Starting phenix.real_space_refine on Tue Sep 15 13:35:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0y_22618/09_2026/7k0y_22618.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0y_22618/09_2026/7k0y_22618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0y_22618/09_2026/7k0y_22618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0y_22618/09_2026/7k0y_22618.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0y_22618/09_2026/7k0y_22618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0y_22618/09_2026/7k0y_22618.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 71 5.49 5 S 233 5.16 5 C 25304 2.51 5 N 6762 2.21 5 O 7465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39835 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 29107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3669, 29107 Classifications: {'peptide': 3669} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 3512} Chain breaks: 16 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 28, 'ASP:plan': 1, 'GLN:plan1': 8, 'ARG:plan': 9, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 3973 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 490, 3957 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 490, 3957 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 bond proxies already assigned to first conformer: 4016 Chain: "C" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5247 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 9.62, per 1000 atoms: 0.24 Number of scatterers: 39835 At special positions: 0 Unit cell: (133.4, 176.32, 241.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 233 16.00 P 71 15.00 O 7465 8.00 N 6762 7.00 C 25304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 2.0 seconds 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9234 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 12 sheets defined 56.8% alpha, 4.1% beta 37 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 5.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 4.603A pdb=" N LEU A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.658A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.596A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.144A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 removed outlier: 3.686A pdb=" N ILE A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.961A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.564A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 4.454A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.668A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.939A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.731A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.834A pdb=" N ARG A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.961A pdb=" N GLN A 281 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 328 removed outlier: 4.336A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 355 through 370 removed outlier: 4.053A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 397 removed outlier: 4.654A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.149A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.581A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.729A pdb=" N PHE A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 634 removed outlier: 3.729A pdb=" N ASN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 658 removed outlier: 3.714A pdb=" N LEU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 4.030A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 718 removed outlier: 3.792A pdb=" N LEU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.969A pdb=" N TYR A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 749 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 752 through 758 removed outlier: 3.629A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.268A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.745A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.914A pdb=" N ALA A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.955A pdb=" N LEU A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 878 through 883 removed outlier: 3.871A pdb=" N TYR A 883 " --> pdb=" O MET A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 4.285A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 945 removed outlier: 3.903A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.404A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.861A pdb=" N LEU A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix removed outlier: 4.198A pdb=" N ILE A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 993 " --> pdb=" O MET A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1018 removed outlier: 3.571A pdb=" N ALA A1008 " --> pdb=" O GLN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 removed outlier: 3.812A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A1043 " --> pdb=" O TRP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1074 Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.787A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1114 Processing helix chain 'A' and resid 1123 through 1133 removed outlier: 4.158A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1175 Processing helix chain 'A' and resid 1180 through 1193 removed outlier: 4.127A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1216 removed outlier: 3.512A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1252 through 1267 removed outlier: 4.611A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1277 through 1283 removed outlier: 3.586A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A1283 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 removed outlier: 3.586A pdb=" N PHE A1296 " --> pdb=" O LYS A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1335 removed outlier: 4.344A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1349 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.505A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1404 Processing helix chain 'A' and resid 1412 through 1420 Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1446 through 1462 removed outlier: 3.541A pdb=" N ALA A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.797A pdb=" N ILE A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1490 Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 3.897A pdb=" N LEU A1515 " --> pdb=" O ALA A1511 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A1516 " --> pdb=" O SER A1512 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A1518 " --> pdb=" O LEU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1556 through 1564 removed outlier: 4.327A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1564 " --> pdb=" O TYR A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.747A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1585 removed outlier: 4.417A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.995A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1623 removed outlier: 4.228A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A1617 " --> pdb=" O HIS A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1629 removed outlier: 5.790A pdb=" N LYS A1627 " --> pdb=" O GLN A1624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A1629 " --> pdb=" O TRP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 4.340A pdb=" N LYS A1642 " --> pdb=" O PRO A1638 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET A1643 " --> pdb=" O LEU A1639 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.894A pdb=" N THR A1673 " --> pdb=" O PRO A1669 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A1679 " --> pdb=" O TYR A1675 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1694 removed outlier: 3.699A pdb=" N GLY A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN A1691 " --> pdb=" O HIS A1687 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A1692 " --> pdb=" O LEU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1719 Processing helix chain 'A' and resid 1735 through 1753 removed outlier: 3.594A pdb=" N LYS A1745 " --> pdb=" O ASP A1741 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A1752 " --> pdb=" O ASP A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1767 removed outlier: 3.717A pdb=" N MET A1762 " --> pdb=" O LEU A1758 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS A1767 " --> pdb=" O THR A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 4.027A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.977A pdb=" N GLN A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1830 removed outlier: 4.101A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A1824 " --> pdb=" O VAL A1820 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 4.105A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 4.383A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A1883 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 4.002A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A1923 " --> pdb=" O CYS A1919 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A1924 " --> pdb=" O TYR A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1954 removed outlier: 3.524A pdb=" N LEU A1939 " --> pdb=" O GLU A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1967 Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.876A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.624A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2016 Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2126 through 2134 Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.608A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2161 removed outlier: 3.611A pdb=" N TYR A2160 " --> pdb=" O PHE A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2174 Processing helix chain 'A' and resid 2182 through 2196 removed outlier: 4.005A pdb=" N VAL A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A2188 " --> pdb=" O TYR A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 4.043A pdb=" N LYS A2246 " --> pdb=" O VAL A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2284 removed outlier: 3.587A pdb=" N ILE A2274 " --> pdb=" O ASN A2270 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A2284 " --> pdb=" O VAL A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 3.850A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2315 through 2333 removed outlier: 3.818A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2356 removed outlier: 3.644A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A2356 " --> pdb=" O HIS A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2371 removed outlier: 3.811A pdb=" N CYS A2363 " --> pdb=" O LYS A2359 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2385 through 2389 removed outlier: 4.004A pdb=" N PHE A2389 " --> pdb=" O LEU A2386 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2402 removed outlier: 4.066A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2403 through 2405 No H-bonds generated for 'chain 'A' and resid 2403 through 2405' Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2420 through 2424 Processing helix chain 'A' and resid 2430 through 2442 removed outlier: 4.055A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A2439 " --> pdb=" O CYS A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2455 removed outlier: 3.604A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2483 removed outlier: 3.536A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A2482 " --> pdb=" O MET A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2503 Processing helix chain 'A' and resid 2507 through 2511 removed outlier: 3.841A pdb=" N ILE A2511 " --> pdb=" O GLN A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2534 through 2542 Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.351A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2790 Processing helix chain 'A' and resid 2791 through 2799 Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.529A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 4.486A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 4.299A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A2859 " --> pdb=" O VAL A2855 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A2860 " --> pdb=" O SER A2856 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2881 removed outlier: 4.046A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2897 removed outlier: 3.822A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2931 removed outlier: 3.560A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2958 removed outlier: 4.024A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2977 Processing helix chain 'A' and resid 2987 through 3004 Processing helix chain 'A' and resid 3009 through 3017 Processing helix chain 'A' and resid 3036 through 3053 removed outlier: 3.811A pdb=" N LEU A3041 " --> pdb=" O GLN A3037 " (cutoff:3.500A) Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3061 through 3069 Processing helix chain 'A' and resid 3076 through 3081 removed outlier: 3.753A pdb=" N HIS A3081 " --> pdb=" O ILE A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3091 Processing helix chain 'A' and resid 3097 through 3115 removed outlier: 3.620A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.660A pdb=" N SER A3146 " --> pdb=" O ILE A3142 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 removed outlier: 3.908A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.581A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3231 removed outlier: 3.891A pdb=" N ILE A3231 " --> pdb=" O ILE A3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3227 through 3231' Processing helix chain 'A' and resid 3231 through 3249 removed outlier: 4.451A pdb=" N SER A3237 " --> pdb=" O SER A3233 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A3241 " --> pdb=" O SER A3237 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 3.592A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3269 removed outlier: 3.546A pdb=" N THR A3268 " --> pdb=" O GLU A3265 " (cutoff:3.500A) Processing helix chain 'A' and resid 3272 through 3288 removed outlier: 3.640A pdb=" N HIS A3285 " --> pdb=" O CYS A3281 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A3288 " --> pdb=" O SER A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3295 through 3303 Processing helix chain 'A' and resid 3320 through 3341 removed outlier: 3.707A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3350 removed outlier: 3.824A pdb=" N ALA A3349 " --> pdb=" O ALA A3346 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3371 through 3394 removed outlier: 4.824A pdb=" N LEU A3377 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN A3390 " --> pdb=" O SER A3386 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.663A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A3429 " --> pdb=" O ARG A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3433 through 3440 Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.803A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3461 through 3463 No H-bonds generated for 'chain 'A' and resid 3461 through 3463' Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.825A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 removed outlier: 4.049A pdb=" N GLU A3486 " --> pdb=" O LEU A3482 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3530 through 3538 removed outlier: 3.733A pdb=" N ILE A3534 " --> pdb=" O VAL A3530 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3562 Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3594 removed outlier: 4.170A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.382A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3627 removed outlier: 4.174A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3641 through 3651 removed outlier: 4.038A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3670 removed outlier: 4.359A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3776 removed outlier: 3.744A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 removed outlier: 3.501A pdb=" N SER A3782 " --> pdb=" O ASP A3778 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A3783 " --> pdb=" O SER A3779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3778 through 3783' Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 4.494A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A3827 " --> pdb=" O GLU A3823 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 3.884A pdb=" N TYR A3839 " --> pdb=" O PRO A3835 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3860 removed outlier: 3.690A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.804A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 4.169A pdb=" N LEU A3898 " --> pdb=" O PRO A3894 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 Processing helix chain 'A' and resid 3978 through 3992 removed outlier: 3.994A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3996 through 4002 Processing helix chain 'A' and resid 4003 through 4008 Processing helix chain 'A' and resid 4016 through 4023 Processing helix chain 'A' and resid 4039 through 4053 Processing helix chain 'A' and resid 4057 through 4069 removed outlier: 3.847A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A4067 " --> pdb=" O GLU A4063 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.723A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4119 removed outlier: 4.175A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 4.373A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.701A pdb=" N ASP B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.797A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.240A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 Processing helix chain 'B' and resid 511 through 519 removed outlier: 3.917A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 88 through 96 removed outlier: 4.237A pdb=" N ILE C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 removed outlier: 4.061A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.554A pdb=" N ASP C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.021A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 4.122A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.940A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.571A pdb=" N PHE C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.743A pdb=" N LYS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 626 Processing helix chain 'C' and resid 628 through 649 removed outlier: 3.690A pdb=" N PHE C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET C 633 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 644 " --> pdb=" O ARG C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 669 Processing helix chain 'C' and resid 671 through 680 Processing helix chain 'C' and resid 698 through 705 Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 894 Processing sheet with id=AA2, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 6.899A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.622A pdb=" N ASP B 36 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA B 84 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 38 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR B 88 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 42 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 272 removed outlier: 5.492A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 349 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA7, first strand: chain 'B' and resid 298 through 303 Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.963A pdb=" N ARG B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 318 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 84 removed outlier: 7.144A pdb=" N HIS C 80 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N LEU C 58 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS C 82 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU C 56 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA C 8 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA C 55 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 10 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL C 57 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 12 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE C 59 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET C 14 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 9 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLU C 133 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C 11 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE C 135 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS C 13 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 130 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN C 162 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 247 through 253 removed outlier: 6.585A pdb=" N TYR C 264 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 364 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 339 through 346 removed outlier: 3.764A pdb=" N CYS C 339 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 464 through 466 1627 hydrogen bonds defined for protein. 4793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 15.79 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7444 1.32 - 1.45: 10025 1.45 - 1.57: 22812 1.57 - 1.70: 142 1.70 - 1.82: 368 Bond restraints: 40791 Sorted by residual: bond pdb=" CG ASN A 356 " pdb=" OD1 ASN A 356 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.60e+01 bond pdb=" CG ASN A 356 " pdb=" ND2 ASN A 356 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.20e+01 bond pdb=" C3' DT F 16 " pdb=" O3' DT F 16 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.77e+01 bond pdb=" C3' DT D 22 " pdb=" O3' DT D 22 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.73e+01 bond pdb=" CA LEU B 337 " pdb=" C LEU B 337 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.34e-02 5.57e+03 1.52e+01 ... (remaining 40786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 54914 4.65 - 9.29: 465 9.29 - 13.94: 48 13.94 - 18.59: 2 18.59 - 23.23: 2 Bond angle restraints: 55431 Sorted by residual: angle pdb=" C LEU A2122 " pdb=" N PRO A2123 " pdb=" CA PRO A2123 " ideal model delta sigma weight residual 119.84 138.80 -18.96 1.25e+00 6.40e-01 2.30e+02 angle pdb=" C GLU A3895 " pdb=" CA GLU A3895 " pdb=" CB GLU A3895 " ideal model delta sigma weight residual 110.90 127.15 -16.25 1.58e+00 4.01e-01 1.06e+02 angle pdb=" C TYR B 530 " pdb=" N PRO B 531 " pdb=" CA PRO B 531 " ideal model delta sigma weight residual 120.38 110.00 10.38 1.03e+00 9.43e-01 1.01e+02 angle pdb=" N VAL A1773 " pdb=" CA VAL A1773 " pdb=" C VAL A1773 " ideal model delta sigma weight residual 113.42 102.35 11.07 1.17e+00 7.31e-01 8.95e+01 angle pdb=" C LYS A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta sigma weight residual 119.84 130.89 -11.05 1.25e+00 6.40e-01 7.81e+01 ... (remaining 55426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 20892 17.69 - 35.38: 2887 35.38 - 53.07: 764 53.07 - 70.76: 134 70.76 - 88.45: 49 Dihedral angle restraints: 24726 sinusoidal: 10560 harmonic: 14166 Sorted by residual: dihedral pdb=" C GLU A3895 " pdb=" N GLU A3895 " pdb=" CA GLU A3895 " pdb=" CB GLU A3895 " ideal model delta harmonic sigma weight residual -122.60 -137.49 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA PRO A 473 " pdb=" C PRO A 473 " pdb=" N VAL A 474 " pdb=" CA VAL A 474 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA LEU A1165 " pdb=" C LEU A1165 " pdb=" N LEU A1166 " pdb=" CA LEU A1166 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 24723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5469 0.093 - 0.186: 754 0.186 - 0.279: 66 0.279 - 0.372: 2 0.372 - 0.465: 2 Chirality restraints: 6293 Sorted by residual: chirality pdb=" CA PRO A2887 " pdb=" N PRO A2887 " pdb=" C PRO A2887 " pdb=" CB PRO A2887 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA GLU A3895 " pdb=" N GLU A3895 " pdb=" C GLU A3895 " pdb=" CB GLU A3895 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA PRO A3894 " pdb=" N PRO A3894 " pdb=" C PRO A3894 " pdb=" CB PRO A3894 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 6290 not shown) Planarity restraints: 6795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A2572 " 0.028 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C TYR A2572 " -0.097 2.00e-02 2.50e+03 pdb=" O TYR A2572 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO A2573 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1727 " -0.487 9.50e-02 1.11e+02 2.18e-01 2.91e+01 pdb=" NE ARG A1727 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A1727 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1727 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1727 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3835 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO A3836 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A3836 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A3836 " 0.058 5.00e-02 4.00e+02 ... (remaining 6792 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 253 2.49 - 3.09: 26171 3.09 - 3.70: 59710 3.70 - 4.30: 80483 4.30 - 4.90: 132938 Nonbonded interactions: 299555 Sorted by model distance: nonbonded pdb=" O ASN A3697 " pdb=" O GLU A3698 " model vdw 1.890 3.040 nonbonded pdb=" O GLN A1771 " pdb=" O HIS A1772 " model vdw 1.897 3.040 nonbonded pdb=" O LYS B 245 " pdb=" CG2 VAL B 246 " model vdw 2.038 3.460 nonbonded pdb=" O TYR B 530 " pdb=" O PRO B 531 " model vdw 2.107 3.040 nonbonded pdb=" O SER A 842 " pdb=" OG SER A 842 " model vdw 2.188 3.040 ... (remaining 299550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 4 through 24) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 50.680 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 0.113 40791 Z= 0.435 Angle : 1.189 23.232 55431 Z= 0.661 Chirality : 0.064 0.465 6293 Planarity : 0.009 0.218 6795 Dihedral : 17.597 88.454 15492 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.90 % Favored : 84.58 % Rotamer: Outliers : 1.27 % Allowed : 12.64 % Favored : 86.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.48 % 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: -5.42 (0.09), residues: 4768 helix: -3.09 (0.07), residues: 2631 sheet: -2.46 (0.33), residues: 202 loop : -4.40 (0.11), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 79 TYR 0.039 0.003 TYR A 651 PHE 0.042 0.003 PHE A2260 TRP 0.044 0.003 TRP A2196 HIS 0.019 0.002 HIS A2787 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.43 (40791) covalent geometry : angle 1.18906 / 0.66 (55431) hydrogen bonds : bond 0.11400 / 7.64 ( 1719) hydrogen bonds : angle 6.31021 / 4.37 ( 4977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 535 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.8416 (mmtp) cc_final: 0.7636 (ttmt) REVERT: A 441 MET cc_start: 0.7053 (tpt) cc_final: 0.6810 (tpp) REVERT: A 520 LYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3011 (pttm) REVERT: A 857 GLN cc_start: 0.7643 (mt0) cc_final: 0.7069 (tm-30) REVERT: A 1220 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 1256 TRP cc_start: 0.7385 (t60) cc_final: 0.7142 (t60) REVERT: A 1426 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 1430 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 1727 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6986 (tmm-80) REVERT: A 1768 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6320 (mtm180) REVERT: A 2281 MET cc_start: 0.8783 (tpp) cc_final: 0.8233 (mmt) REVERT: A 3154 GLN cc_start: 0.7988 (pp30) cc_final: 0.7487 (pp30) REVERT: A 3273 LEU cc_start: 0.8001 (mt) cc_final: 0.7749 (mt) REVERT: A 3610 TYR cc_start: 0.7173 (t80) cc_final: 0.6909 (t80) REVERT: A 3698 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5729 (mm-30) REVERT: A 3729 MET cc_start: 0.8139 (mmp) cc_final: 0.7871 (tpp) REVERT: A 3791 TYR cc_start: 0.7844 (p90) cc_final: 0.7612 (p90) REVERT: B 203 MET cc_start: 0.5829 (mmp) cc_final: 0.5567 (mmm) REVERT: B 249 LYS cc_start: 0.6854 (tptt) cc_final: 0.6378 (ttpp) REVERT: B 453 MET cc_start: 0.6532 (mmm) cc_final: 0.5771 (tpp) REVERT: B 525 PHE cc_start: 0.4526 (t80) cc_final: 0.3947 (t80) REVERT: B 526 LYS cc_start: 0.7676 (ttmm) cc_final: 0.7318 (tptt) REVERT: C 250 ARG cc_start: 0.4547 (ttm170) cc_final: 0.4340 (mtm180) REVERT: C 430 LEU cc_start: 0.8580 (mt) cc_final: 0.8355 (mp) REVERT: C 431 ARG cc_start: 0.7180 (ptt90) cc_final: 0.6734 (ptm160) REVERT: C 631 TYR cc_start: 0.8048 (m-10) cc_final: 0.7809 (m-80) REVERT: C 643 ARG cc_start: 0.7819 (tmm160) cc_final: 0.7521 (ttm170) outliers start: 52 outliers final: 21 residues processed: 581 average time/residue: 0.2654 time to fit residues: 251.5697 Evaluate side-chains 408 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 383 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 617 PRO Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1727 ARG Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 3698 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain C residue 629 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 10.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS A 109 ASN A 325 ASN A 344 GLN A 454 GLN A 833 HIS A1049 GLN A1126 GLN A1142 HIS A1146 ASN A1175 HIS A1280 GLN A1457 GLN A1459 HIS A1589 ASN A1598 ASN A1624 GLN A1738 ASN A1957 ASN A2016 ASN A2177 ASN A2270 ASN A2365 ASN A2795 GLN A2885 GLN A2954 GLN A3113 ASN A3459 ASN A3510 GLN A3524 ASN A3564 GLN A3569 GLN A3573 ASN A3671 ASN ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3743 HIS B 98 ASN B 360 HIS B 405 ASN B 423 GLN B 515 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 76 ASN C 201 GLN C 290 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 ASN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.146171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120005 restraints weight = 92364.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118800 restraints weight = 92724.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.119738 restraints weight = 82714.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120583 restraints weight = 56878.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121049 restraints weight = 49875.824| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40791 Z= 0.155 Angle : 0.756 21.662 55431 Z= 0.387 Chirality : 0.045 0.244 6293 Planarity : 0.006 0.080 6795 Dihedral : 14.135 84.937 6001 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.11 % Favored : 87.68 % Rotamer: Outliers : 2.45 % Allowed : 15.61 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % 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: -4.21 (0.10), residues: 4768 helix: -1.89 (0.09), residues: 2662 sheet: -2.16 (0.35), residues: 201 loop : -4.21 (0.11), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 431 TYR 0.021 0.002 TYR A2316 PHE 0.026 0.001 PHE A2260 TRP 0.021 0.001 TRP A1256 HIS 0.007 0.001 HIS A2426 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (40791) covalent geometry : angle 0.75593 / 0.39 (55431) hydrogen bonds : bond 0.04865 / 3.20 ( 1719) hydrogen bonds : angle 5.21364 / 3.62 ( 4977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 432 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 357 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7506 (ttpt) REVERT: A 441 MET cc_start: 0.6940 (tpt) cc_final: 0.6685 (tpp) REVERT: A 518 LYS cc_start: 0.4259 (OUTLIER) cc_final: 0.2979 (mmmt) REVERT: A 726 LEU cc_start: 0.8412 (mt) cc_final: 0.7994 (tp) REVERT: A 857 GLN cc_start: 0.7657 (mt0) cc_final: 0.6863 (tm-30) REVERT: A 880 MET cc_start: 0.7851 (mmt) cc_final: 0.7456 (mmm) REVERT: A 1099 PHE cc_start: 0.5490 (OUTLIER) cc_final: 0.4200 (p90) REVERT: A 1256 TRP cc_start: 0.7447 (t60) cc_final: 0.6879 (t60) REVERT: A 1426 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 1430 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 1463 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 1768 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6419 (mtm180) REVERT: A 1905 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7298 (mm) REVERT: A 2281 MET cc_start: 0.8851 (tpp) cc_final: 0.8203 (mmt) REVERT: A 2504 ASP cc_start: 0.8404 (t0) cc_final: 0.7947 (t0) REVERT: A 3154 GLN cc_start: 0.7955 (pp30) cc_final: 0.7423 (pp30) REVERT: A 3554 PHE cc_start: 0.7825 (t80) cc_final: 0.7619 (t80) REVERT: A 3698 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6058 (mm-30) REVERT: A 3729 MET cc_start: 0.8242 (mmp) cc_final: 0.7992 (tpp) REVERT: B 203 MET cc_start: 0.5610 (mmp) cc_final: 0.5272 (mmm) REVERT: B 249 LYS cc_start: 0.6601 (tptt) cc_final: 0.6043 (ttpp) REVERT: B 453 MET cc_start: 0.6527 (mmm) cc_final: 0.5447 (mmt) REVERT: B 526 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7472 (tptt) REVERT: C 84 MET cc_start: 0.6143 (tpt) cc_final: 0.5931 (tpt) REVERT: C 610 GLU cc_start: 0.7382 (tp30) cc_final: 0.6948 (tp30) outliers start: 102 outliers final: 61 residues processed: 509 average time/residue: 0.2464 time to fit residues: 209.5372 Evaluate side-chains 441 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 374 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2146 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2358 ASP Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 3016 THR Chi-restraints excluded: chain A residue 3117 ILE Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3683 CYS Chi-restraints excluded: chain A residue 3698 GLU Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 629 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 61 optimal weight: 2.9990 chunk 484 optimal weight: 20.0000 chunk 368 optimal weight: 2.9990 chunk 342 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 483 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 333 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1625 HIS ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2838 GLN A3113 ASN A3459 ASN A3704 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 GLN ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.144829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118537 restraints weight = 78111.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117429 restraints weight = 93130.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.118470 restraints weight = 85212.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119808 restraints weight = 54693.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119895 restraints weight = 49270.574| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40791 Z= 0.181 Angle : 0.737 21.635 55431 Z= 0.376 Chirality : 0.045 0.188 6293 Planarity : 0.005 0.072 6795 Dihedral : 14.045 105.146 5989 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.37 % Favored : 86.45 % Rotamer: Outliers : 3.16 % Allowed : 17.48 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % 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: -3.74 (0.11), residues: 4768 helix: -1.41 (0.09), residues: 2661 sheet: -2.12 (0.34), residues: 212 loop : -4.14 (0.11), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 470 TYR 0.022 0.002 TYR A2316 PHE 0.026 0.002 PHE A2260 TRP 0.016 0.001 TRP A1256 HIS 0.008 0.001 HIS A3924 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (40791) covalent geometry : angle 0.73736 / 0.38 (55431) hydrogen bonds : bond 0.04689 / 3.07 ( 1719) hydrogen bonds : angle 5.10081 / 3.55 ( 4977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 390 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 357 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7621 (ttpt) REVERT: A 441 MET cc_start: 0.6983 (tpt) cc_final: 0.6734 (tpp) REVERT: A 518 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.3119 (mmmt) REVERT: A 520 LYS cc_start: 0.4197 (OUTLIER) cc_final: 0.3259 (ptpt) REVERT: A 857 GLN cc_start: 0.7689 (mt0) cc_final: 0.6947 (tm-30) REVERT: A 879 MET cc_start: 0.8424 (ttp) cc_final: 0.8177 (ttm) REVERT: A 880 MET cc_start: 0.7978 (mmt) cc_final: 0.7577 (mmm) REVERT: A 978 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7184 (tp-100) REVERT: A 1099 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.4185 (p90) REVERT: A 1145 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6766 (tt) REVERT: A 1171 TRP cc_start: 0.6508 (t60) cc_final: 0.6170 (t60) REVERT: A 1256 TRP cc_start: 0.7432 (t60) cc_final: 0.6915 (t60) REVERT: A 1463 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (pp) REVERT: A 1768 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6266 (mtm180) REVERT: A 1905 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7181 (mm) REVERT: A 2126 MET cc_start: 0.6263 (ptm) cc_final: 0.6020 (ptt) REVERT: A 2281 MET cc_start: 0.8897 (tpp) cc_final: 0.8296 (mmt) REVERT: A 2504 ASP cc_start: 0.8258 (t0) cc_final: 0.7878 (t0) REVERT: A 2899 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.3890 (pmt-80) REVERT: A 3154 GLN cc_start: 0.7974 (pp30) cc_final: 0.7482 (pp30) REVERT: A 3173 MET cc_start: 0.7560 (mmm) cc_final: 0.7336 (mmm) REVERT: A 3414 MET cc_start: 0.8705 (mmm) cc_final: 0.8481 (mmm) REVERT: A 3450 MET cc_start: 0.7714 (ttm) cc_final: 0.7473 (ttt) REVERT: A 3729 MET cc_start: 0.8357 (mmp) cc_final: 0.8142 (tpp) REVERT: A 3842 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.6966 (t60) REVERT: A 3846 MET cc_start: 0.8032 (tpp) cc_final: 0.7781 (tpt) REVERT: B 249 LYS cc_start: 0.6540 (tptt) cc_final: 0.5972 (ttpp) REVERT: B 453 MET cc_start: 0.6472 (mmm) cc_final: 0.5414 (mmt) REVERT: B 526 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7456 (tptt) REVERT: C 610 GLU cc_start: 0.7372 (tp30) cc_final: 0.6928 (tp30) REVERT: C 731 MET cc_start: 0.3919 (mmp) cc_final: 0.3361 (ttm) outliers start: 132 outliers final: 93 residues processed: 495 average time/residue: 0.2377 time to fit residues: 200.4102 Evaluate side-chains 474 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 372 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 982 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1926 ASN Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2382 VAL Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 2938 VAL Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 2987 THR Chi-restraints excluded: chain A residue 3016 THR Chi-restraints excluded: chain A residue 3097 ASP Chi-restraints excluded: chain A residue 3117 ILE Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3499 ILE Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3752 VAL Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3845 LYS Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 329 optimal weight: 0.3980 chunk 406 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 391 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 426 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 chunk 317 optimal weight: 0.0870 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN A1476 HIS A3122 HIS A3459 ASN A3605 ASN A3704 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 511 HIS C 653 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.120318 restraints weight = 78934.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119859 restraints weight = 69477.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120684 restraints weight = 56822.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121116 restraints weight = 45523.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121337 restraints weight = 40324.179| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 40791 Z= 0.121 Angle : 0.663 22.061 55431 Z= 0.337 Chirality : 0.042 0.261 6293 Planarity : 0.005 0.066 6795 Dihedral : 13.738 75.733 5985 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.02 % Favored : 88.86 % Rotamer: Outliers : 2.95 % Allowed : 18.87 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.16 (0.11), residues: 4768 helix: -0.88 (0.10), residues: 2654 sheet: -1.86 (0.36), residues: 199 loop : -3.98 (0.12), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 431 TYR 0.022 0.001 TYR A1411 PHE 0.038 0.001 PHE A3554 TRP 0.017 0.001 TRP A1256 HIS 0.008 0.001 HIS A1476 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (40791) covalent geometry : angle 0.66331 / 0.34 (55431) hydrogen bonds : bond 0.03835 / 2.49 ( 1719) hydrogen bonds : angle 4.69796 / 3.27 ( 4977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 437 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7681 (pp) REVERT: A 357 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7408 (ttpt) REVERT: A 441 MET cc_start: 0.6918 (tpt) cc_final: 0.6679 (tpp) REVERT: A 487 LEU cc_start: 0.8595 (mt) cc_final: 0.8288 (mt) REVERT: A 518 LYS cc_start: 0.4430 (OUTLIER) cc_final: 0.3083 (mmmt) REVERT: A 520 LYS cc_start: 0.3936 (OUTLIER) cc_final: 0.3614 (ptpt) REVERT: A 563 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 720 GLN cc_start: 0.6034 (tm-30) cc_final: 0.5745 (tm-30) REVERT: A 726 LEU cc_start: 0.8465 (mt) cc_final: 0.8081 (tp) REVERT: A 857 GLN cc_start: 0.7745 (mt0) cc_final: 0.7047 (tm-30) REVERT: A 879 MET cc_start: 0.8303 (ttt) cc_final: 0.7963 (ttm) REVERT: A 880 MET cc_start: 0.8003 (mmt) cc_final: 0.7468 (mmm) REVERT: A 1145 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6939 (tt) REVERT: A 1256 TRP cc_start: 0.7267 (t60) cc_final: 0.6734 (t60) REVERT: A 1679 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6187 (pp) REVERT: A 1768 ARG cc_start: 0.6840 (mtm-85) cc_final: 0.6438 (mtm180) REVERT: A 1890 HIS cc_start: 0.5207 (OUTLIER) cc_final: 0.3954 (t70) REVERT: A 1905 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7070 (mm) REVERT: A 2281 MET cc_start: 0.8970 (tpp) cc_final: 0.8450 (mmt) REVERT: A 2284 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7368 (t70) REVERT: A 2799 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7599 (mp-120) REVERT: A 2899 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.4051 (pmt-80) REVERT: A 3154 GLN cc_start: 0.7860 (pp30) cc_final: 0.7421 (pp30) REVERT: A 3414 MET cc_start: 0.8712 (mmm) cc_final: 0.8424 (mmm) REVERT: A 3450 MET cc_start: 0.7922 (ttm) cc_final: 0.7610 (ttt) REVERT: A 3729 MET cc_start: 0.8390 (mmp) cc_final: 0.8118 (tpp) REVERT: A 3842 TRP cc_start: 0.8007 (OUTLIER) cc_final: 0.6847 (t60) REVERT: A 3846 MET cc_start: 0.8136 (tpp) cc_final: 0.7887 (tpt) REVERT: B 81 ASP cc_start: 0.7294 (m-30) cc_final: 0.6948 (m-30) REVERT: B 167 MET cc_start: 0.7827 (ttm) cc_final: 0.7596 (ttm) REVERT: B 453 MET cc_start: 0.6450 (mmm) cc_final: 0.5435 (mmt) REVERT: B 526 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7539 (tptt) REVERT: C 267 ILE cc_start: 0.8233 (mp) cc_final: 0.8024 (mt) REVERT: C 412 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7358 (pt) REVERT: C 610 GLU cc_start: 0.7501 (tp30) cc_final: 0.7062 (tp30) REVERT: C 642 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5734 (m-10) REVERT: C 731 MET cc_start: 0.3973 (mmp) cc_final: 0.3407 (ttm) outliers start: 123 outliers final: 66 residues processed: 538 average time/residue: 0.2356 time to fit residues: 214.1711 Evaluate side-chains 460 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 380 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1722 PHE Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2284 ASP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3117 ILE Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3459 ASN Chi-restraints excluded: chain A residue 3499 ILE Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3752 VAL Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 653 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 199 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 433 optimal weight: 6.9990 chunk 339 optimal weight: 1.9990 chunk 466 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 126 optimal weight: 0.0370 chunk 385 optimal weight: 8.9990 chunk 442 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1779 GLN A3459 ASN A3760 GLN B 359 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121096 restraints weight = 91417.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120489 restraints weight = 79866.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121833 restraints weight = 72447.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121920 restraints weight = 51496.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122506 restraints weight = 45995.080| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 40791 Z= 0.122 Angle : 0.659 21.303 55431 Z= 0.332 Chirality : 0.042 0.249 6293 Planarity : 0.005 0.064 6795 Dihedral : 13.643 74.073 5980 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.25 % Favored : 88.63 % Rotamer: Outliers : 3.02 % Allowed : 19.76 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.91 (0.12), residues: 4768 helix: -0.65 (0.10), residues: 2657 sheet: -1.70 (0.36), residues: 198 loop : -3.91 (0.12), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1184 TYR 0.021 0.001 TYR A1411 PHE 0.023 0.001 PHE A1297 TRP 0.012 0.001 TRP A2479 HIS 0.008 0.001 HIS A2225 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (40791) covalent geometry : angle 0.65879 / 0.33 (55431) hydrogen bonds : bond 0.03772 / 2.45 ( 1719) hydrogen bonds : angle 4.60917 / 3.21 ( 4977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 405 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7699 (pp) REVERT: A 357 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7511 (ttmt) REVERT: A 441 MET cc_start: 0.6912 (tpt) cc_final: 0.6690 (tpp) REVERT: A 487 LEU cc_start: 0.8547 (mt) cc_final: 0.8289 (mt) REVERT: A 518 LYS cc_start: 0.4443 (OUTLIER) cc_final: 0.3123 (mmmt) REVERT: A 563 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8568 (mp) REVERT: A 720 GLN cc_start: 0.6021 (tm-30) cc_final: 0.5723 (tm-30) REVERT: A 726 LEU cc_start: 0.8385 (mt) cc_final: 0.8146 (tp) REVERT: A 857 GLN cc_start: 0.7570 (mt0) cc_final: 0.6781 (tm-30) REVERT: A 879 MET cc_start: 0.8287 (ttt) cc_final: 0.7953 (ttm) REVERT: A 880 MET cc_start: 0.7906 (mmt) cc_final: 0.7556 (mmm) REVERT: A 1015 ASP cc_start: 0.8048 (t0) cc_final: 0.7712 (t0) REVERT: A 1145 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6922 (tt) REVERT: A 1256 TRP cc_start: 0.7164 (t60) cc_final: 0.6694 (t60) REVERT: A 1478 SER cc_start: 0.8064 (t) cc_final: 0.7780 (t) REVERT: A 1679 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6243 (pp) REVERT: A 1890 HIS cc_start: 0.5342 (OUTLIER) cc_final: 0.4024 (t70) REVERT: A 1905 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7123 (mm) REVERT: A 2284 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7401 (t70) REVERT: A 2443 MET cc_start: 0.7776 (ttp) cc_final: 0.7222 (ttp) REVERT: A 2799 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7612 (mp-120) REVERT: A 2899 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.3889 (pmt-80) REVERT: A 3154 GLN cc_start: 0.7830 (pp30) cc_final: 0.7468 (pp30) REVERT: A 3450 MET cc_start: 0.7954 (ttm) cc_final: 0.7663 (ttt) REVERT: A 3729 MET cc_start: 0.8361 (mmp) cc_final: 0.8114 (tpp) REVERT: A 3842 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.6921 (t60) REVERT: A 3846 MET cc_start: 0.8301 (tpp) cc_final: 0.7989 (tpt) REVERT: B 81 ASP cc_start: 0.7300 (m-30) cc_final: 0.7038 (m-30) REVERT: B 167 MET cc_start: 0.7784 (ttm) cc_final: 0.7582 (ttm) REVERT: B 217 TYR cc_start: 0.3443 (OUTLIER) cc_final: 0.2639 (m-10) REVERT: B 453 MET cc_start: 0.6473 (mmm) cc_final: 0.5469 (mmt) REVERT: B 526 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7508 (tptt) REVERT: C 267 ILE cc_start: 0.8319 (mp) cc_final: 0.8115 (mt) REVERT: C 412 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7262 (pt) REVERT: C 505 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6778 (pp) REVERT: C 610 GLU cc_start: 0.7521 (tp30) cc_final: 0.7018 (tp30) REVERT: C 642 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5836 (m-10) REVERT: C 647 ILE cc_start: 0.5171 (OUTLIER) cc_final: 0.4941 (mt) REVERT: C 653 GLN cc_start: 0.7183 (pp30) cc_final: 0.6502 (pt0) REVERT: C 654 ARG cc_start: 0.5995 (ttp-110) cc_final: 0.5729 (ttp-170) REVERT: C 731 MET cc_start: 0.4441 (mmp) cc_final: 0.3887 (ttm) outliers start: 126 outliers final: 83 residues processed: 506 average time/residue: 0.2402 time to fit residues: 205.1030 Evaluate side-chains 477 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 378 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 300 TRP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 982 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2284 ASP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2458 VAL Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3117 ILE Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3845 LYS Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 647 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 333 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 374 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 466 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1374 GLN A1457 GLN A2865 HIS A3423 GLN A3787 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121793 restraints weight = 81624.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120791 restraints weight = 95225.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122426 restraints weight = 86852.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122422 restraints weight = 55969.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123372 restraints weight = 50182.796| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40791 Z= 0.124 Angle : 0.651 20.866 55431 Z= 0.327 Chirality : 0.042 0.252 6293 Planarity : 0.005 0.062 6795 Dihedral : 13.570 72.814 5974 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.35 % Favored : 88.52 % Rotamer: Outliers : 3.37 % Allowed : 19.91 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.74 (0.12), residues: 4768 helix: -0.51 (0.10), residues: 2659 sheet: -1.68 (0.36), residues: 198 loop : -3.85 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 431 TYR 0.023 0.001 TYR A 762 PHE 0.026 0.001 PHE A3554 TRP 0.010 0.001 TRP A1256 HIS 0.007 0.001 HIS A3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (40791) covalent geometry : angle 0.65123 / 0.33 (55431) hydrogen bonds : bond 0.03714 / 2.42 ( 1719) hydrogen bonds : angle 4.55966 / 3.17 ( 4977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 396 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7781 (pp) REVERT: A 357 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7555 (ttmt) REVERT: A 518 LYS cc_start: 0.4482 (OUTLIER) cc_final: 0.3095 (mmmt) REVERT: A 520 LYS cc_start: 0.4100 (OUTLIER) cc_final: 0.3570 (pttp) REVERT: A 533 HIS cc_start: 0.7439 (m-70) cc_final: 0.7237 (m-70) REVERT: A 563 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 720 GLN cc_start: 0.5958 (tm-30) cc_final: 0.5627 (tm-30) REVERT: A 726 LEU cc_start: 0.8379 (mt) cc_final: 0.8158 (tp) REVERT: A 857 GLN cc_start: 0.7622 (mt0) cc_final: 0.6874 (tm-30) REVERT: A 879 MET cc_start: 0.8286 (ttt) cc_final: 0.7946 (ttm) REVERT: A 880 MET cc_start: 0.7941 (mmt) cc_final: 0.7595 (mmm) REVERT: A 1015 ASP cc_start: 0.8033 (t0) cc_final: 0.7745 (t0) REVERT: A 1089 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.5443 (t80) REVERT: A 1145 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6853 (tt) REVERT: A 1478 SER cc_start: 0.8078 (t) cc_final: 0.7833 (t) REVERT: A 1890 HIS cc_start: 0.5379 (OUTLIER) cc_final: 0.3986 (t70) REVERT: A 1905 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7135 (mm) REVERT: A 2083 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7651 (pp) REVERT: A 2799 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7627 (mp-120) REVERT: A 2899 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.3895 (pmt-80) REVERT: A 3154 GLN cc_start: 0.7777 (pp30) cc_final: 0.7411 (pp30) REVERT: A 3414 MET cc_start: 0.8742 (mmm) cc_final: 0.8106 (mmm) REVERT: A 3450 MET cc_start: 0.7790 (ttm) cc_final: 0.7514 (ttt) REVERT: A 3683 CYS cc_start: 0.7506 (m) cc_final: 0.7006 (m) REVERT: A 3729 MET cc_start: 0.8260 (mmp) cc_final: 0.8009 (tpp) REVERT: B 217 TYR cc_start: 0.3579 (OUTLIER) cc_final: 0.2870 (m-10) REVERT: B 453 MET cc_start: 0.6539 (mmm) cc_final: 0.5128 (tpp) REVERT: B 525 PHE cc_start: 0.4915 (t80) cc_final: 0.4614 (t80) REVERT: B 526 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7436 (tptt) REVERT: C 412 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7217 (pt) REVERT: C 505 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6819 (pp) REVERT: C 610 GLU cc_start: 0.7350 (tp30) cc_final: 0.6904 (tp30) REVERT: C 642 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5766 (m-10) REVERT: C 647 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.5155 (mt) REVERT: C 731 MET cc_start: 0.4471 (mmp) cc_final: 0.3907 (ttm) outliers start: 141 outliers final: 99 residues processed: 511 average time/residue: 0.2393 time to fit residues: 208.2081 Evaluate side-chains 491 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 376 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 300 TRP Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 982 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2274 ILE Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2421 VAL Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 2987 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3097 ASP Chi-restraints excluded: chain A residue 3117 ILE Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3752 VAL Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3845 LYS Chi-restraints excluded: chain A residue 3937 VAL Chi-restraints excluded: chain A residue 3948 SER Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 647 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 270 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 466 optimal weight: 9.9990 chunk 373 optimal weight: 5.9990 chunk 357 optimal weight: 0.7980 chunk 291 optimal weight: 0.0170 chunk 235 optimal weight: 0.2980 chunk 188 optimal weight: 0.1980 chunk 416 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.150761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124128 restraints weight = 82374.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123834 restraints weight = 89075.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125190 restraints weight = 80638.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125242 restraints weight = 51820.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126370 restraints weight = 46493.871| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 40791 Z= 0.111 Angle : 0.647 20.721 55431 Z= 0.323 Chirality : 0.041 0.272 6293 Planarity : 0.004 0.062 6795 Dihedral : 13.415 69.654 5974 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.32 % Favored : 89.57 % Rotamer: Outliers : 2.78 % Allowed : 20.78 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.48 (0.12), residues: 4768 helix: -0.31 (0.10), residues: 2660 sheet: -1.53 (0.37), residues: 197 loop : -3.70 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 431 TYR 0.021 0.001 TYR A1411 PHE 0.025 0.001 PHE A1297 TRP 0.023 0.001 TRP A2479 HIS 0.005 0.001 HIS A3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (40791) covalent geometry : angle 0.64703 / 0.32 (55431) hydrogen bonds : bond 0.03384 / 2.19 ( 1719) hydrogen bonds : angle 4.39833 / 3.05 ( 4977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 425 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (pp) REVERT: A 357 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7554 (ttmt) REVERT: A 518 LYS cc_start: 0.4424 (OUTLIER) cc_final: 0.3073 (mmmt) REVERT: A 520 LYS cc_start: 0.3831 (OUTLIER) cc_final: 0.3361 (pttp) REVERT: A 563 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 720 GLN cc_start: 0.5936 (tm-30) cc_final: 0.5595 (tm-30) REVERT: A 857 GLN cc_start: 0.7642 (mt0) cc_final: 0.6826 (tm-30) REVERT: A 879 MET cc_start: 0.8212 (ttt) cc_final: 0.7833 (ttm) REVERT: A 880 MET cc_start: 0.7896 (mmt) cc_final: 0.7515 (mmm) REVERT: A 1015 ASP cc_start: 0.7938 (t0) cc_final: 0.7715 (t0) REVERT: A 1089 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5462 (t80) REVERT: A 1145 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6976 (tt) REVERT: A 1890 HIS cc_start: 0.5372 (OUTLIER) cc_final: 0.3981 (t70) REVERT: A 1905 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7017 (mm) REVERT: A 1927 MET cc_start: 0.8175 (mpp) cc_final: 0.7936 (mpp) REVERT: A 2083 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7581 (pp) REVERT: A 2379 MET cc_start: 0.8349 (tpp) cc_final: 0.8121 (tpp) REVERT: A 2799 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7581 (mp-120) REVERT: A 2899 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.4028 (pmt-80) REVERT: A 3154 GLN cc_start: 0.7806 (pp30) cc_final: 0.7417 (pp30) REVERT: A 3414 MET cc_start: 0.8681 (mmm) cc_final: 0.8007 (mmm) REVERT: A 3450 MET cc_start: 0.7930 (ttm) cc_final: 0.7629 (ttt) REVERT: A 3683 CYS cc_start: 0.7422 (m) cc_final: 0.6897 (m) REVERT: A 3751 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8366 (mp) REVERT: A 3842 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.6869 (t60) REVERT: A 3918 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8572 (pp) REVERT: A 3948 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.6752 (t) REVERT: A 3974 MET cc_start: 0.7197 (mpp) cc_final: 0.6809 (mtm) REVERT: A 4005 PHE cc_start: 0.6355 (m-80) cc_final: 0.6126 (m-80) REVERT: A 4110 GLN cc_start: 0.7686 (tp40) cc_final: 0.7384 (tt0) REVERT: B 217 TYR cc_start: 0.3575 (OUTLIER) cc_final: 0.3081 (m-10) REVERT: B 453 MET cc_start: 0.6519 (mmm) cc_final: 0.5054 (tpp) REVERT: B 525 PHE cc_start: 0.5001 (t80) cc_final: 0.4745 (t80) REVERT: B 526 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7489 (tptt) REVERT: C 280 ASP cc_start: 0.7650 (p0) cc_final: 0.7371 (p0) REVERT: C 412 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7139 (pt) REVERT: C 610 GLU cc_start: 0.7292 (tp30) cc_final: 0.6881 (tp30) REVERT: C 642 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5410 (m-10) REVERT: C 731 MET cc_start: 0.4452 (mmp) cc_final: 0.3901 (ttm) outliers start: 116 outliers final: 73 residues processed: 518 average time/residue: 0.2314 time to fit residues: 204.1588 Evaluate side-chains 482 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 391 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 300 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 982 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2251 ILE Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 2953 THR Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3351 ILE Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3463 LEU Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3751 LEU Chi-restraints excluded: chain A residue 3752 VAL Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3948 SER Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 642 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 447 optimal weight: 0.4980 chunk 356 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 358 optimal weight: 0.9990 chunk 265 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 385 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 43 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 = 0.4038 r_free = 0.4038 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.122633 restraints weight = 82638.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121978 restraints weight = 99756.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123365 restraints weight = 90356.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123441 restraints weight = 57419.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124211 restraints weight = 51619.482| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40791 Z= 0.133 Angle : 0.660 19.464 55431 Z= 0.330 Chirality : 0.043 0.277 6293 Planarity : 0.005 0.063 6795 Dihedral : 13.442 69.058 5972 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.35 % Favored : 88.52 % Rotamer: Outliers : 2.88 % Allowed : 20.75 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.43 (0.12), residues: 4768 helix: -0.28 (0.10), residues: 2664 sheet: -1.49 (0.37), residues: 199 loop : -3.67 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3474 TYR 0.022 0.001 TYR A 762 PHE 0.024 0.001 PHE A2260 TRP 0.016 0.001 TRP A3842 HIS 0.008 0.001 HIS A3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (40791) covalent geometry : angle 0.66043 / 0.33 (55431) hydrogen bonds : bond 0.03635 / 2.37 ( 1719) hydrogen bonds : angle 4.46341 / 3.10 ( 4977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 400 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8352 (mmm) cc_final: 0.8106 (mmm) REVERT: A 162 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7799 (pp) REVERT: A 357 LYS cc_start: 0.7989 (mmtp) cc_final: 0.7480 (ttpt) REVERT: A 518 LYS cc_start: 0.4401 (OUTLIER) cc_final: 0.3041 (mmmt) REVERT: A 520 LYS cc_start: 0.3862 (OUTLIER) cc_final: 0.3397 (pttp) REVERT: A 720 GLN cc_start: 0.5960 (tm-30) cc_final: 0.5615 (tm-30) REVERT: A 857 GLN cc_start: 0.7644 (mt0) cc_final: 0.6889 (tm-30) REVERT: A 879 MET cc_start: 0.8288 (ttt) cc_final: 0.7947 (ttm) REVERT: A 880 MET cc_start: 0.7908 (mmt) cc_final: 0.7574 (mmm) REVERT: A 1015 ASP cc_start: 0.8003 (t0) cc_final: 0.7775 (t0) REVERT: A 1145 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7061 (tt) REVERT: A 1890 HIS cc_start: 0.5390 (OUTLIER) cc_final: 0.3974 (t70) REVERT: A 1905 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7066 (mm) REVERT: A 2083 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7581 (pp) REVERT: A 2424 MET cc_start: 0.7991 (ttm) cc_final: 0.7756 (ttp) REVERT: A 2799 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7642 (mp-120) REVERT: A 2899 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.3972 (pmt-80) REVERT: A 3414 MET cc_start: 0.8739 (mmm) cc_final: 0.8226 (mmm) REVERT: A 3450 MET cc_start: 0.7810 (ttm) cc_final: 0.7536 (tmm) REVERT: A 3842 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.6863 (t60) REVERT: A 3918 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 3948 SER cc_start: 0.7177 (OUTLIER) cc_final: 0.6609 (t) REVERT: A 3974 MET cc_start: 0.7185 (mpp) cc_final: 0.6702 (mtm) REVERT: A 4005 PHE cc_start: 0.6358 (m-80) cc_final: 0.6134 (m-80) REVERT: B 217 TYR cc_start: 0.3532 (OUTLIER) cc_final: 0.2967 (m-10) REVERT: B 432 PHE cc_start: 0.7661 (m-80) cc_final: 0.6942 (t80) REVERT: B 453 MET cc_start: 0.6515 (mmm) cc_final: 0.5014 (tpp) REVERT: B 526 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7415 (tptt) REVERT: C 280 ASP cc_start: 0.7676 (p0) cc_final: 0.7416 (p0) REVERT: C 412 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7072 (pt) REVERT: C 610 GLU cc_start: 0.7275 (tp30) cc_final: 0.6884 (tp30) REVERT: C 622 GLN cc_start: 0.7197 (tp-100) cc_final: 0.6289 (pt0) REVERT: C 642 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5981 (m-10) REVERT: C 731 MET cc_start: 0.4488 (mmp) cc_final: 0.3931 (ttm) outliers start: 120 outliers final: 90 residues processed: 497 average time/residue: 0.2399 time to fit residues: 202.9336 Evaluate side-chains 485 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 380 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 982 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1382 ILE Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2251 ILE Chi-restraints excluded: chain A residue 2271 SER Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2467 THR Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2877 SER Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3097 ASP Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3463 LEU Chi-restraints excluded: chain A residue 3499 ILE Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3752 VAL Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3824 GLU Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3948 SER Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 642 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 442 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 chunk 317 optimal weight: 0.9990 chunk 406 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 314 optimal weight: 0.0170 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 152 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.150278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124179 restraints weight = 81995.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124401 restraints weight = 93677.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125340 restraints weight = 83451.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125683 restraints weight = 52464.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126728 restraints weight = 46662.463| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 40791 Z= 0.113 Angle : 0.653 19.558 55431 Z= 0.325 Chirality : 0.042 0.407 6293 Planarity : 0.004 0.065 6795 Dihedral : 13.354 67.397 5972 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.62 % Favored : 89.28 % Rotamer: Outliers : 2.62 % Allowed : 21.42 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.28 (0.12), residues: 4768 helix: -0.17 (0.10), residues: 2676 sheet: -1.34 (0.37), residues: 196 loop : -3.61 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 502 TYR 0.021 0.001 TYR A1411 PHE 0.041 0.001 PHE A1297 TRP 0.010 0.001 TRP A3842 HIS 0.007 0.001 HIS A3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (40791) covalent geometry : angle 0.65342 / 0.32 (55431) hydrogen bonds : bond 0.03388 / 2.20 ( 1719) hydrogen bonds : angle 4.33343 / 3.01 ( 4977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 401 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7860 (pp) REVERT: A 357 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7666 (ttmt) REVERT: A 366 TYR cc_start: 0.7032 (t80) cc_final: 0.6633 (t80) REVERT: A 384 MET cc_start: 0.7560 (mtt) cc_final: 0.6976 (mtt) REVERT: A 518 LYS cc_start: 0.4395 (OUTLIER) cc_final: 0.3038 (mmmt) REVERT: A 520 LYS cc_start: 0.3937 (OUTLIER) cc_final: 0.3427 (pttp) REVERT: A 563 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 720 GLN cc_start: 0.5910 (tm-30) cc_final: 0.5562 (tm-30) REVERT: A 857 GLN cc_start: 0.7619 (mt0) cc_final: 0.6853 (tm-30) REVERT: A 879 MET cc_start: 0.8194 (ttt) cc_final: 0.7815 (ttm) REVERT: A 880 MET cc_start: 0.7879 (mmt) cc_final: 0.7543 (mmm) REVERT: A 1145 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7245 (tt) REVERT: A 1890 HIS cc_start: 0.5292 (OUTLIER) cc_final: 0.3722 (t70) REVERT: A 1927 MET cc_start: 0.8029 (mpp) cc_final: 0.7739 (mpp) REVERT: A 2083 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7567 (pp) REVERT: A 2424 MET cc_start: 0.7882 (ttm) cc_final: 0.7656 (ttp) REVERT: A 2799 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7588 (mp-120) REVERT: A 2899 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.4047 (pmt-80) REVERT: A 3330 LEU cc_start: 0.8467 (mm) cc_final: 0.8186 (mt) REVERT: A 3414 MET cc_start: 0.8712 (mmm) cc_final: 0.8025 (mmm) REVERT: A 3450 MET cc_start: 0.7805 (ttm) cc_final: 0.7543 (ttt) REVERT: A 3683 CYS cc_start: 0.7316 (m) cc_final: 0.6815 (m) REVERT: A 3751 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 3842 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.6789 (t60) REVERT: A 3918 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8493 (pp) REVERT: A 3948 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.6799 (t) REVERT: A 3974 MET cc_start: 0.7160 (mpp) cc_final: 0.6825 (mtm) REVERT: A 4005 PHE cc_start: 0.6369 (m-80) cc_final: 0.6112 (m-80) REVERT: B 217 TYR cc_start: 0.3746 (OUTLIER) cc_final: 0.3242 (m-10) REVERT: B 432 PHE cc_start: 0.7552 (m-80) cc_final: 0.6849 (t80) REVERT: B 453 MET cc_start: 0.6460 (mmm) cc_final: 0.5736 (tpp) REVERT: B 526 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7371 (tptt) REVERT: C 280 ASP cc_start: 0.7467 (p0) cc_final: 0.7202 (p0) REVERT: C 412 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7052 (pt) REVERT: C 610 GLU cc_start: 0.7253 (tp30) cc_final: 0.6971 (tp30) REVERT: C 731 MET cc_start: 0.4950 (mmp) cc_final: 0.4231 (ttm) outliers start: 109 outliers final: 81 residues processed: 489 average time/residue: 0.2367 time to fit residues: 196.6570 Evaluate side-chains 474 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 378 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 300 TRP Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 982 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2251 ILE Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3463 LEU Chi-restraints excluded: chain A residue 3499 ILE Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3751 LEU Chi-restraints excluded: chain A residue 3752 VAL Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3948 SER Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 156 optimal weight: 0.0020 chunk 77 optimal weight: 2.9990 chunk 344 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 423 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 281 optimal weight: 0.7980 chunk 89 optimal weight: 0.0470 chunk 73 optimal weight: 10.0000 chunk 307 optimal weight: 0.0060 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 HIS A2275 GLN A2283 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3748 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125276 restraints weight = 99651.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123979 restraints weight = 86628.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125354 restraints weight = 81440.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125691 restraints weight = 53245.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126563 restraints weight = 47085.893| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 40791 Z= 0.112 Angle : 0.654 18.863 55431 Z= 0.324 Chirality : 0.041 0.356 6293 Planarity : 0.004 0.067 6795 Dihedral : 13.265 65.902 5972 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.49 % Favored : 89.40 % Rotamer: Outliers : 2.33 % Allowed : 21.84 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.10 (0.12), residues: 4768 helix: -0.01 (0.11), residues: 2668 sheet: -1.25 (0.38), residues: 195 loop : -3.55 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3324 TYR 0.020 0.001 TYR A1411 PHE 0.040 0.001 PHE A3554 TRP 0.011 0.001 TRP A2479 HIS 0.010 0.001 HIS A2225 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (40791) covalent geometry : angle 0.65363 / 0.32 (55431) hydrogen bonds : bond 0.03237 / 2.10 ( 1719) hydrogen bonds : angle 4.25687 / 2.96 ( 4977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 410 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7771 (pp) REVERT: A 357 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7483 (ttpt) REVERT: A 366 TYR cc_start: 0.7039 (t80) cc_final: 0.6632 (t80) REVERT: A 384 MET cc_start: 0.7624 (mtt) cc_final: 0.7081 (mtt) REVERT: A 518 LYS cc_start: 0.4317 (OUTLIER) cc_final: 0.2883 (mmmt) REVERT: A 720 GLN cc_start: 0.5967 (tm-30) cc_final: 0.5630 (tm-30) REVERT: A 857 GLN cc_start: 0.7510 (mt0) cc_final: 0.6685 (tm-30) REVERT: A 879 MET cc_start: 0.8245 (ttt) cc_final: 0.7854 (ttm) REVERT: A 880 MET cc_start: 0.7897 (mmt) cc_final: 0.7522 (mmm) REVERT: A 1145 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7535 (tt) REVERT: A 1426 GLN cc_start: 0.8285 (tm-30) cc_final: 0.8054 (tp-100) REVERT: A 1430 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 1583 MET cc_start: 0.8521 (mtm) cc_final: 0.8091 (mtm) REVERT: A 1589 ASN cc_start: 0.7977 (m110) cc_final: 0.7649 (m110) REVERT: A 1641 THR cc_start: 0.8723 (p) cc_final: 0.8425 (p) REVERT: A 1890 HIS cc_start: 0.5232 (OUTLIER) cc_final: 0.3682 (t70) REVERT: A 1927 MET cc_start: 0.8167 (mpp) cc_final: 0.7819 (mpp) REVERT: A 2083 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7527 (pp) REVERT: A 2424 MET cc_start: 0.7861 (ttm) cc_final: 0.7652 (ttp) REVERT: A 2799 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7556 (mp-120) REVERT: A 2899 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.4129 (pmt-80) REVERT: A 3414 MET cc_start: 0.8705 (mmm) cc_final: 0.8039 (mmm) REVERT: A 3450 MET cc_start: 0.7804 (ttm) cc_final: 0.7515 (tmm) REVERT: A 3683 CYS cc_start: 0.7521 (m) cc_final: 0.6955 (m) REVERT: A 3842 TRP cc_start: 0.8068 (OUTLIER) cc_final: 0.6726 (t60) REVERT: A 3918 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8548 (pp) REVERT: A 3948 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.6828 (t) REVERT: A 3974 MET cc_start: 0.7112 (mpp) cc_final: 0.6844 (mtm) REVERT: A 4005 PHE cc_start: 0.6400 (m-80) cc_final: 0.6148 (m-80) REVERT: A 4110 GLN cc_start: 0.7788 (tp40) cc_final: 0.7474 (tt0) REVERT: B 217 TYR cc_start: 0.3218 (OUTLIER) cc_final: 0.2842 (m-10) REVERT: B 363 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7954 (ttm170) REVERT: B 432 PHE cc_start: 0.7543 (m-80) cc_final: 0.6932 (t80) REVERT: B 453 MET cc_start: 0.6437 (mmm) cc_final: 0.5747 (tpp) REVERT: B 526 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7453 (tptt) REVERT: C 280 ASP cc_start: 0.7399 (p0) cc_final: 0.7115 (p0) REVERT: C 412 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7063 (pt) REVERT: C 434 MET cc_start: 0.8157 (ppp) cc_final: 0.7808 (ppp) REVERT: C 610 GLU cc_start: 0.7353 (tp30) cc_final: 0.7003 (tp30) REVERT: C 622 GLN cc_start: 0.7354 (tp-100) cc_final: 0.6673 (pt0) REVERT: C 731 MET cc_start: 0.4866 (mmp) cc_final: 0.4177 (ttm) outliers start: 97 outliers final: 70 residues processed: 492 average time/residue: 0.2400 time to fit residues: 199.9148 Evaluate side-chains 467 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 385 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 884 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1036 PHE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1175 HIS Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1673 THR Chi-restraints excluded: chain A residue 1696 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1762 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1919 CYS Chi-restraints excluded: chain A residue 2083 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2249 LEU Chi-restraints excluded: chain A residue 2251 ILE Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2484 TYR Chi-restraints excluded: chain A residue 2491 THR Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2799 GLN Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2888 VAL Chi-restraints excluded: chain A residue 2899 ARG Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3259 LEU Chi-restraints excluded: chain A residue 3433 VAL Chi-restraints excluded: chain A residue 3434 ILE Chi-restraints excluded: chain A residue 3463 LEU Chi-restraints excluded: chain A residue 3535 ILE Chi-restraints excluded: chain A residue 3625 LEU Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3791 TYR Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3948 SER Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4112 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 420 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 438 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 285 optimal weight: 0.5980 chunk 436 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 462 optimal weight: 1.9990 chunk 435 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124635 restraints weight = 94371.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123524 restraints weight = 84707.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124842 restraints weight = 79712.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124975 restraints weight = 59484.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125897 restraints weight = 49979.337| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40791 Z= 0.114 Angle : 0.656 18.025 55431 Z= 0.324 Chirality : 0.042 0.365 6293 Planarity : 0.004 0.068 6795 Dihedral : 13.254 66.049 5972 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.41 % Favored : 89.49 % Rotamer: Outliers : 2.15 % Allowed : 22.26 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.07 (0.12), residues: 4768 helix: 0.00 (0.10), residues: 2672 sheet: -1.23 (0.38), residues: 196 loop : -3.53 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1712 TYR 0.034 0.001 TYR A1411 PHE 0.036 0.001 PHE A1297 TRP 0.049 0.001 TRP A1356 HIS 0.009 0.001 HIS A3516 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (40791) covalent geometry : angle 0.65564 / 0.32 (55431) hydrogen bonds : bond 0.03273 / 2.13 ( 1719) hydrogen bonds : angle 4.25998 / 2.97 ( 4977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7251.62 seconds wall clock time: 126 minutes 16.15 seconds (7576.15 seconds total)