Starting phenix.real_space_refine on Fri Feb 6 01:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9li7_63113/02_2026/9li7_63113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9li7_63113/02_2026/9li7_63113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9li7_63113/02_2026/9li7_63113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9li7_63113/02_2026/9li7_63113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9li7_63113/02_2026/9li7_63113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9li7_63113/02_2026/9li7_63113.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.078 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 104 5.16 5 C 13822 2.51 5 N 3604 2.21 5 O 3822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21352 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1351, 10676 Classifications: {'peptide': 1351} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1295} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 12.38, per 1000 atoms: 0.58 Number of scatterers: 21352 At special positions: 0 Unit cell: (177.1, 111.1, 146.3, 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 104 16.00 O 3822 8.00 N 3604 7.00 C 13822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " distance=2.02 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 32 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5028 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 10 sheets defined 54.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.746A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.601A pdb=" N ASN A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.542A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.661A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 128 removed outlier: 3.626A pdb=" N PHE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 162 removed outlier: 4.487A pdb=" N ILE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.712A pdb=" N LEU A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.368A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.680A pdb=" N SER A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.574A pdb=" N MET A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.569A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.589A pdb=" N PHE A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.740A pdb=" N ILE A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.535A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 486 removed outlier: 3.791A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.509A pdb=" N PHE A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.637A pdb=" N ARG A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 517' Processing helix chain 'A' and resid 519 through 546 removed outlier: 3.630A pdb=" N LEU A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Proline residue: A 533 - end of helix removed outlier: 3.833A pdb=" N THR A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.511A pdb=" N PHE A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.708A pdb=" N PHE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 590 removed outlier: 3.534A pdb=" N MET A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.686A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 removed outlier: 3.774A pdb=" N ILE A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 removed outlier: 3.710A pdb=" N ILE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.622A pdb=" N TYR A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.913A pdb=" N VAL A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 782 removed outlier: 3.761A pdb=" N GLN A 777 " --> pdb=" O HIS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.982A pdb=" N VAL A 805 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 829 removed outlier: 3.847A pdb=" N SER A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 838 removed outlier: 3.751A pdb=" N ASN A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 916 removed outlier: 3.585A pdb=" N GLN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.863A pdb=" N LEU A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 931 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 957 through 981 removed outlier: 3.711A pdb=" N LEU A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 962 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP A 980 " --> pdb=" O THR A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 removed outlier: 4.102A pdb=" N TYR A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1011 removed outlier: 4.164A pdb=" N PHE A1008 " --> pdb=" O PRO A1004 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1018 removed outlier: 3.721A pdb=" N ILE A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1030 through 1043 removed outlier: 3.740A pdb=" N GLN A1041 " --> pdb=" O MET A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1056 removed outlier: 3.864A pdb=" N VAL A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 3.630A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1077 through 1091 removed outlier: 4.051A pdb=" N GLU A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1084 " --> pdb=" O THR A1080 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A1088 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1097 Processing helix chain 'A' and resid 1125 through 1131 removed outlier: 4.173A pdb=" N ASN A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1144 removed outlier: 3.800A pdb=" N TRP A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.591A pdb=" N TRP A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1167 removed outlier: 3.600A pdb=" N GLY A1167 " --> pdb=" O MET A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1175 through 1187 removed outlier: 3.786A pdb=" N GLY A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A1185 " --> pdb=" O LEU A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1197 removed outlier: 4.507A pdb=" N THR A1194 " --> pdb=" O THR A1190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1207 Processing helix chain 'A' and resid 1207 through 1214 removed outlier: 3.874A pdb=" N GLU A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 3.781A pdb=" N ALA A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A1290 " --> pdb=" O LEU A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 removed outlier: 3.756A pdb=" N LYS A1309 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A1310 " --> pdb=" O VAL A1307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1306 through 1310' Processing helix chain 'A' and resid 1311 through 1317 removed outlier: 3.510A pdb=" N LEU A1315 " --> pdb=" O GLY A1311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1317 " --> pdb=" O MET A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1354 removed outlier: 3.521A pdb=" N GLU A1350 " --> pdb=" O ALA A1346 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A1351 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A1352 " --> pdb=" O LEU A1348 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A1353 " --> pdb=" O TRP A1349 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A1354 " --> pdb=" O GLU A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1363 removed outlier: 3.798A pdb=" N ILE A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 removed outlier: 4.021A pdb=" N GLN A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1393 removed outlier: 3.639A pdb=" N SER A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1424 removed outlier: 4.157A pdb=" N LYS A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 41 through 56 removed outlier: 3.747A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.602A pdb=" N ASN B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 94 removed outlier: 3.542A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.661A pdb=" N ILE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 128 removed outlier: 3.627A pdb=" N PHE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 162 removed outlier: 4.487A pdb=" N ILE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 192 removed outlier: 3.711A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 292 through 297 removed outlier: 4.369A pdb=" N ASN B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.680A pdb=" N SER B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.574A pdb=" N MET B 338 " --> pdb=" O PRO B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 363 through 373 removed outlier: 3.569A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.589A pdb=" N PHE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 440 through 445 removed outlier: 3.739A pdb=" N ILE B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.534A pdb=" N LEU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 486 removed outlier: 3.791A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.509A pdb=" N PHE B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 508 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.636A pdb=" N ARG B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 517' Processing helix chain 'B' and resid 519 through 546 removed outlier: 3.630A pdb=" N LEU B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix removed outlier: 3.833A pdb=" N THR B 537 " --> pdb=" O PRO B 533 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.511A pdb=" N PHE B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.709A pdb=" N PHE B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.534A pdb=" N MET B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 573 " --> pdb=" O PRO B 569 " (cutoff:3.500A) Proline residue: B 574 - end of helix removed outlier: 3.686A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 664 removed outlier: 3.774A pdb=" N ILE B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 removed outlier: 3.710A pdb=" N ILE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 700 " --> pdb=" O ASP B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 removed outlier: 3.623A pdb=" N TYR B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 716 " --> pdb=" O ALA B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 724 Processing helix chain 'B' and resid 744 through 756 removed outlier: 3.913A pdb=" N VAL B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 782 removed outlier: 3.762A pdb=" N GLN B 777 " --> pdb=" O HIS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.982A pdb=" N VAL B 805 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 829 removed outlier: 3.847A pdb=" N SER B 827 " --> pdb=" O GLU B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 838 removed outlier: 3.750A pdb=" N ASN B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 916 removed outlier: 3.586A pdb=" N GLN B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.863A pdb=" N LEU B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 931 " --> pdb=" O CYS B 927 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU B 932 " --> pdb=" O TYR B 928 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 946 Processing helix chain 'B' and resid 957 through 981 removed outlier: 3.711A pdb=" N LEU B 961 " --> pdb=" O LEU B 957 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 962 " --> pdb=" O PHE B 958 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 968 " --> pdb=" O ALA B 964 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN B 970 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR B 974 " --> pdb=" O GLN B 970 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 980 " --> pdb=" O THR B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1001 removed outlier: 4.102A pdb=" N TYR B 987 " --> pdb=" O MET B 983 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS B 990 " --> pdb=" O LEU B 986 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 991 " --> pdb=" O TYR B 987 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1011 removed outlier: 4.165A pdb=" N PHE B1008 " --> pdb=" O PRO B1004 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS B1009 " --> pdb=" O MET B1005 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B1010 " --> pdb=" O SER B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1018 removed outlier: 3.722A pdb=" N ILE B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN B1018 " --> pdb=" O GLY B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1030 Processing helix chain 'B' and resid 1030 through 1043 removed outlier: 3.739A pdb=" N GLN B1041 " --> pdb=" O MET B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1056 removed outlier: 3.864A pdb=" N VAL B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1064 removed outlier: 3.630A pdb=" N LEU B1060 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B1064 " --> pdb=" O LEU B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1067 No H-bonds generated for 'chain 'B' and resid 1065 through 1067' Processing helix chain 'B' and resid 1068 through 1073 Processing helix chain 'B' and resid 1077 through 1091 removed outlier: 4.051A pdb=" N GLU B1083 " --> pdb=" O ASN B1079 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B1084 " --> pdb=" O THR B1080 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B1088 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B1091 " --> pdb=" O MET B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1097 Processing helix chain 'B' and resid 1125 through 1131 removed outlier: 4.173A pdb=" N ASN B1129 " --> pdb=" O SER B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1144 removed outlier: 3.801A pdb=" N TRP B1142 " --> pdb=" O GLY B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.591A pdb=" N TRP B1156 " --> pdb=" O GLY B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1167 removed outlier: 3.600A pdb=" N GLY B1167 " --> pdb=" O MET B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1174 No H-bonds generated for 'chain 'B' and resid 1172 through 1174' Processing helix chain 'B' and resid 1175 through 1187 removed outlier: 3.785A pdb=" N GLY B1180 " --> pdb=" O ALA B1176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B1185 " --> pdb=" O LEU B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1197 removed outlier: 4.507A pdb=" N THR B1194 " --> pdb=" O THR B1190 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1207 Processing helix chain 'B' and resid 1207 through 1214 removed outlier: 3.874A pdb=" N GLU B1211 " --> pdb=" O LEU B1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1290 removed outlier: 3.781A pdb=" N ALA B1288 " --> pdb=" O SER B1284 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B1290 " --> pdb=" O LEU B1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1310 removed outlier: 3.755A pdb=" N LYS B1309 " --> pdb=" O ASP B1306 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B1310 " --> pdb=" O VAL B1307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1306 through 1310' Processing helix chain 'B' and resid 1311 through 1317 removed outlier: 3.510A pdb=" N LEU B1315 " --> pdb=" O GLY B1311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1317 " --> pdb=" O MET B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1344 through 1354 removed outlier: 3.520A pdb=" N GLU B1350 " --> pdb=" O ALA B1346 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B1351 " --> pdb=" O ASP B1347 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B1352 " --> pdb=" O LEU B1348 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B1353 " --> pdb=" O TRP B1349 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B1354 " --> pdb=" O GLU B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1363 removed outlier: 3.799A pdb=" N ILE B1361 " --> pdb=" O LEU B1357 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B1363 " --> pdb=" O ASP B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1385 removed outlier: 4.020A pdb=" N GLN B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1393 removed outlier: 3.639A pdb=" N SER B1390 " --> pdb=" O LEU B1386 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG B1391 " --> pdb=" O LEU B1387 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B1392 " --> pdb=" O SER B1388 " (cutoff:3.500A) Processing helix chain 'B' and resid 1413 through 1424 removed outlier: 4.156A pdb=" N LYS B1419 " --> pdb=" O ALA B1415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 632 through 639 removed outlier: 4.756A pdb=" N GLY A 619 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN A 636 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG A 617 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 638 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER A 615 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 615 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 675 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 760 through 764 removed outlier: 6.495A pdb=" N TYR A 761 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A 795 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE A 763 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 644 " --> pdb=" O ARG A 807 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 809 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 646 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A 811 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 648 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HIS A 812 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1259 through 1262 removed outlier: 6.279A pdb=" N HIS A1260 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A1249 " --> pdb=" O HIS A1260 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A1262 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A1247 " --> pdb=" O LYS A1297 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS A1297 " --> pdb=" O VAL A1247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1272 through 1274 Processing sheet with id=AA5, first strand: chain 'A' and resid 1321 through 1322 removed outlier: 3.549A pdb=" N ILE A1322 " --> pdb=" O VAL A1401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 632 through 639 removed outlier: 4.756A pdb=" N GLY B 619 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN B 636 " --> pdb=" O ARG B 617 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG B 617 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP B 638 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER B 615 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 615 " --> pdb=" O THR B 675 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 675 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 760 through 764 removed outlier: 6.494A pdb=" N TYR B 761 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 795 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 763 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 644 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL B 809 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA B 646 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL B 811 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 648 " --> pdb=" O VAL B 811 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HIS B 812 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 816 " --> pdb=" O HIS B 812 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1259 through 1262 removed outlier: 6.279A pdb=" N HIS B1260 " --> pdb=" O LEU B1249 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B1249 " --> pdb=" O HIS B1260 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B1262 " --> pdb=" O VAL B1247 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B1247 " --> pdb=" O LYS B1297 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS B1297 " --> pdb=" O VAL B1247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1272 through 1274 Processing sheet with id=AB1, first strand: chain 'B' and resid 1321 through 1322 removed outlier: 3.549A pdb=" N ILE B1322 " --> pdb=" O VAL B1401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 662 hydrogen bonds defined for protein. 1962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.19 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: 6737 1.34 - 1.46: 4283 1.46 - 1.57: 10622 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 21822 Sorted by residual: bond pdb=" CA LEU B 551 " pdb=" CB LEU B 551 " ideal model delta sigma weight residual 1.539 1.425 0.114 4.88e-02 4.20e+02 5.45e+00 bond pdb=" CA LEU A 551 " pdb=" CB LEU A 551 " ideal model delta sigma weight residual 1.539 1.426 0.114 4.88e-02 4.20e+02 5.44e+00 bond pdb=" CG LEU B 438 " pdb=" CD1 LEU B 438 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CG LEU A 438 " pdb=" CD1 LEU A 438 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.87e+00 bond pdb=" CB ASN B 960 " pdb=" CG ASN B 960 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.28e+00 ... (remaining 21817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 28155 2.15 - 4.30: 1227 4.30 - 6.45: 155 6.45 - 8.60: 59 8.60 - 10.75: 22 Bond angle restraints: 29618 Sorted by residual: angle pdb=" N ILE B1155 " pdb=" CA ILE B1155 " pdb=" C ILE B1155 " ideal model delta sigma weight residual 112.96 106.54 6.42 1.00e+00 1.00e+00 4.12e+01 angle pdb=" N ILE A1155 " pdb=" CA ILE A1155 " pdb=" C ILE A1155 " ideal model delta sigma weight residual 112.96 106.58 6.38 1.00e+00 1.00e+00 4.07e+01 angle pdb=" C GLN A 395 " pdb=" N THR A 396 " pdb=" CA THR A 396 " ideal model delta sigma weight residual 121.54 131.74 -10.20 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C GLN B 395 " pdb=" N THR B 396 " pdb=" CA THR B 396 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C LYS A 165 " pdb=" CA LYS A 165 " pdb=" CB LYS A 165 " ideal model delta sigma weight residual 111.48 103.23 8.25 1.59e+00 3.96e-01 2.69e+01 ... (remaining 29613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 12156 15.49 - 30.99: 624 30.99 - 46.48: 178 46.48 - 61.98: 6 61.98 - 77.47: 12 Dihedral angle restraints: 12976 sinusoidal: 5170 harmonic: 7806 Sorted by residual: dihedral pdb=" CA SER A1107 " pdb=" C SER A1107 " pdb=" N THR A1108 " pdb=" CA THR A1108 " ideal model delta harmonic sigma weight residual 180.00 147.40 32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA SER B1107 " pdb=" C SER B1107 " pdb=" N THR B1108 " pdb=" CA THR B1108 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA TYR B 168 " pdb=" C TYR B 168 " pdb=" N SER B 169 " pdb=" CA SER B 169 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 12973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2111 0.051 - 0.101: 1021 0.101 - 0.152: 237 0.152 - 0.202: 21 0.202 - 0.252: 10 Chirality restraints: 3400 Sorted by residual: chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 96 " pdb=" CA ILE B 96 " pdb=" CG1 ILE B 96 " pdb=" CG2 ILE B 96 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 354 " pdb=" CA VAL A 354 " pdb=" CG1 VAL A 354 " pdb=" CG2 VAL A 354 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3397 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 945 " -0.023 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP B 945 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 945 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 945 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 945 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 945 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 945 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 945 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 945 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 945 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 945 " 0.023 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP A 945 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 945 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 945 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 945 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 945 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 945 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 945 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 945 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 945 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 423 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO A 424 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.043 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6053 2.80 - 3.33: 18289 3.33 - 3.85: 32838 3.85 - 4.38: 37774 4.38 - 4.90: 64643 Nonbonded interactions: 159597 Sorted by model distance: nonbonded pdb=" OG SER B 278 " pdb=" O LEU B 291 " model vdw 2.281 3.040 nonbonded pdb=" OG SER A 278 " pdb=" O LEU A 291 " model vdw 2.281 3.040 nonbonded pdb=" O ASN A 575 " pdb=" OG1 THR A 578 " model vdw 2.318 3.040 nonbonded pdb=" O ASN B 575 " pdb=" OG1 THR B 578 " model vdw 2.318 3.040 nonbonded pdb=" O LEU A 175 " pdb=" OG SER A 178 " model vdw 2.335 3.040 ... (remaining 159592 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 0.114 21824 Z= 0.403 Angle : 1.051 10.746 29622 Z= 0.548 Chirality : 0.058 0.252 3400 Planarity : 0.007 0.078 3732 Dihedral : 10.683 77.472 7942 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.29 (0.10), residues: 2682 helix: -4.66 (0.05), residues: 1534 sheet: -3.50 (0.44), residues: 96 loop : -3.15 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1015 TYR 0.024 0.002 TYR A 959 PHE 0.031 0.003 PHE B1329 TRP 0.053 0.003 TRP B 945 HIS 0.006 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00941 (21822) covalent geometry : angle 1.05075 (29618) SS BOND : bond 0.00838 ( 2) SS BOND : angle 0.33688 ( 4) hydrogen bonds : bond 0.34203 ( 662) hydrogen bonds : angle 10.77406 ( 1962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TRP cc_start: 0.6617 (t60) cc_final: 0.6239 (t60) REVERT: A 90 PHE cc_start: 0.8544 (t80) cc_final: 0.8235 (t80) REVERT: A 127 MET cc_start: 0.8317 (tmm) cc_final: 0.8076 (tmm) REVERT: A 294 LEU cc_start: 0.8298 (mm) cc_final: 0.7937 (mt) REVERT: A 747 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7480 (mtm110) REVERT: A 836 MET cc_start: 0.1993 (mmm) cc_final: 0.1397 (ptt) REVERT: A 1076 TYR cc_start: 0.8645 (t80) cc_final: 0.8373 (t80) REVERT: A 1118 MET cc_start: 0.7697 (mmt) cc_final: 0.7181 (mmp) REVERT: A 1430 MET cc_start: 0.8258 (mmm) cc_final: 0.7880 (mmt) REVERT: B 55 TRP cc_start: 0.6710 (t60) cc_final: 0.6325 (t60) REVERT: B 90 PHE cc_start: 0.8557 (t80) cc_final: 0.8233 (t80) REVERT: B 127 MET cc_start: 0.8234 (tmm) cc_final: 0.7959 (tmm) REVERT: B 129 LEU cc_start: 0.8608 (tp) cc_final: 0.8282 (tt) REVERT: B 242 MET cc_start: 0.7235 (ttm) cc_final: 0.6989 (ttm) REVERT: B 836 MET cc_start: 0.2136 (mmm) cc_final: 0.1542 (ptt) REVERT: B 983 MET cc_start: 0.8200 (mmt) cc_final: 0.7942 (mmt) REVERT: B 1430 MET cc_start: 0.8329 (mmm) cc_final: 0.7869 (mmt) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1820 time to fit residues: 81.0108 Evaluate side-chains 206 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 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 24 ASN A 412 GLN A 437 GLN A1078 GLN A1129 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN A1435 HIS B 24 ASN B 412 GLN B 437 GLN B1078 GLN B1129 ASN ** B1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1383 GLN B1435 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.169737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125788 restraints weight = 36151.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121664 restraints weight = 22281.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122269 restraints weight = 27954.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122562 restraints weight = 19995.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122664 restraints weight = 15781.208| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21824 Z= 0.130 Angle : 0.667 9.824 29622 Z= 0.342 Chirality : 0.042 0.197 3400 Planarity : 0.005 0.050 3732 Dihedral : 6.005 28.609 2930 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.12 % Allowed : 6.91 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.13), residues: 2682 helix: -3.14 (0.10), residues: 1514 sheet: -3.20 (0.49), residues: 94 loop : -2.68 (0.16), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 792 TYR 0.026 0.001 TYR B1076 PHE 0.019 0.001 PHE B 763 TRP 0.019 0.001 TRP A 945 HIS 0.003 0.001 HIS B 773 Details of bonding type rmsd covalent geometry : bond 0.00275 (21822) covalent geometry : angle 0.66727 (29618) SS BOND : bond 0.00442 ( 2) SS BOND : angle 0.79986 ( 4) hydrogen bonds : bond 0.05470 ( 662) hydrogen bonds : angle 5.67730 ( 1962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9151 (mm) cc_final: 0.8878 (tt) REVERT: A 127 MET cc_start: 0.8315 (tmm) cc_final: 0.8025 (tmm) REVERT: A 157 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 682 TYR cc_start: 0.7138 (t80) cc_final: 0.6767 (t80) REVERT: A 755 TYR cc_start: 0.7900 (t80) cc_final: 0.7516 (t80) REVERT: A 836 MET cc_start: 0.1856 (mmm) cc_final: 0.1475 (ptt) REVERT: A 1430 MET cc_start: 0.8223 (mmm) cc_final: 0.7840 (mmt) REVERT: B 6 ILE cc_start: 0.9169 (mm) cc_final: 0.8926 (tt) REVERT: B 55 TRP cc_start: 0.6417 (t60) cc_final: 0.6189 (t60) REVERT: B 127 MET cc_start: 0.8284 (tmm) cc_final: 0.7986 (tmm) REVERT: B 157 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7953 (mm) REVERT: B 242 MET cc_start: 0.7123 (ttm) cc_final: 0.6711 (ttm) REVERT: B 620 TYR cc_start: 0.7848 (m-80) cc_final: 0.7413 (m-80) REVERT: B 682 TYR cc_start: 0.7226 (t80) cc_final: 0.6818 (t80) REVERT: B 755 TYR cc_start: 0.7845 (t80) cc_final: 0.7523 (t80) REVERT: B 836 MET cc_start: 0.2468 (mmm) cc_final: 0.1857 (ptt) REVERT: B 1164 MET cc_start: 0.9239 (ttp) cc_final: 0.8930 (ttt) REVERT: B 1430 MET cc_start: 0.8302 (mmm) cc_final: 0.7840 (mmt) outliers start: 26 outliers final: 11 residues processed: 251 average time/residue: 0.1391 time to fit residues: 54.9495 Evaluate side-chains 216 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 76 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 12 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 257 optimal weight: 0.0970 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 259 optimal weight: 0.1980 chunk 255 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 193 HIS ** B1324 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.170208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115064 restraints weight = 36262.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117075 restraints weight = 20708.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116559 restraints weight = 13806.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117381 restraints weight = 15395.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117068 restraints weight = 13321.724| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21824 Z= 0.111 Angle : 0.593 8.752 29622 Z= 0.300 Chirality : 0.041 0.136 3400 Planarity : 0.004 0.042 3732 Dihedral : 5.380 26.668 2930 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.46 % Allowed : 8.58 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.14), residues: 2682 helix: -2.19 (0.12), residues: 1498 sheet: -2.97 (0.48), residues: 98 loop : -2.29 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.027 0.001 TYR A1076 PHE 0.022 0.001 PHE A 568 TRP 0.013 0.001 TRP B 945 HIS 0.004 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00239 (21822) covalent geometry : angle 0.59324 (29618) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.55955 ( 4) hydrogen bonds : bond 0.04561 ( 662) hydrogen bonds : angle 4.91690 ( 1962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9162 (mm) cc_final: 0.8835 (tt) REVERT: A 125 MET cc_start: 0.8264 (mmm) cc_final: 0.7558 (tpt) REVERT: A 127 MET cc_start: 0.8370 (tmm) cc_final: 0.8099 (tmm) REVERT: A 135 TYR cc_start: 0.6141 (p90) cc_final: 0.5323 (p90) REVERT: A 746 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9103 (mp10) REVERT: A 836 MET cc_start: 0.1555 (mmm) cc_final: 0.1258 (ptt) REVERT: A 1430 MET cc_start: 0.8336 (mmm) cc_final: 0.8132 (mmt) REVERT: A 1456 GLU cc_start: 0.6986 (mp0) cc_final: 0.6773 (mp0) REVERT: B 6 ILE cc_start: 0.9160 (mm) cc_final: 0.8842 (tt) REVERT: B 55 TRP cc_start: 0.6374 (t60) cc_final: 0.6083 (t60) REVERT: B 67 CYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6918 (t) REVERT: B 125 MET cc_start: 0.8319 (mmm) cc_final: 0.7634 (tpt) REVERT: B 127 MET cc_start: 0.8394 (tmm) cc_final: 0.8108 (tmm) REVERT: B 135 TYR cc_start: 0.6308 (p90) cc_final: 0.5633 (p90) REVERT: B 157 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (mm) REVERT: B 589 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7821 (tpp80) REVERT: B 682 TYR cc_start: 0.7025 (t80) cc_final: 0.6461 (t80) REVERT: B 836 MET cc_start: 0.1938 (mmm) cc_final: 0.1559 (ptt) REVERT: B 1164 MET cc_start: 0.9212 (ttp) cc_final: 0.8946 (ttt) REVERT: B 1430 MET cc_start: 0.8401 (mmm) cc_final: 0.8140 (mmt) REVERT: B 1456 GLU cc_start: 0.7012 (mp0) cc_final: 0.6791 (mp0) outliers start: 34 outliers final: 13 residues processed: 244 average time/residue: 0.1329 time to fit residues: 51.2059 Evaluate side-chains 214 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1413 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 267 optimal weight: 0.9980 chunk 202 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN A 401 ASN B1336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.169084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.125475 restraints weight = 36157.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122044 restraints weight = 27959.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122366 restraints weight = 24453.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122612 restraints weight = 19126.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122839 restraints weight = 17310.279| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21824 Z= 0.131 Angle : 0.583 8.426 29622 Z= 0.294 Chirality : 0.042 0.139 3400 Planarity : 0.003 0.044 3732 Dihedral : 5.122 23.977 2930 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.63 % Allowed : 9.57 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.15), residues: 2682 helix: -1.67 (0.13), residues: 1482 sheet: -2.34 (0.60), residues: 78 loop : -2.13 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 589 TYR 0.025 0.001 TYR A1076 PHE 0.013 0.001 PHE B 763 TRP 0.014 0.001 TRP B 945 HIS 0.003 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00300 (21822) covalent geometry : angle 0.58333 (29618) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.57941 ( 4) hydrogen bonds : bond 0.04122 ( 662) hydrogen bonds : angle 4.63439 ( 1962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9150 (mm) cc_final: 0.8859 (tt) REVERT: A 127 MET cc_start: 0.8410 (tmm) cc_final: 0.8146 (tmm) REVERT: A 242 MET cc_start: 0.7013 (ttm) cc_final: 0.6741 (ttm) REVERT: A 682 TYR cc_start: 0.7076 (t80) cc_final: 0.6593 (t80) REVERT: A 746 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: A 836 MET cc_start: 0.1435 (mmm) cc_final: 0.1190 (ptt) REVERT: A 1148 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 1430 MET cc_start: 0.8182 (mmm) cc_final: 0.7875 (mmt) REVERT: A 1438 ASN cc_start: 0.8946 (m-40) cc_final: 0.8621 (t0) REVERT: B 6 ILE cc_start: 0.9138 (mm) cc_final: 0.8865 (tt) REVERT: B 55 TRP cc_start: 0.6430 (t60) cc_final: 0.6200 (t60) REVERT: B 127 MET cc_start: 0.8370 (tmm) cc_final: 0.8130 (tmm) REVERT: B 135 TYR cc_start: 0.6310 (p90) cc_final: 0.5602 (p90) REVERT: B 682 TYR cc_start: 0.7242 (t80) cc_final: 0.6662 (t80) REVERT: B 836 MET cc_start: 0.1849 (mmm) cc_final: 0.1564 (ptt) REVERT: B 1148 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 1164 MET cc_start: 0.9245 (ttp) cc_final: 0.8954 (ttt) REVERT: B 1430 MET cc_start: 0.8216 (mmm) cc_final: 0.7845 (mmt) outliers start: 38 outliers final: 21 residues processed: 237 average time/residue: 0.1264 time to fit residues: 48.0066 Evaluate side-chains 225 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1413 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 178 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN B 24 ASN B 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.166992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110894 restraints weight = 36260.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112879 restraints weight = 21387.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.111922 restraints weight = 14977.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112284 restraints weight = 17619.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112392 restraints weight = 15145.399| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21824 Z= 0.179 Angle : 0.616 10.562 29622 Z= 0.308 Chirality : 0.044 0.160 3400 Planarity : 0.003 0.040 3732 Dihedral : 5.137 23.025 2930 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.97 % Allowed : 9.83 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.15), residues: 2682 helix: -1.42 (0.13), residues: 1488 sheet: -2.22 (0.61), residues: 78 loop : -2.12 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1146 TYR 0.028 0.002 TYR A1076 PHE 0.023 0.001 PHE A 568 TRP 0.020 0.001 TRP B 945 HIS 0.004 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00423 (21822) covalent geometry : angle 0.61624 (29618) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.80198 ( 4) hydrogen bonds : bond 0.04374 ( 662) hydrogen bonds : angle 4.68322 ( 1962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8092 (mmm) cc_final: 0.7456 (tpt) REVERT: A 127 MET cc_start: 0.8567 (tmm) cc_final: 0.8183 (tmm) REVERT: A 135 TYR cc_start: 0.6113 (p90) cc_final: 0.5520 (p90) REVERT: A 242 MET cc_start: 0.7183 (ttm) cc_final: 0.6924 (ttm) REVERT: A 420 MET cc_start: 0.7986 (mmm) cc_final: 0.7461 (mmm) REVERT: A 682 TYR cc_start: 0.7105 (t80) cc_final: 0.6592 (t80) REVERT: A 746 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.9055 (pm20) REVERT: A 836 MET cc_start: 0.1370 (mmm) cc_final: 0.1108 (ptt) REVERT: A 1148 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: A 1430 MET cc_start: 0.8264 (mmm) cc_final: 0.8053 (mmt) REVERT: A 1438 ASN cc_start: 0.8965 (m-40) cc_final: 0.8655 (t0) REVERT: B 55 TRP cc_start: 0.6425 (t60) cc_final: 0.6107 (t60) REVERT: B 125 MET cc_start: 0.8107 (mmm) cc_final: 0.7487 (tpt) REVERT: B 127 MET cc_start: 0.8527 (tmm) cc_final: 0.8144 (tmm) REVERT: B 135 TYR cc_start: 0.6301 (p90) cc_final: 0.5635 (p90) REVERT: B 242 MET cc_start: 0.7118 (ttm) cc_final: 0.6833 (ttm) REVERT: B 589 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7877 (tpp80) REVERT: B 682 TYR cc_start: 0.7207 (t80) cc_final: 0.6802 (t80) REVERT: B 755 TYR cc_start: 0.7583 (t80) cc_final: 0.7353 (t80) REVERT: B 836 MET cc_start: 0.1826 (mmm) cc_final: 0.1482 (ptt) REVERT: B 1118 MET cc_start: 0.7138 (mmp) cc_final: 0.6673 (mmm) REVERT: B 1148 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 1164 MET cc_start: 0.9214 (ttp) cc_final: 0.8928 (ttt) REVERT: B 1430 MET cc_start: 0.8310 (mmm) cc_final: 0.8041 (mmt) outliers start: 46 outliers final: 25 residues processed: 230 average time/residue: 0.1401 time to fit residues: 52.2760 Evaluate side-chains 222 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1351 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 256 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 207 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 228 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 268 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A1336 ASN B 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.170623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113872 restraints weight = 36200.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115679 restraints weight = 22350.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.116371 restraints weight = 16613.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.116387 restraints weight = 15053.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.116600 restraints weight = 14467.763| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21824 Z= 0.095 Angle : 0.552 8.106 29622 Z= 0.277 Chirality : 0.041 0.192 3400 Planarity : 0.003 0.042 3732 Dihedral : 4.771 22.416 2930 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.37 % Allowed : 10.77 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2682 helix: -1.00 (0.14), residues: 1478 sheet: -1.97 (0.62), residues: 78 loop : -1.96 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.026 0.001 TYR A1076 PHE 0.008 0.001 PHE A 26 TRP 0.012 0.001 TRP B 289 HIS 0.003 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00208 (21822) covalent geometry : angle 0.55244 (29618) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.36169 ( 4) hydrogen bonds : bond 0.03489 ( 662) hydrogen bonds : angle 4.37317 ( 1962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8095 (mmm) cc_final: 0.7471 (tpt) REVERT: A 127 MET cc_start: 0.8586 (tmm) cc_final: 0.8240 (tmm) REVERT: A 135 TYR cc_start: 0.6062 (p90) cc_final: 0.5495 (p90) REVERT: A 191 PHE cc_start: 0.8252 (t80) cc_final: 0.8024 (t80) REVERT: A 682 TYR cc_start: 0.7130 (t80) cc_final: 0.6847 (t80) REVERT: A 746 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8989 (pm20) REVERT: A 968 PHE cc_start: 0.7732 (m-80) cc_final: 0.7247 (m-10) REVERT: A 1148 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 1430 MET cc_start: 0.8258 (mmm) cc_final: 0.8055 (mmt) REVERT: A 1438 ASN cc_start: 0.8899 (m-40) cc_final: 0.8602 (t0) REVERT: B 125 MET cc_start: 0.8123 (mmm) cc_final: 0.7481 (tpt) REVERT: B 127 MET cc_start: 0.8527 (tmm) cc_final: 0.8211 (tmm) REVERT: B 135 TYR cc_start: 0.6171 (p90) cc_final: 0.5557 (p90) REVERT: B 191 PHE cc_start: 0.8218 (t80) cc_final: 0.7967 (t80) REVERT: B 682 TYR cc_start: 0.7209 (t80) cc_final: 0.6808 (t80) REVERT: B 836 MET cc_start: 0.1615 (mmm) cc_final: 0.1318 (ptt) REVERT: B 968 PHE cc_start: 0.7814 (m-80) cc_final: 0.7601 (m-10) REVERT: B 1148 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: B 1164 MET cc_start: 0.9199 (ttp) cc_final: 0.8966 (ttm) REVERT: B 1430 MET cc_start: 0.8267 (mmm) cc_final: 0.8036 (mmt) outliers start: 32 outliers final: 24 residues processed: 226 average time/residue: 0.1388 time to fit residues: 51.3130 Evaluate side-chains 219 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1057 THR Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1321 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 198 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 169 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 117 optimal weight: 0.1980 chunk 203 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A1336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.169095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111668 restraints weight = 36277.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114261 restraints weight = 22346.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114907 restraints weight = 14294.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114896 restraints weight = 14738.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115014 restraints weight = 13590.369| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21824 Z= 0.128 Angle : 0.574 7.389 29622 Z= 0.285 Chirality : 0.042 0.187 3400 Planarity : 0.003 0.039 3732 Dihedral : 4.747 22.276 2930 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.42 % Allowed : 11.20 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2682 helix: -0.86 (0.14), residues: 1480 sheet: -1.98 (0.60), residues: 78 loop : -1.77 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1124 TYR 0.033 0.001 TYR B 755 PHE 0.024 0.001 PHE B 568 TRP 0.014 0.001 TRP A 289 HIS 0.003 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00299 (21822) covalent geometry : angle 0.57401 (29618) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.54954 ( 4) hydrogen bonds : bond 0.03733 ( 662) hydrogen bonds : angle 4.37332 ( 1962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8146 (mmm) cc_final: 0.7485 (tpt) REVERT: A 127 MET cc_start: 0.8651 (tmm) cc_final: 0.8243 (tmm) REVERT: A 135 TYR cc_start: 0.6113 (p90) cc_final: 0.5588 (p90) REVERT: A 682 TYR cc_start: 0.7240 (t80) cc_final: 0.6995 (t80) REVERT: A 746 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.9022 (pm20) REVERT: A 1148 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 1438 ASN cc_start: 0.8890 (m-40) cc_final: 0.8604 (t0) REVERT: B 125 MET cc_start: 0.8165 (mmm) cc_final: 0.7487 (tpt) REVERT: B 127 MET cc_start: 0.8591 (tmm) cc_final: 0.8208 (tmm) REVERT: B 135 TYR cc_start: 0.6102 (p90) cc_final: 0.5588 (p90) REVERT: B 682 TYR cc_start: 0.7208 (t80) cc_final: 0.6909 (t80) REVERT: B 836 MET cc_start: 0.1777 (mmm) cc_final: 0.1423 (ptt) REVERT: B 1148 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 1164 MET cc_start: 0.9208 (ttp) cc_final: 0.8971 (ttm) outliers start: 33 outliers final: 24 residues processed: 212 average time/residue: 0.1402 time to fit residues: 48.5671 Evaluate side-chains 209 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1057 THR Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1351 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 69 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 chunk 256 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 229 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.169564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126000 restraints weight = 36072.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122223 restraints weight = 22919.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122690 restraints weight = 28121.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122876 restraints weight = 20512.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.123101 restraints weight = 16285.026| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21824 Z= 0.125 Angle : 0.574 8.964 29622 Z= 0.286 Chirality : 0.042 0.171 3400 Planarity : 0.003 0.039 3732 Dihedral : 4.693 21.640 2930 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.37 % Allowed : 11.33 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2682 helix: -0.70 (0.14), residues: 1482 sheet: -1.86 (0.61), residues: 78 loop : -1.67 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 589 TYR 0.027 0.001 TYR A1076 PHE 0.013 0.001 PHE A 763 TRP 0.016 0.001 TRP A 289 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00294 (21822) covalent geometry : angle 0.57382 (29618) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.53853 ( 4) hydrogen bonds : bond 0.03634 ( 662) hydrogen bonds : angle 4.31589 ( 1962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8117 (mmm) cc_final: 0.7466 (tpt) REVERT: A 127 MET cc_start: 0.8646 (tmm) cc_final: 0.8241 (tmm) REVERT: A 135 TYR cc_start: 0.6105 (p90) cc_final: 0.5600 (p90) REVERT: A 242 MET cc_start: 0.7150 (ttm) cc_final: 0.6726 (ttm) REVERT: A 682 TYR cc_start: 0.7215 (t80) cc_final: 0.7002 (t80) REVERT: A 746 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8981 (pm20) REVERT: A 1148 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 1438 ASN cc_start: 0.8870 (m-40) cc_final: 0.8604 (t0) REVERT: B 125 MET cc_start: 0.8153 (mmm) cc_final: 0.7479 (tpt) REVERT: B 127 MET cc_start: 0.8576 (tmm) cc_final: 0.8218 (tmm) REVERT: B 135 TYR cc_start: 0.6270 (p90) cc_final: 0.5756 (p90) REVERT: B 242 MET cc_start: 0.7065 (ttm) cc_final: 0.6633 (ttm) REVERT: B 836 MET cc_start: 0.1701 (mmm) cc_final: 0.1410 (ptt) REVERT: B 1148 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 1164 MET cc_start: 0.9214 (ttp) cc_final: 0.8919 (ttt) REVERT: B 1438 ASN cc_start: 0.8972 (t0) cc_final: 0.8599 (t0) outliers start: 32 outliers final: 23 residues processed: 213 average time/residue: 0.1367 time to fit residues: 48.1358 Evaluate side-chains 212 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1057 THR Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 207 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 189 optimal weight: 0.0970 chunk 154 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.165727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109007 restraints weight = 36375.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109893 restraints weight = 22277.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110029 restraints weight = 16960.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110171 restraints weight = 16129.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110249 restraints weight = 15697.873| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21824 Z= 0.240 Angle : 0.664 7.691 29622 Z= 0.330 Chirality : 0.047 0.220 3400 Planarity : 0.004 0.036 3732 Dihedral : 5.045 22.584 2930 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.42 % Allowed : 11.50 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2682 helix: -0.83 (0.14), residues: 1476 sheet: -2.05 (0.60), residues: 78 loop : -1.67 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1124 TYR 0.031 0.002 TYR A1076 PHE 0.027 0.002 PHE A 568 TRP 0.022 0.001 TRP A 945 HIS 0.006 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00575 (21822) covalent geometry : angle 0.66365 (29618) SS BOND : bond 0.00137 ( 2) SS BOND : angle 1.04242 ( 4) hydrogen bonds : bond 0.04480 ( 662) hydrogen bonds : angle 4.62881 ( 1962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8205 (mmm) cc_final: 0.7581 (tpt) REVERT: A 127 MET cc_start: 0.8757 (tmm) cc_final: 0.8268 (tmm) REVERT: A 135 TYR cc_start: 0.6333 (p90) cc_final: 0.5808 (p90) REVERT: A 242 MET cc_start: 0.7348 (ttm) cc_final: 0.7000 (ttm) REVERT: A 746 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9041 (pm20) REVERT: A 1148 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: A 1438 ASN cc_start: 0.8875 (m-40) cc_final: 0.8604 (t0) REVERT: B 125 MET cc_start: 0.8219 (mmm) cc_final: 0.7602 (tpt) REVERT: B 127 MET cc_start: 0.8715 (tmm) cc_final: 0.8252 (tmm) REVERT: B 135 TYR cc_start: 0.6490 (p90) cc_final: 0.5972 (p90) REVERT: B 242 MET cc_start: 0.7349 (ttm) cc_final: 0.6997 (ttm) REVERT: B 836 MET cc_start: 0.1632 (mmm) cc_final: 0.1379 (ptt) REVERT: B 1148 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: B 1164 MET cc_start: 0.9226 (ttp) cc_final: 0.8946 (ttt) REVERT: B 1438 ASN cc_start: 0.9017 (t0) cc_final: 0.8691 (t0) outliers start: 33 outliers final: 27 residues processed: 207 average time/residue: 0.1393 time to fit residues: 47.2839 Evaluate side-chains 210 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 ILE Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 4 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.167551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110075 restraints weight = 36290.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111796 restraints weight = 23379.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111991 restraints weight = 17236.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112102 restraints weight = 15700.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112165 restraints weight = 15273.622| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21824 Z= 0.154 Angle : 0.610 8.091 29622 Z= 0.305 Chirality : 0.043 0.201 3400 Planarity : 0.003 0.039 3732 Dihedral : 4.901 22.456 2930 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.20 % Allowed : 11.89 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.16), residues: 2682 helix: -0.68 (0.14), residues: 1474 sheet: -2.29 (0.59), residues: 76 loop : -1.58 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1124 TYR 0.029 0.001 TYR A1076 PHE 0.011 0.001 PHE A 26 TRP 0.020 0.001 TRP B 289 HIS 0.005 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00365 (21822) covalent geometry : angle 0.61043 (29618) SS BOND : bond 0.00008 ( 2) SS BOND : angle 0.64295 ( 4) hydrogen bonds : bond 0.03931 ( 662) hydrogen bonds : angle 4.47862 ( 1962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8189 (mmm) cc_final: 0.7615 (tpt) REVERT: A 127 MET cc_start: 0.8738 (tmm) cc_final: 0.8249 (tmm) REVERT: A 135 TYR cc_start: 0.6190 (p90) cc_final: 0.5682 (p90) REVERT: A 242 MET cc_start: 0.7283 (ttm) cc_final: 0.6921 (ttm) REVERT: A 746 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.9053 (pm20) REVERT: A 968 PHE cc_start: 0.7914 (m-80) cc_final: 0.7640 (m-10) REVERT: A 1148 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: A 1438 ASN cc_start: 0.8873 (m-40) cc_final: 0.8592 (t0) REVERT: B 125 MET cc_start: 0.8203 (mmm) cc_final: 0.7629 (tpt) REVERT: B 127 MET cc_start: 0.8715 (tmm) cc_final: 0.8239 (tmm) REVERT: B 135 TYR cc_start: 0.6495 (p90) cc_final: 0.5977 (p90) REVERT: B 242 MET cc_start: 0.7214 (ttm) cc_final: 0.6856 (ttm) REVERT: B 836 MET cc_start: 0.1547 (mmm) cc_final: 0.1330 (ptt) REVERT: B 1148 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 1164 MET cc_start: 0.9219 (ttp) cc_final: 0.8939 (ttt) REVERT: B 1438 ASN cc_start: 0.8999 (t0) cc_final: 0.8727 (t0) outliers start: 28 outliers final: 23 residues processed: 205 average time/residue: 0.1341 time to fit residues: 45.4078 Evaluate side-chains 209 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 746 GLN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1238 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 ILE Chi-restraints excluded: chain B residue 1118 MET Chi-restraints excluded: chain B residue 1148 GLU Chi-restraints excluded: chain B residue 1238 SER Chi-restraints excluded: chain B residue 1321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 220 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 ASN ** B1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.167735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109430 restraints weight = 36206.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113171 restraints weight = 21144.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.112757 restraints weight = 14892.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113000 restraints weight = 12978.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113277 restraints weight = 12668.675| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21824 Z= 0.149 Angle : 0.607 8.076 29622 Z= 0.301 Chirality : 0.043 0.226 3400 Planarity : 0.003 0.038 3732 Dihedral : 4.847 22.484 2930 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.12 % Allowed : 12.15 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2682 helix: -0.56 (0.14), residues: 1474 sheet: -2.00 (0.52), residues: 98 loop : -1.57 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1124 TYR 0.028 0.001 TYR A1076 PHE 0.025 0.001 PHE B 568 TRP 0.022 0.001 TRP B 289 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00356 (21822) covalent geometry : angle 0.60681 (29618) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.60937 ( 4) hydrogen bonds : bond 0.03856 ( 662) hydrogen bonds : angle 4.43533 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.02 seconds wall clock time: 58 minutes 54.03 seconds (3534.03 seconds total)