 0.7940 (mtm) cc_final: 0.7480 (mtm) REVERT: C 650 MET cc_start: 0.8223 (mmm) cc_final: 0.7740 (mmm) outliers start: 56 outliers final: 36 residues processed: 297 average time/residue: 0.1403 time to fit residues: 69.4080 Evaluate side-chains 290 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 902 GLN Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 189 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 257 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN A 927 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 = 0.3521 r_free = 0.3521 target = 0.099319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083249 restraints weight = 59830.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085865 restraints weight = 30593.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.087612 restraints weight = 19352.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088772 restraints weight = 14074.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089500 restraints weight = 11290.193| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24740 Z= 0.161 Angle : 0.563 9.550 33340 Z= 0.285 Chirality : 0.041 0.254 3594 Planarity : 0.003 0.048 4182 Dihedral : 4.398 32.941 3158 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.03 % Allowed : 13.55 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2859 helix: 1.00 (0.13), residues: 1687 sheet: -0.59 (0.80), residues: 43 loop : -0.60 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 946 TYR 0.029 0.001 TYR A1242 PHE 0.019 0.001 PHE A 312 TRP 0.014 0.002 TRP B 896 HIS 0.007 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00373 (24727) covalent geometry : angle 0.56268 (33314) SS BOND : bond 0.00254 ( 13) SS BOND : angle 1.03437 ( 26) hydrogen bonds : bond 0.03441 ( 1057) hydrogen bonds : angle 4.24053 ( 3087) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: A 377 GLU cc_start: 0.8173 (tp30) cc_final: 0.7711 (tm-30) REVERT: A 454 MET cc_start: 0.8724 (mmm) cc_final: 0.8409 (mmm) REVERT: A 553 ASN cc_start: 0.8480 (m110) cc_final: 0.8096 (p0) REVERT: A 567 TYR cc_start: 0.8156 (t80) cc_final: 0.7269 (t80) REVERT: A 626 MET cc_start: 0.8230 (tpp) cc_final: 0.7193 (tpp) REVERT: A 678 THR cc_start: 0.8447 (p) cc_final: 0.7960 (m) REVERT: A 781 MET cc_start: 0.8326 (mmp) cc_final: 0.8086 (mtp) REVERT: A 807 MET cc_start: 0.8955 (mmm) cc_final: 0.7628 (mmm) REVERT: A 814 TYR cc_start: 0.9182 (t80) cc_final: 0.8589 (t80) REVERT: A 1030 THR cc_start: 0.8977 (p) cc_final: 0.8745 (t) REVERT: A 1097 MET cc_start: 0.7995 (tpp) cc_final: 0.7597 (tpp) REVERT: A 1146 GLU cc_start: 0.8635 (tp30) cc_final: 0.8249 (mm-30) REVERT: A 1308 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7423 (mpp) REVERT: A 1316 MET cc_start: 0.8699 (mmm) cc_final: 0.8432 (tpp) REVERT: A 1329 ASP cc_start: 0.8181 (t0) cc_final: 0.7975 (t0) REVERT: B 121 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 125 TYR cc_start: 0.8774 (t80) cc_final: 0.8508 (t80) REVERT: B 278 LYS cc_start: 0.8416 (tttp) cc_final: 0.8058 (pttt) REVERT: B 359 LYS cc_start: 0.8701 (tttt) cc_final: 0.8118 (tppt) REVERT: B 379 ASP cc_start: 0.5758 (t0) cc_final: 0.5282 (t0) REVERT: B 384 TYR cc_start: 0.8186 (t80) cc_final: 0.7847 (t80) REVERT: B 396 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7327 (tpt-90) REVERT: B 437 ILE cc_start: 0.8672 (mm) cc_final: 0.8289 (mm) REVERT: B 509 ASN cc_start: 0.8195 (m-40) cc_final: 0.7903 (m-40) REVERT: B 769 MET cc_start: 0.6748 (mtt) cc_final: 0.6107 (mtt) REVERT: B 892 SER cc_start: 0.9098 (p) cc_final: 0.8830 (t) REVERT: B 914 MET cc_start: 0.7937 (mmm) cc_final: 0.7191 (tpt) REVERT: B 918 MET cc_start: 0.7833 (ptt) cc_final: 0.7594 (ptm) REVERT: B 980 ASP cc_start: 0.8517 (m-30) cc_final: 0.8214 (m-30) REVERT: B 1054 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6628 (tt) REVERT: C 59 SER cc_start: 0.9644 (m) cc_final: 0.9118 (t) REVERT: C 75 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8839 (tm-30) REVERT: C 114 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8782 (mp0) REVERT: C 121 MET cc_start: 0.8975 (mmm) cc_final: 0.8593 (mmm) REVERT: C 320 TYR cc_start: 0.8388 (m-80) cc_final: 0.8164 (m-10) REVERT: C 534 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7433 (mtm110) REVERT: C 629 ILE cc_start: 0.9019 (mt) cc_final: 0.8028 (mt) REVERT: C 633 MET cc_start: 0.7978 (mtm) cc_final: 0.7515 (mtm) REVERT: C 650 MET cc_start: 0.8152 (mmm) cc_final: 0.7678 (mmm) outliers start: 55 outliers final: 43 residues processed: 284 average time/residue: 0.1381 time to fit residues: 66.0895 Evaluate side-chains 290 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 HIS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 259 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 chunk 170 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 = 0.3542 r_free = 0.3542 target = 0.100540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085599 restraints weight = 58220.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088206 restraints weight = 29016.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089949 restraints weight = 17879.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091014 restraints weight = 12652.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091798 restraints weight = 10074.437| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24740 Z= 0.119 Angle : 0.534 9.225 33340 Z= 0.269 Chirality : 0.040 0.258 3594 Planarity : 0.003 0.047 4182 Dihedral : 4.347 32.510 3158 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.99 % Allowed : 13.70 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.16), residues: 2859 helix: 1.06 (0.13), residues: 1686 sheet: -0.57 (0.80), residues: 43 loop : -0.55 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 946 TYR 0.026 0.001 TYR A1242 PHE 0.022 0.001 PHE A 312 TRP 0.008 0.001 TRP B 827 HIS 0.007 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00277 (24727) covalent geometry : angle 0.53341 (33314) SS BOND : bond 0.00212 ( 13) SS BOND : angle 0.97160 ( 26) hydrogen bonds : bond 0.03309 ( 1057) hydrogen bonds : angle 4.18931 ( 3087) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.974 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: A 135 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: A 377 GLU cc_start: 0.8156 (tp30) cc_final: 0.7781 (tm-30) REVERT: A 553 ASN cc_start: 0.8450 (m110) cc_final: 0.7939 (p0) REVERT: A 567 TYR cc_start: 0.8147 (t80) cc_final: 0.7123 (t80) REVERT: A 626 MET cc_start: 0.8134 (tpp) cc_final: 0.7149 (tpp) REVERT: A 645 TRP cc_start: 0.8356 (t60) cc_final: 0.8011 (t60) REVERT: A 781 MET cc_start: 0.8290 (mmp) cc_final: 0.8081 (mtp) REVERT: A 807 MET cc_start: 0.8900 (mmm) cc_final: 0.7556 (mmm) REVERT: A 814 TYR cc_start: 0.9149 (t80) cc_final: 0.8598 (t80) REVERT: A 1030 THR cc_start: 0.8984 (p) cc_final: 0.8742 (t) REVERT: A 1097 MET cc_start: 0.8062 (tpp) cc_final: 0.7662 (tpp) REVERT: A 1146 GLU cc_start: 0.8581 (tp30) cc_final: 0.8272 (mm-30) REVERT: A 1297 MET cc_start: 0.9057 (mmm) cc_final: 0.8820 (mmm) REVERT: A 1308 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: A 1316 MET cc_start: 0.8695 (mmm) cc_final: 0.8100 (tpt) REVERT: A 1329 ASP cc_start: 0.8057 (t0) cc_final: 0.7722 (t0) REVERT: B 121 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (mt) REVERT: B 125 TYR cc_start: 0.8687 (t80) cc_final: 0.8443 (t80) REVERT: B 278 LYS cc_start: 0.8360 (tttp) cc_final: 0.8035 (pttt) REVERT: B 359 LYS cc_start: 0.8683 (tttt) cc_final: 0.8129 (tppt) REVERT: B 379 ASP cc_start: 0.5480 (t0) cc_final: 0.5044 (t0) REVERT: B 384 TYR cc_start: 0.8159 (t80) cc_final: 0.7838 (t80) REVERT: B 396 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7340 (tpt-90) REVERT: B 437 ILE cc_start: 0.8697 (mm) cc_final: 0.8325 (mm) REVERT: B 509 ASN cc_start: 0.8115 (m-40) cc_final: 0.7813 (m-40) REVERT: B 695 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 769 MET cc_start: 0.6609 (mtt) cc_final: 0.6221 (mtt) REVERT: B 892 SER cc_start: 0.9097 (p) cc_final: 0.8826 (t) REVERT: B 914 MET cc_start: 0.7853 (mmm) cc_final: 0.7114 (tpt) REVERT: B 918 MET cc_start: 0.7784 (ptt) cc_final: 0.7539 (ptm) REVERT: B 922 MET cc_start: 0.7511 (ppp) cc_final: 0.7177 (ppp) REVERT: B 980 ASP cc_start: 0.8442 (m-30) cc_final: 0.8177 (m-30) REVERT: B 1054 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6687 (tt) REVERT: C 59 SER cc_start: 0.9611 (m) cc_final: 0.9102 (t) REVERT: C 75 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8868 (tm-30) REVERT: C 114 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8815 (mp0) REVERT: C 121 MET cc_start: 0.8925 (mmm) cc_final: 0.8558 (mmm) REVERT: C 164 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8798 (mmmt) REVERT: C 534 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7450 (mtm110) REVERT: C 629 ILE cc_start: 0.8995 (mt) cc_final: 0.8031 (mt) REVERT: C 633 MET cc_start: 0.7936 (mtm) cc_final: 0.7477 (mtm) REVERT: C 650 MET cc_start: 0.8165 (mmm) cc_final: 0.7773 (mmm) outliers start: 54 outliers final: 41 residues processed: 302 average time/residue: 0.1423 time to fit residues: 71.2940 Evaluate side-chains 293 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1308 MET Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 684 ILE Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 1035 HIS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 235 optimal weight: 0.0370 chunk 144 optimal weight: 0.3980 chunk 224 optimal weight: 8.9990 chunk 223 optimal weight: 0.0970 chunk 189 optimal weight: 0.1980 chunk 232 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 241 optimal weight: 0.2980 chunk 217 optimal weight: 0.3980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 693 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 = 0.3570 r_free = 0.3570 target = 0.102058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086472 restraints weight = 58938.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089181 restraints weight = 29602.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090969 restraints weight = 18363.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092167 restraints weight = 13164.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092790 restraints weight = 10435.113| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24740 Z= 0.100 Angle : 0.541 11.435 33340 Z= 0.269 Chirality : 0.039 0.264 3594 Planarity : 0.003 0.047 4182 Dihedral : 4.293 31.441 3158 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.47 % Allowed : 14.62 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2859 helix: 1.08 (0.13), residues: 1688 sheet: -0.51 (0.81), residues: 43 loop : -0.54 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 946 TYR 0.025 0.001 TYR A1154 PHE 0.032 0.001 PHE A 312 TRP 0.021 0.001 TRP A 602 HIS 0.013 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00224 (24727) covalent geometry : angle 0.54024 (33314) SS BOND : bond 0.00170 ( 13) SS BOND : angle 0.92785 ( 26) hydrogen bonds : bond 0.03256 ( 1057) hydrogen bonds : angle 4.13967 ( 3087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3436.94 seconds wall clock time: 60 minutes 49.48 seconds (3649.48 seconds total)