Starting phenix.real_space_refine on Fri Jun 20 22:11:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mrw_23959/06_2025/7mrw_23959.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mrw_23959/06_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_23959/06_2025/7mrw_23959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mrw_23959/06_2025/7mrw_23959.map" model { file = "/net/cci-nas-00/data/ceres_data/7mrw_23959/06_2025/7mrw_23959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mrw_23959/06_2025/7mrw_23959.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.93, per 1000 atoms: 0.54 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: 5.36 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.50 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: 7.82 Time building geometry restraints manager: 6.48 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: 2.270 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: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 50.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.005 TRP B 557 HIS 0.013 0.003 HIS C 278 PHE 0.052 0.004 PHE A 253 TYR 0.033 0.003 TYR A 467 ARG 0.014 0.001 ARG C 549 Details of bonding type rmsd hydrogen bonds : bond 0.29589 ( 1057) hydrogen bonds : angle 10.01286 ( 3087) SS BOND : bond 0.00731 ( 13) SS BOND : angle 2.21192 ( 26) covalent geometry : bond 0.00891 (24727) covalent geometry : angle 1.00113 (33314) *********************** 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 : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.3458 time to fit residues: 310.3938 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 : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.9980 chunk 217 optimal weight: 0.0970 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084366 restraints weight = 58713.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086976 restraints weight = 29435.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088718 restraints weight = 18311.690| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24740 Z= 0.164 Angle : 0.634 10.576 33340 Z= 0.338 Chirality : 0.042 0.169 3594 Planarity : 0.004 0.063 4182 Dihedral : 5.601 41.064 3158 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.39 % Allowed : 6.92 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.13), residues: 2859 helix: -1.60 (0.10), residues: 1696 sheet: -0.37 (0.74), residues: 53 loop : -1.17 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 645 HIS 0.009 0.001 HIS B 458 PHE 0.030 0.002 PHE A 614 TYR 0.026 0.002 TYR A1242 ARG 0.010 0.001 ARG B1082 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 1057) hydrogen bonds : angle 5.22870 ( 3087) SS BOND : bond 0.00817 ( 13) SS BOND : angle 1.64980 ( 26) covalent geometry : bond 0.00364 (24727) covalent geometry : angle 0.63216 (33314) *********************** 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: 65 poor density : 357 time to evaluate : 2.791 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: 0.7888 (m-80) cc_final: 0.7658 (m-80) REVERT: A 352 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8861 (t) REVERT: A 377 GLU cc_start: 0.8193 (tp30) cc_final: 0.7907 (tp30) REVERT: A 463 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8013 (mppt) REVERT: A 595 TYR cc_start: 0.9327 (t80) cc_final: 0.8818 (t80) REVERT: A 781 MET cc_start: 0.8675 (mmp) cc_final: 0.8143 (mtp) REVERT: A 788 VAL cc_start: 0.9463 (t) cc_final: 0.9207 (p) REVERT: A 807 MET cc_start: 0.8925 (mmm) cc_final: 0.7356 (mmm) REVERT: A 814 TYR cc_start: 0.9028 (t80) cc_final: 0.8673 (t80) REVERT: A 970 LEU cc_start: 0.9009 (mt) cc_final: 0.8446 (mt) REVERT: A 974 MET cc_start: 0.7756 (mtm) cc_final: 0.6895 (mtm) REVERT: A 1146 GLU cc_start: 0.8712 (tp30) cc_final: 0.8389 (mm-30) REVERT: A 1209 MET cc_start: 0.8751 (mmm) cc_final: 0.8420 (mmt) REVERT: A 1220 MET cc_start: 0.6960 (ptm) cc_final: 0.6606 (ptm) REVERT: A 1308 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7519 (mmt) REVERT: A 1329 ASP cc_start: 0.8347 (t0) cc_final: 0.7982 (t0) REVERT: B 73 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (p0) REVERT: B 152 ASN cc_start: 0.8777 (m-40) cc_final: 0.8560 (m110) REVERT: B 246 SER cc_start: 0.9439 (m) cc_final: 0.9045 (t) REVERT: B 359 LYS cc_start: 0.8765 (tttt) cc_final: 0.8053 (tppt) REVERT: B 365 MET cc_start: 0.8669 (mmm) cc_final: 0.8354 (mmp) REVERT: B 384 TYR cc_start: 0.8039 (t80) cc_final: 0.7547 (t80) REVERT: B 396 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7414 (tpt170) REVERT: B 437 ILE cc_start: 0.8729 (mm) cc_final: 0.8209 (mm) REVERT: B 522 LEU cc_start: 0.8403 (tp) cc_final: 0.8194 (tt) REVERT: B 545 TRP cc_start: 0.8888 (t60) cc_final: 0.8674 (t60) REVERT: B 861 GLU cc_start: 0.8687 (tp30) cc_final: 0.8455 (tp30) REVERT: B 918 MET cc_start: 0.8064 (ptt) cc_final: 0.7829 (ptt) REVERT: B 980 ASP cc_start: 0.8699 (m-30) cc_final: 0.8323 (m-30) REVERT: C 59 SER cc_start: 0.9672 (m) cc_final: 0.9134 (t) REVERT: C 75 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 121 MET cc_start: 0.8998 (mmm) cc_final: 0.8798 (mmm) REVERT: C 164 LYS cc_start: 0.9235 (mmtp) cc_final: 0.8933 (mmtt) REVERT: C 534 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7320 (mtm110) REVERT: C 650 MET cc_start: 0.8308 (mmm) cc_final: 0.7617 (mmm) outliers start: 65 outliers final: 30 residues processed: 402 average time/residue: 0.3528 time to fit residues: 227.5399 Evaluate side-chains 297 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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 352 VAL Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 587 ASP 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 1166 SER 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 73 ASN 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 241 SER Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 901 ILE Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain B residue 1029 ILE 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 Chi-restraints excluded: chain C residue 554 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 187 optimal weight: 0.0070 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 178 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 282 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 ASN B 729 ASN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** 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 = 0.3554 r_free = 0.3554 target = 0.100987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085414 restraints weight = 58842.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088036 restraints weight = 29548.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089807 restraints weight = 18455.261| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24740 Z= 0.120 Angle : 0.548 9.010 33340 Z= 0.288 Chirality : 0.040 0.185 3594 Planarity : 0.003 0.059 4182 Dihedral : 5.032 38.688 3158 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.99 % Allowed : 9.35 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 2859 helix: -0.64 (0.12), residues: 1696 sheet: -0.40 (0.71), residues: 53 loop : -0.94 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 645 HIS 0.009 0.001 HIS B 458 PHE 0.027 0.001 PHE A 402 TYR 0.022 0.001 TYR A1242 ARG 0.003 0.000 ARG A 610 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 1057) hydrogen bonds : angle 4.74226 ( 3087) SS BOND : bond 0.00246 ( 13) SS BOND : angle 1.19153 ( 26) covalent geometry : bond 0.00265 (24727) covalent geometry : angle 0.54677 (33314) *********************** 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 379 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 325 time to evaluate : 3.070 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: 0.7621 (mt-10) cc_final: 0.7087 (tt0) REVERT: A 312 PHE cc_start: 0.7638 (m-80) cc_final: 0.7363 (m-80) REVERT: A 352 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8780 (t) REVERT: A 392 MET cc_start: 0.7550 (mmt) cc_final: 0.7311 (tpp) REVERT: A 393 MET cc_start: 0.8384 (mtp) cc_final: 0.7853 (mtt) REVERT: A 595 TYR cc_start: 0.9249 (t80) cc_final: 0.8721 (t80) REVERT: A 628 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 764 MET cc_start: 0.7724 (mtp) cc_final: 0.7493 (mtp) REVERT: A 781 MET cc_start: 0.8595 (mmp) cc_final: 0.8133 (mtp) REVERT: A 788 VAL cc_start: 0.9416 (t) cc_final: 0.9182 (p) REVERT: A 807 MET cc_start: 0.8727 (mmm) cc_final: 0.7708 (mmm) REVERT: A 814 TYR cc_start: 0.9047 (t80) cc_final: 0.8813 (t80) REVERT: A 1030 THR cc_start: 0.8953 (p) cc_final: 0.8750 (t) REVERT: A 1045 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8257 (tpp) REVERT: A 1146 GLU cc_start: 0.8603 (tp30) cc_final: 0.8313 (mm-30) REVERT: A 1220 MET cc_start: 0.7065 (ptm) cc_final: 0.6788 (ptm) REVERT: A 1308 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7300 (mmt) REVERT: A 1329 ASP cc_start: 0.8092 (t0) cc_final: 0.7736 (t0) REVERT: B 246 SER cc_start: 0.9176 (m) cc_final: 0.8734 (t) REVERT: B 278 LYS cc_start: 0.8493 (tttp) cc_final: 0.8158 (pttt) REVERT: B 349 ILE cc_start: 0.6879 (mm) cc_final: 0.6378 (mm) REVERT: B 359 LYS cc_start: 0.8804 (tttt) cc_final: 0.8195 (tppt) REVERT: B 365 MET cc_start: 0.8516 (mmm) cc_final: 0.8205 (mmp) REVERT: B 379 ASP cc_start: 0.7009 (t0) cc_final: 0.6594 (t70) REVERT: B 384 TYR cc_start: 0.7940 (t80) cc_final: 0.7562 (t80) REVERT: B 396 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7467 (tpt-90) REVERT: B 886 MET cc_start: 0.8685 (ttp) cc_final: 0.8464 (ttp) REVERT: B 906 TYR cc_start: 0.9053 (t80) cc_final: 0.8796 (t80) REVERT: B 918 MET cc_start: 0.7812 (ptt) cc_final: 0.7414 (ptm) REVERT: B 941 MET cc_start: 0.8689 (ttm) cc_final: 0.8321 (tpp) REVERT: B 977 ASP cc_start: 0.9018 (m-30) cc_final: 0.8813 (m-30) REVERT: B 980 ASP cc_start: 0.8675 (m-30) cc_final: 0.8330 (m-30) REVERT: B 1054 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6606 (tt) REVERT: C 59 SER cc_start: 0.9626 (m) cc_final: 0.9131 (t) REVERT: C 75 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8712 (tm-30) REVERT: C 121 MET cc_start: 0.9005 (mmm) cc_final: 0.8763 (mmm) REVERT: C 164 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8924 (mmtt) REVERT: C 450 GLU cc_start: 0.8426 (tp30) cc_final: 0.8143 (mm-30) REVERT: C 534 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7382 (mtm110) REVERT: C 633 MET cc_start: 0.7940 (mtm) cc_final: 0.7567 (mtm) REVERT: C 650 MET cc_start: 0.8191 (mmm) cc_final: 0.7698 (mmm) outliers start: 54 outliers final: 27 residues processed: 363 average time/residue: 0.3244 time to fit residues: 195.3498 Evaluate side-chains 290 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 352 VAL 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 854 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1045 MET 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 450 ASN Chi-restraints excluded: chain B residue 538 THR 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 891 LEU Chi-restraints excluded: chain B residue 929 LEU 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 474 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 157 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 629 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 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** ** B1024 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 = 0.3516 r_free = 0.3516 target = 0.098672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083048 restraints weight = 59829.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085620 restraints weight = 30337.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087356 restraints weight = 19099.974| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24740 Z= 0.163 Angle : 0.563 9.670 33340 Z= 0.292 Chirality : 0.041 0.206 3594 Planarity : 0.003 0.062 4182 Dihedral : 4.842 37.486 3158 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.32 % Allowed : 10.35 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2859 helix: -0.06 (0.12), residues: 1690 sheet: -0.49 (0.70), residues: 53 loop : -0.84 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 545 HIS 0.008 0.001 HIS B 458 PHE 0.021 0.001 PHE A 607 TYR 0.027 0.001 TYR A1242 ARG 0.002 0.000 ARG B 738 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1057) hydrogen bonds : angle 4.58444 ( 3087) SS BOND : bond 0.00280 ( 13) SS BOND : angle 1.21662 ( 26) covalent geometry : bond 0.00374 (24727) covalent geometry : angle 0.56232 (33314) *********************** 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 336 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 2.937 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 62 MET cc_start: 0.8393 (mtp) cc_final: 0.8115 (mtp) REVERT: A 140 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7333 (tt0) REVERT: A 352 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8765 (t) REVERT: A 377 GLU cc_start: 0.8204 (tp30) cc_final: 0.7942 (tp30) REVERT: A 392 MET cc_start: 0.7604 (mmt) cc_final: 0.7304 (tpp) REVERT: A 393 MET cc_start: 0.8449 (mtp) cc_final: 0.7919 (mtt) REVERT: A 781 MET cc_start: 0.8534 (mmp) cc_final: 0.8139 (mtp) REVERT: A 788 VAL cc_start: 0.9516 (t) cc_final: 0.9295 (p) REVERT: A 807 MET cc_start: 0.8795 (mmm) cc_final: 0.7678 (mmm) REVERT: A 814 TYR cc_start: 0.9108 (t80) cc_final: 0.8722 (t80) REVERT: A 1012 ILE cc_start: 0.5489 (OUTLIER) cc_final: 0.5076 (mt) REVERT: A 1030 THR cc_start: 0.8962 (p) cc_final: 0.8741 (t) REVERT: A 1146 GLU cc_start: 0.8629 (tp30) cc_final: 0.8324 (mm-30) REVERT: A 1221 TYR cc_start: 0.8320 (m-10) cc_final: 0.8058 (m-10) REVERT: A 1308 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7386 (mpp) REVERT: A 1329 ASP cc_start: 0.8244 (t0) cc_final: 0.8033 (t0) REVERT: A 1348 CYS cc_start: 0.7237 (m) cc_final: 0.6968 (p) REVERT: B 278 LYS cc_start: 0.8429 (tttp) cc_final: 0.8060 (ptmt) REVERT: B 359 LYS cc_start: 0.8803 (tttt) cc_final: 0.8173 (tppt) REVERT: B 384 TYR cc_start: 0.7985 (t80) cc_final: 0.7614 (t80) REVERT: B 396 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7535 (tpt-90) REVERT: B 509 ASN cc_start: 0.8352 (m-40) cc_final: 0.8070 (m-40) REVERT: B 847 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8022 (tt) REVERT: B 914 MET cc_start: 0.7823 (mmm) cc_final: 0.7164 (tpt) REVERT: B 918 MET cc_start: 0.7884 (ptt) cc_final: 0.7545 (ptm) REVERT: B 977 ASP cc_start: 0.8992 (m-30) cc_final: 0.8790 (m-30) REVERT: B 980 ASP cc_start: 0.8616 (m-30) cc_final: 0.8320 (m-30) REVERT: B 1054 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6655 (tt) REVERT: C 59 SER cc_start: 0.9615 (m) cc_final: 0.9101 (t) REVERT: C 75 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8844 (tm-30) REVERT: C 114 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: C 450 GLU cc_start: 0.8333 (tp30) cc_final: 0.8116 (mm-30) REVERT: C 534 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7415 (mtm110) REVERT: C 629 ILE cc_start: 0.8920 (mt) cc_final: 0.8089 (mt) REVERT: C 633 MET cc_start: 0.7968 (mtm) cc_final: 0.7574 (mtm) REVERT: C 650 MET cc_start: 0.8233 (mmm) cc_final: 0.7703 (mmm) outliers start: 63 outliers final: 37 residues processed: 320 average time/residue: 0.3359 time to fit residues: 179.0235 Evaluate side-chains 285 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 2.862 ------------------------------------------------------------------------------- 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 352 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 622 VAL 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 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 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 547 ASP Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 ILE Chi-restraints excluded: chain B residue 929 LEU 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 474 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 159 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 23 optimal weight: 0.0170 chunk 262 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 152 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 HIS 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 = 0.100541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084627 restraints weight = 59631.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087261 restraints weight = 30431.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089041 restraints weight = 19208.262| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3605 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= 0.109 Angle : 0.507 9.064 33340 Z= 0.262 Chirality : 0.039 0.198 3594 Planarity : 0.003 0.063 4182 Dihedral : 4.572 35.818 3158 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.10 % Allowed : 11.30 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 2859 helix: 0.37 (0.12), residues: 1700 sheet: -0.51 (0.71), residues: 53 loop : -0.73 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 545 HIS 0.008 0.001 HIS B 458 PHE 0.026 0.001 PHE A 261 TYR 0.018 0.001 TYR A1242 ARG 0.002 0.000 ARG A 957 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 1057) hydrogen bonds : angle 4.35221 ( 3087) SS BOND : bond 0.00194 ( 13) SS BOND : angle 1.03592 ( 26) covalent geometry : bond 0.00247 (24727) covalent geometry : angle 0.50673 (33314) *********************** 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 350 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 293 time to evaluate : 2.835 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: 0.7630 (mt-10) cc_final: 0.7346 (tt0) REVERT: A 352 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8756 (t) REVERT: A 377 GLU cc_start: 0.8158 (tp30) cc_final: 0.7918 (tp30) REVERT: A 392 MET cc_start: 0.7566 (mmt) cc_final: 0.7320 (tpp) REVERT: A 393 MET cc_start: 0.8456 (mtp) cc_final: 0.7943 (mtt) REVERT: A 781 MET cc_start: 0.8465 (mmp) cc_final: 0.8098 (mtp) REVERT: A 788 VAL cc_start: 0.9474 (t) cc_final: 0.9223 (p) REVERT: A 807 MET cc_start: 0.8682 (mmm) cc_final: 0.7420 (mmm) REVERT: A 814 TYR cc_start: 0.9103 (t80) cc_final: 0.8875 (t80) REVERT: A 1012 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.5092 (mt) REVERT: A 1020 LEU cc_start: 0.8793 (mm) cc_final: 0.8537 (mm) REVERT: A 1030 THR cc_start: 0.8993 (p) cc_final: 0.8774 (t) REVERT: A 1050 MET cc_start: 0.7729 (mmp) cc_final: 0.7502 (mmp) REVERT: A 1146 GLU cc_start: 0.8569 (tp30) cc_final: 0.8261 (mm-30) REVERT: A 1308 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: A 1329 ASP cc_start: 0.8054 (t0) cc_final: 0.7623 (t0) REVERT: B 121 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 125 TYR cc_start: 0.8751 (t80) cc_final: 0.8390 (t80) REVERT: B 278 LYS cc_start: 0.8435 (tttp) cc_final: 0.8122 (pttt) REVERT: B 280 MET cc_start: 0.8280 (mmm) cc_final: 0.8059 (tpp) REVERT: B 359 LYS cc_start: 0.8782 (tttt) cc_final: 0.8153 (tppt) REVERT: B 384 TYR cc_start: 0.8013 (t80) cc_final: 0.7692 (t80) REVERT: B 396 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7432 (tpt-90) REVERT: B 509 ASN cc_start: 0.8293 (m-40) cc_final: 0.7980 (m-40) REVERT: B 518 MET cc_start: 0.8123 (mtm) cc_final: 0.7918 (mtm) REVERT: B 847 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 892 SER cc_start: 0.8973 (p) cc_final: 0.8743 (t) REVERT: B 918 MET cc_start: 0.7985 (ptt) cc_final: 0.7529 (ptm) REVERT: B 922 MET cc_start: 0.7303 (ppp) cc_final: 0.7065 (ppp) REVERT: B 980 ASP cc_start: 0.8599 (m-30) cc_final: 0.8319 (m-30) REVERT: B 1054 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6545 (tt) REVERT: C 59 SER cc_start: 0.9624 (m) cc_final: 0.9126 (t) REVERT: C 75 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8809 (tm-30) REVERT: C 114 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8750 (mp0) REVERT: C 121 MET cc_start: 0.8992 (mmm) cc_final: 0.8533 (mmm) REVERT: C 534 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7386 (mtm110) REVERT: C 629 ILE cc_start: 0.8960 (mt) cc_final: 0.8081 (mt) REVERT: C 633 MET cc_start: 0.7962 (mtm) cc_final: 0.7530 (mtm) REVERT: C 650 MET cc_start: 0.8239 (mmm) cc_final: 0.7699 (mmm) outliers start: 57 outliers final: 29 residues processed: 335 average time/residue: 0.3360 time to fit residues: 187.5514 Evaluate side-chains 285 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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 352 VAL Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 622 VAL 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 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 743 SER 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 158 ILE Chi-restraints excluded: chain C residue 176 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 282 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 278 optimal weight: 0.0020 overall best weight: 1.3194 ------------------------------------------------------------------------------- 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** A1158 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083345 restraints weight = 59340.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085920 restraints weight = 30282.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087651 restraints weight = 19103.126| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3738 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= 0.145 Angle : 0.526 8.955 33340 Z= 0.272 Chirality : 0.040 0.215 3594 Planarity : 0.003 0.066 4182 Dihedral : 4.505 34.797 3158 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.43 % Allowed : 12.19 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2859 helix: 0.63 (0.13), residues: 1699 sheet: -0.55 (0.71), residues: 53 loop : -0.71 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 545 HIS 0.007 0.001 HIS B 458 PHE 0.019 0.001 PHE B 510 TYR 0.026 0.001 TYR A1242 ARG 0.002 0.000 ARG B 738 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 1057) hydrogen bonds : angle 4.31019 ( 3087) SS BOND : bond 0.00315 ( 13) SS BOND : angle 1.13730 ( 26) covalent geometry : bond 0.00335 (24727) covalent geometry : angle 0.52519 (33314) *********************** 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 321 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 2.836 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: 0.7648 (mt-10) cc_final: 0.7407 (tt0) REVERT: A 352 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8731 (t) REVERT: A 392 MET cc_start: 0.7637 (mmt) cc_final: 0.7434 (tpp) REVERT: A 747 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8724 (tmm-80) REVERT: A 781 MET cc_start: 0.8494 (mmp) cc_final: 0.8159 (mtp) REVERT: A 788 VAL cc_start: 0.9489 (t) cc_final: 0.9255 (p) REVERT: A 807 MET cc_start: 0.8809 (mmm) cc_final: 0.7576 (mmm) REVERT: A 814 TYR cc_start: 0.9154 (t80) cc_final: 0.8722 (t80) REVERT: A 1012 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5184 (mt) REVERT: A 1020 LEU cc_start: 0.8895 (mm) cc_final: 0.8552 (mm) REVERT: A 1030 THR cc_start: 0.9013 (p) cc_final: 0.8770 (t) REVERT: A 1146 GLU cc_start: 0.8591 (tp30) cc_final: 0.8289 (mm-30) REVERT: A 1221 TYR cc_start: 0.8271 (m-10) cc_final: 0.7902 (m-10) REVERT: A 1308 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7380 (mpp) REVERT: A 1329 ASP cc_start: 0.8200 (t0) cc_final: 0.7811 (t0) REVERT: B 121 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8728 (mt) REVERT: B 125 TYR cc_start: 0.8756 (t80) cc_final: 0.8436 (t80) REVERT: B 278 LYS cc_start: 0.8418 (tttp) cc_final: 0.8124 (pttt) REVERT: B 359 LYS cc_start: 0.8756 (tttt) cc_final: 0.8129 (tppt) REVERT: B 384 TYR cc_start: 0.8113 (t80) cc_final: 0.7772 (t80) REVERT: B 396 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7458 (tpt-90) REVERT: B 509 ASN cc_start: 0.8359 (m-40) cc_final: 0.8065 (m-40) REVERT: B 847 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7972 (tt) REVERT: B 892 SER cc_start: 0.9012 (p) cc_final: 0.8708 (t) REVERT: B 918 MET cc_start: 0.7777 (ptt) cc_final: 0.7390 (ptm) REVERT: B 980 ASP cc_start: 0.8582 (m-30) cc_final: 0.8244 (m-30) REVERT: B 1054 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6607 (tt) REVERT: C 59 SER cc_start: 0.9632 (m) cc_final: 0.9120 (t) REVERT: C 75 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8843 (tm-30) REVERT: C 114 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: C 121 MET cc_start: 0.9013 (mmm) cc_final: 0.8541 (mmm) REVERT: C 366 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7284 (mp0) REVERT: C 534 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7422 (mtm110) REVERT: C 633 MET cc_start: 0.8034 (mtm) cc_final: 0.7778 (mtm) REVERT: C 650 MET cc_start: 0.8300 (mmm) cc_final: 0.7844 (mmm) outliers start: 66 outliers final: 43 residues processed: 301 average time/residue: 0.3165 time to fit residues: 158.0953 Evaluate side-chains 287 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 VAL 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 811 ILE Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 904 VAL 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 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 518 MET 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 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 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 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 341 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 138 optimal weight: 0.0970 chunk 119 optimal weight: 0.0980 chunk 166 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ** 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 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.085479 restraints weight = 58949.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088121 restraints weight = 29831.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089879 restraints weight = 18633.755| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3963 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= 0.102 Angle : 0.511 11.429 33340 Z= 0.259 Chirality : 0.039 0.230 3594 Planarity : 0.003 0.061 4182 Dihedral : 4.359 33.626 3158 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.14 % Allowed : 12.85 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2859 helix: 0.86 (0.13), residues: 1689 sheet: -0.40 (0.80), residues: 43 loop : -0.63 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 896 HIS 0.007 0.001 HIS B 458 PHE 0.019 0.001 PHE A 607 TYR 0.021 0.001 TYR A1242 ARG 0.002 0.000 ARG A 957 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1057) hydrogen bonds : angle 4.17650 ( 3087) SS BOND : bond 0.00188 ( 13) SS BOND : angle 0.99506 ( 26) covalent geometry : bond 0.00232 (24727) covalent geometry : angle 0.51073 (33314) *********************** 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 333 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 2.545 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: 0.8996 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: A 352 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8703 (t) REVERT: A 377 GLU cc_start: 0.8040 (tp30) cc_final: 0.7664 (tp30) REVERT: A 781 MET cc_start: 0.8442 (mmp) cc_final: 0.8091 (mtp) REVERT: A 788 VAL cc_start: 0.9487 (t) cc_final: 0.9244 (p) REVERT: A 807 MET cc_start: 0.8802 (mmm) cc_final: 0.7496 (mmm) REVERT: A 814 TYR cc_start: 0.9072 (t80) cc_final: 0.8721 (t80) REVERT: A 1012 ILE cc_start: 0.5415 (OUTLIER) cc_final: 0.5190 (mt) REVERT: A 1020 LEU cc_start: 0.8827 (mm) cc_final: 0.8539 (mm) REVERT: A 1030 THR cc_start: 0.9003 (p) cc_final: 0.8767 (t) REVERT: A 1146 GLU cc_start: 0.8565 (tp30) cc_final: 0.8257 (mm-30) REVERT: A 1308 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7319 (mmm) REVERT: A 1329 ASP cc_start: 0.8088 (t0) cc_final: 0.7820 (t0) REVERT: B 121 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8670 (mt) REVERT: B 125 TYR cc_start: 0.8742 (t80) cc_final: 0.8431 (t80) REVERT: B 278 LYS cc_start: 0.8427 (tttp) cc_final: 0.8043 (pttt) REVERT: B 359 LYS cc_start: 0.8736 (tttt) cc_final: 0.8148 (tppt) REVERT: B 384 TYR cc_start: 0.8084 (t80) cc_final: 0.7758 (t80) REVERT: B 396 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7353 (tpt-90) REVERT: B 509 ASN cc_start: 0.8334 (m-40) cc_final: 0.8055 (m-40) REVERT: B 847 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7935 (tt) REVERT: B 892 SER cc_start: 0.9042 (p) cc_final: 0.8831 (t) REVERT: B 918 MET cc_start: 0.7776 (ptt) cc_final: 0.7472 (ptm) REVERT: B 980 ASP cc_start: 0.8550 (m-30) cc_final: 0.8243 (m-30) REVERT: B 1054 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6508 (tt) REVERT: C 59 SER cc_start: 0.9628 (m) cc_final: 0.9142 (t) REVERT: C 75 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8851 (tm-30) REVERT: C 114 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8797 (mp0) REVERT: C 121 MET cc_start: 0.9014 (mmm) cc_final: 0.8614 (mmm) REVERT: C 366 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7265 (mp0) REVERT: C 534 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7373 (mtm110) REVERT: C 650 MET cc_start: 0.8240 (mmm) cc_final: 0.7790 (mmm) outliers start: 58 outliers final: 36 residues processed: 317 average time/residue: 0.3361 time to fit residues: 176.3139 Evaluate side-chains 286 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 2.866 ------------------------------------------------------------------------------- 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 352 VAL Chi-restraints excluded: chain A residue 515 ILE 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 854 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1015 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 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 586 LEU 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 779 VAL 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 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 314 VAL Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 474 LEU 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 640 ASP 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 111 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 286 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A 891 ASN ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.101225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085426 restraints weight = 59247.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088082 restraints weight = 30334.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089856 restraints weight = 19098.305| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4106 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= 0.109 Angle : 0.520 9.383 33340 Z= 0.262 Chirality : 0.039 0.240 3594 Planarity : 0.003 0.057 4182 Dihedral : 4.291 32.694 3158 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.99 % Allowed : 13.51 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2859 helix: 0.98 (0.13), residues: 1690 sheet: -0.35 (0.80), residues: 43 loop : -0.60 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 896 HIS 0.007 0.001 HIS B 458 PHE 0.036 0.001 PHE A1214 TYR 0.022 0.001 TYR A1242 ARG 0.010 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 1057) hydrogen bonds : angle 4.14805 ( 3087) SS BOND : bond 0.00203 ( 13) SS BOND : angle 0.96589 ( 26) covalent geometry : bond 0.00253 (24727) covalent geometry : angle 0.51947 (33314) *********************** 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 323 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 3.016 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: A 135 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: A 352 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8648 (t) REVERT: A 553 ASN cc_start: 0.8423 (m110) cc_final: 0.7862 (p0) REVERT: A 781 MET cc_start: 0.8403 (mmp) cc_final: 0.8105 (mtp) REVERT: A 807 MET cc_start: 0.8895 (mmm) cc_final: 0.7541 (mmm) REVERT: A 814 TYR cc_start: 0.9113 (t80) cc_final: 0.8614 (t80) REVERT: A 1020 LEU cc_start: 0.8736 (mm) cc_final: 0.8450 (mm) REVERT: A 1030 THR cc_start: 0.9007 (p) cc_final: 0.8754 (t) REVERT: A 1146 GLU cc_start: 0.8541 (tp30) cc_final: 0.8291 (mm-30) REVERT: A 1308 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7317 (mmm) REVERT: A 1316 MET cc_start: 0.8677 (mmm) cc_final: 0.8464 (tpp) REVERT: B 121 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8660 (mt) REVERT: B 125 TYR cc_start: 0.8720 (t80) cc_final: 0.8416 (t80) REVERT: B 278 LYS cc_start: 0.8419 (tttp) cc_final: 0.8102 (pttt) REVERT: B 349 ILE cc_start: 0.6737 (mm) cc_final: 0.6360 (mm) REVERT: B 359 LYS cc_start: 0.8722 (tttt) cc_final: 0.8152 (tppt) REVERT: B 384 TYR cc_start: 0.8065 (t80) cc_final: 0.7763 (t80) REVERT: B 396 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7310 (tpt-90) REVERT: B 509 ASN cc_start: 0.8299 (m-40) cc_final: 0.8006 (m-40) REVERT: B 897 ASN cc_start: 0.8609 (t0) cc_final: 0.7943 (t0) REVERT: B 918 MET cc_start: 0.7830 (ptt) cc_final: 0.7494 (ptm) REVERT: B 980 ASP cc_start: 0.8502 (m-30) cc_final: 0.8204 (m-30) REVERT: B 1054 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6524 (tt) REVERT: C 59 SER cc_start: 0.9605 (m) cc_final: 0.9124 (t) REVERT: C 71 TYR cc_start: 0.8585 (m-80) cc_final: 0.8345 (m-80) REVERT: C 75 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 114 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8806 (mp0) REVERT: C 121 MET cc_start: 0.8991 (mmm) cc_final: 0.8602 (mmm) REVERT: C 211 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8460 (mtt-85) REVERT: C 366 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7176 (mp0) REVERT: C 534 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7396 (mtm110) REVERT: C 633 MET cc_start: 0.7916 (mtm) cc_final: 0.7682 (mtm) REVERT: C 650 MET cc_start: 0.8199 (mmm) cc_final: 0.7768 (mmm) outliers start: 54 outliers final: 40 residues processed: 310 average time/residue: 0.3334 time to fit residues: 171.2205 Evaluate side-chains 293 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 3.012 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 515 ILE 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 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 1015 SER Chi-restraints excluded: chain A residue 1099 ILE 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 B residue 121 LEU Chi-restraints excluded: chain B residue 150 ILE 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 684 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 929 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 314 VAL Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 474 LEU 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 285 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 125 optimal weight: 0.0670 chunk 145 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 223 optimal weight: 0.0570 chunk 34 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1322 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 HIS ** 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 = 0.3567 r_free = 0.3567 target = 0.101835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086102 restraints weight = 59416.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088771 restraints weight = 30318.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090554 restraints weight = 19043.476| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24740 Z= 0.104 Angle : 0.523 9.294 33340 Z= 0.262 Chirality : 0.039 0.249 3594 Planarity : 0.003 0.053 4182 Dihedral : 4.238 31.708 3158 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 13.92 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2859 helix: 1.06 (0.13), residues: 1696 sheet: -0.33 (0.80), residues: 43 loop : -0.53 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 645 HIS 0.007 0.001 HIS A 136 PHE 0.038 0.001 PHE C 686 TYR 0.022 0.001 TYR A1242 ARG 0.009 0.000 ARG A1347 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 1057) hydrogen bonds : angle 4.11543 ( 3087) SS BOND : bond 0.00190 ( 13) SS BOND : angle 0.91925 ( 26) covalent geometry : bond 0.00239 (24727) covalent geometry : angle 0.52215 (33314) *********************** 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 334 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 2.600 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: A 352 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8552 (t) REVERT: A 376 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 377 GLU cc_start: 0.8176 (tp30) cc_final: 0.7840 (tp30) REVERT: A 553 ASN cc_start: 0.8410 (m110) cc_final: 0.7765 (p0) REVERT: A 567 TYR cc_start: 0.8070 (t80) cc_final: 0.7012 (t80) REVERT: A 602 TRP cc_start: 0.8211 (m100) cc_final: 0.7929 (m100) REVERT: A 781 MET cc_start: 0.8382 (mmp) cc_final: 0.8115 (mtp) REVERT: A 807 MET cc_start: 0.8849 (mmm) cc_final: 0.7444 (mmm) REVERT: A 814 TYR cc_start: 0.9102 (t80) cc_final: 0.8593 (t80) REVERT: A 954 MET cc_start: 0.8016 (tpp) cc_final: 0.7709 (tpp) REVERT: A 1020 LEU cc_start: 0.8710 (mm) cc_final: 0.8415 (mm) REVERT: A 1030 THR cc_start: 0.9006 (p) cc_final: 0.8746 (t) REVERT: A 1146 GLU cc_start: 0.8568 (tp30) cc_final: 0.8311 (mm-30) REVERT: A 1297 MET cc_start: 0.9065 (mmm) cc_final: 0.8777 (mmm) REVERT: A 1308 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7323 (mmm) REVERT: A 1316 MET cc_start: 0.8686 (mmm) cc_final: 0.8220 (tpp) REVERT: B 121 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B 125 TYR cc_start: 0.8707 (t80) cc_final: 0.8397 (t80) REVERT: B 278 LYS cc_start: 0.8423 (tttp) cc_final: 0.8096 (pttt) REVERT: B 349 ILE cc_start: 0.6810 (mm) cc_final: 0.6453 (mm) REVERT: B 359 LYS cc_start: 0.8718 (tttt) cc_final: 0.8158 (tppt) REVERT: B 384 TYR cc_start: 0.8067 (t80) cc_final: 0.7602 (t80) REVERT: B 396 ARG cc_start: 0.7702 (tpp80) cc_final: 0.7231 (tpt-90) REVERT: B 509 ASN cc_start: 0.8274 (m-40) cc_final: 0.7977 (m-40) REVERT: B 897 ASN cc_start: 0.8633 (t0) cc_final: 0.7913 (t0) REVERT: B 918 MET cc_start: 0.7883 (ptt) cc_final: 0.7495 (ptm) REVERT: B 980 ASP cc_start: 0.8492 (m-30) cc_final: 0.8232 (m-30) REVERT: B 1054 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6537 (tt) REVERT: C 59 SER cc_start: 0.9622 (m) cc_final: 0.9161 (t) REVERT: C 71 TYR cc_start: 0.8529 (m-80) cc_final: 0.8285 (m-80) REVERT: C 75 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8877 (tm-30) REVERT: C 114 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8816 (mp0) REVERT: C 121 MET cc_start: 0.9001 (mmm) cc_final: 0.8619 (mmm) REVERT: C 164 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8787 (mmmt) REVERT: C 211 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8414 (mtp180) REVERT: C 366 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7172 (mp0) REVERT: C 534 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7387 (mtm110) REVERT: C 629 ILE cc_start: 0.8956 (mt) cc_final: 0.8546 (mm) REVERT: C 633 MET cc_start: 0.8016 (mtm) cc_final: 0.7731 (mtm) REVERT: C 650 MET cc_start: 0.8152 (mmm) cc_final: 0.7860 (mmm) outliers start: 52 outliers final: 37 residues processed: 319 average time/residue: 0.3287 time to fit residues: 171.7856 Evaluate side-chains 293 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 376 LEU 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 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 1015 SER 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 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 684 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 929 LEU 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 314 VAL Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 474 LEU 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 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 134 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.084922 restraints weight = 59496.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087558 restraints weight = 30444.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089314 restraints weight = 19200.368| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24740 Z= 0.128 Angle : 0.556 15.127 33340 Z= 0.275 Chirality : 0.040 0.256 3594 Planarity : 0.003 0.061 4182 Dihedral : 4.262 31.472 3158 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.95 % Allowed : 14.03 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2859 helix: 1.10 (0.13), residues: 1697 sheet: -0.34 (0.80), residues: 43 loop : -0.52 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 645 HIS 0.007 0.001 HIS B 458 PHE 0.026 0.001 PHE A1214 TYR 0.022 0.001 TYR A1242 ARG 0.008 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1057) hydrogen bonds : angle 4.13732 ( 3087) SS BOND : bond 0.00213 ( 13) SS BOND : angle 0.91889 ( 26) covalent geometry : bond 0.00301 (24727) covalent geometry : angle 0.55577 (33314) ********************** 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 308 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 3.593 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: A 352 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8540 (t) REVERT: A 376 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 377 GLU cc_start: 0.8206 (tp30) cc_final: 0.7887 (tp30) REVERT: A 454 MET cc_start: 0.8709 (mmm) cc_final: 0.8355 (mmp) REVERT: A 553 ASN cc_start: 0.8423 (m110) cc_final: 0.7805 (p0) REVERT: A 567 TYR cc_start: 0.8127 (t80) cc_final: 0.7119 (t80) REVERT: A 602 TRP cc_start: 0.8263 (m100) cc_final: 0.7978 (m100) REVERT: A 781 MET cc_start: 0.8340 (mmp) cc_final: 0.8104 (mtp) REVERT: A 807 MET cc_start: 0.8952 (mmm) cc_final: 0.7572 (mmm) REVERT: A 814 TYR cc_start: 0.9130 (t80) cc_final: 0.8551 (t80) REVERT: A 1020 LEU cc_start: 0.8761 (mm) cc_final: 0.8459 (mm) REVERT: A 1030 THR cc_start: 0.9095 (p) cc_final: 0.8821 (t) REVERT: A 1146 GLU cc_start: 0.8562 (tp30) cc_final: 0.8328 (mm-30) REVERT: A 1297 MET cc_start: 0.9070 (mmm) cc_final: 0.8761 (mmm) REVERT: A 1308 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: A 1316 MET cc_start: 0.8702 (mmm) cc_final: 0.8220 (tpp) REVERT: B 121 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8656 (mt) REVERT: B 125 TYR cc_start: 0.8722 (t80) cc_final: 0.8430 (t80) REVERT: B 245 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 278 LYS cc_start: 0.8427 (tttp) cc_final: 0.8103 (pttt) REVERT: B 349 ILE cc_start: 0.6941 (mm) cc_final: 0.6476 (mm) REVERT: B 359 LYS cc_start: 0.8708 (tttt) cc_final: 0.8143 (tppt) REVERT: B 384 TYR cc_start: 0.8044 (t80) cc_final: 0.7672 (t80) REVERT: B 396 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7249 (tpt-90) REVERT: B 509 ASN cc_start: 0.8139 (m-40) cc_final: 0.7862 (m-40) REVERT: B 918 MET cc_start: 0.7762 (ptt) cc_final: 0.7426 (ptm) REVERT: B 980 ASP cc_start: 0.8495 (m-30) cc_final: 0.8239 (m-30) REVERT: B 1054 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6570 (tt) REVERT: C 59 SER cc_start: 0.9615 (m) cc_final: 0.9132 (t) REVERT: C 71 TYR cc_start: 0.8561 (m-80) cc_final: 0.8309 (m-80) REVERT: C 75 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 114 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8831 (mp0) REVERT: C 121 MET cc_start: 0.8981 (mmm) cc_final: 0.8591 (mmm) REVERT: C 164 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8794 (mmmt) REVERT: C 211 ARG cc_start: 0.8712 (mtt180) cc_final: 0.8401 (mtp180) REVERT: C 366 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7221 (mp0) REVERT: C 534 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7434 (mtm110) REVERT: C 629 ILE cc_start: 0.8975 (mt) cc_final: 0.8540 (mm) REVERT: C 633 MET cc_start: 0.8078 (mtm) cc_final: 0.7809 (mtm) REVERT: C 650 MET cc_start: 0.8194 (mmm) cc_final: 0.7794 (mmm) outliers start: 53 outliers final: 42 residues processed: 294 average time/residue: 0.5215 time to fit residues: 258.2527 Evaluate side-chains 296 residues out of total 2716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 376 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 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 1015 SER 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 121 LEU Chi-restraints excluded: chain B residue 150 ILE 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 684 ILE Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 929 LEU 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 314 VAL Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 474 LEU 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 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 105 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN ** 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 = 0.3556 r_free = 0.3556 target = 0.101282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085669 restraints weight = 59216.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088312 restraints weight = 30194.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090089 restraints weight = 19039.679| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24740 Z= 0.118 Angle : 0.545 12.019 33340 Z= 0.271 Chirality : 0.039 0.257 3594 Planarity : 0.003 0.051 4182 Dihedral : 4.241 31.092 3158 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.88 % Allowed : 14.32 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2859 helix: 1.10 (0.13), residues: 1707 sheet: -0.36 (0.80), residues: 43 loop : -0.52 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 645 HIS 0.007 0.001 HIS B 458 PHE 0.026 0.001 PHE A1214 TYR 0.023 0.001 TYR A1242 ARG 0.007 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 1057) hydrogen bonds : angle 4.11463 ( 3087) SS BOND : bond 0.00189 ( 13) SS BOND : angle 0.87870 ( 26) covalent geometry : bond 0.00274 (24727) covalent geometry : angle 0.54477 (33314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8062.78 seconds wall clock time: 145 minutes 39.80 seconds (8739.80 seconds total)