Starting phenix.real_space_refine on Sun Aug 9 03:11:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qu6_18656/08_2026/8qu6_18656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qu6_18656/08_2026/8qu6_18656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qu6_18656/08_2026/8qu6_18656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qu6_18656/08_2026/8qu6_18656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qu6_18656/08_2026/8qu6_18656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qu6_18656/08_2026/8qu6_18656.map" } resolution = 3.45 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= 0.003 sd= 0.027 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 53 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 20160 2.51 5 N 5773 2.21 5 O 6367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32464 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1779 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8647 Classifications: {'peptide': 1117} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9983 Classifications: {'peptide': 1278} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1220} Chain: "J" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 679 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 616 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2442 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 1 Chain: "H" Number of atoms: 5515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5515 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 36, 'TRANS': 670} Chain breaks: 1 Chain: "P" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "O" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19174 SG CYS D 890 31.802 62.058 87.914 1.00 18.96 S ATOM 19736 SG CYS D 967 34.936 64.171 88.668 1.00 15.04 S ATOM 19778 SG CYS D 974 32.586 63.130 91.413 1.00 14.26 S ATOM 19797 SG CYS D 977 34.651 60.605 89.933 1.00 14.72 S ATOM 12601 SG CYS D 60 31.058 127.018 104.370 1.00 43.45 S ATOM 12619 SG CYS D 62 31.140 130.506 103.198 1.00 42.75 S ATOM 12728 SG CYS D 75 28.099 128.392 102.408 1.00 44.41 S ATOM 12754 SG CYS D 78 32.023 127.290 100.475 1.00 45.00 S Time building chain proxies: 6.58, per 1000 atoms: 0.20 Number of scatterers: 32464 At special positions: 0 Unit cell: (127.541, 168.387, 184.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 108 16.00 P 53 15.00 Mg 1 11.99 O 6367 8.00 N 5773 7.00 C 20160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " Number of angles added : 12 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7440 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 46 sheets defined 45.8% alpha, 14.8% beta 22 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.649A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.108A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.787A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.869A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 4.379A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.533A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.505A pdb=" N ALA C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.423A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 371 through 395 removed outlier: 3.544A pdb=" N ARG C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.789A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 455 through 459 removed outlier: 4.053A pdb=" N ALA C 459 " --> pdb=" O ARG C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.848A pdb=" N ASP C 528 " --> pdb=" O ALA C 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 573 through 577 removed outlier: 4.264A pdb=" N MET C 577 " --> pdb=" O PRO C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.551A pdb=" N ILE C 585 " --> pdb=" O THR C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 591 removed outlier: 3.634A pdb=" N ASP C 591 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.800A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.160A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 806 through 817 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 909 through 913 removed outlier: 3.694A pdb=" N GLY C 912 " --> pdb=" O ASN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 944 through 948 removed outlier: 3.597A pdb=" N SER C 948 " --> pdb=" O ASP C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 981 removed outlier: 3.800A pdb=" N GLY C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1060 through 1071 Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1086 through 1100 Processing helix chain 'C' and resid 1109 through 1122 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.526A pdb=" N LYS D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.691A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 185 removed outlier: 3.865A pdb=" N HIS D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.004A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.687A pdb=" N ALA D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 308 through 311 removed outlier: 4.004A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.950A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.635A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 492 removed outlier: 3.600A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 removed outlier: 3.759A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.595A pdb=" N ARG D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 762 removed outlier: 3.629A pdb=" N GLU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.871A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 Processing helix chain 'D' and resid 844 through 881 removed outlier: 4.043A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 859 " --> pdb=" O ALA D 855 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 860 " --> pdb=" O ARG D 856 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 867 " --> pdb=" O ALA D 863 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 869 " --> pdb=" O ARG D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 944 through 955 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1005 through 1009 removed outlier: 3.507A pdb=" N LEU D1009 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1127 Processing helix chain 'D' and resid 1127 through 1146 Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.900A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D1158 " --> pdb=" O HIS D1154 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN D1161 " --> pdb=" O VAL D1157 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET D1162 " --> pdb=" O ILE D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1194 Processing helix chain 'D' and resid 1210 through 1216 Processing helix chain 'D' and resid 1220 through 1228 removed outlier: 4.080A pdb=" N SER D1226 " --> pdb=" O LEU D1222 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1251 through 1256 removed outlier: 3.616A pdb=" N ILE D1255 " --> pdb=" O GLU D1251 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 removed outlier: 3.626A pdb=" N ASN D1270 " --> pdb=" O SER D1266 " (cutoff:3.500A) Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 106 removed outlier: 3.744A pdb=" N GLU J 95 " --> pdb=" O VAL J 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 46 through 66 Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.533A pdb=" N ALA F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.728A pdb=" N GLN F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 208 removed outlier: 3.604A pdb=" N ALA F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 237 removed outlier: 3.832A pdb=" N ASP F 227 " --> pdb=" O CYS F 223 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 removed outlier: 3.767A pdb=" N VAL F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 273 removed outlier: 3.527A pdb=" N ARG F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.663A pdb=" N LYS F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 301 removed outlier: 3.605A pdb=" N TYR F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 removed outlier: 4.150A pdb=" N VAL F 313 " --> pdb=" O HIS F 309 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 318 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 389 through 403 removed outlier: 3.711A pdb=" N GLN F 399 " --> pdb=" O GLN F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 417 removed outlier: 4.076A pdb=" N VAL F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 435 Processing helix chain 'F' and resid 438 through 454 removed outlier: 3.823A pdb=" N HIS F 454 " --> pdb=" O SER F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 464 Processing helix chain 'H' and resid 3 through 42 Processing helix chain 'H' and resid 45 through 67 Processing helix chain 'H' and resid 93 through 96 removed outlier: 4.039A pdb=" N ASP H 96 " --> pdb=" O ARG H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 106 through 109 Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 175 through 188 Processing helix chain 'H' and resid 204 through 220 removed outlier: 3.661A pdb=" N VAL H 208 " --> pdb=" O GLY H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 224 Processing helix chain 'H' and resid 236 through 246 Processing helix chain 'H' and resid 246 through 253 Processing helix chain 'H' and resid 273 through 281 removed outlier: 4.378A pdb=" N VAL H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.663A pdb=" N VAL H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 Processing helix chain 'H' and resid 333 through 358 removed outlier: 4.601A pdb=" N ALA H 339 " --> pdb=" O ASN H 335 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 384 removed outlier: 3.635A pdb=" N TRP H 370 " --> pdb=" O ASP H 366 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS H 372 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 383 " --> pdb=" O GLY H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 394 Processing helix chain 'H' and resid 399 through 410 removed outlier: 3.574A pdb=" N SER H 410 " --> pdb=" O GLN H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 418 Processing helix chain 'H' and resid 420 through 424 removed outlier: 3.845A pdb=" N LEU H 423 " --> pdb=" O PRO H 420 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP H 424 " --> pdb=" O GLU H 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 420 through 424' Processing helix chain 'H' and resid 434 through 447 removed outlier: 4.464A pdb=" N LEU H 438 " --> pdb=" O SER H 434 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 474 removed outlier: 3.624A pdb=" N MET H 474 " --> pdb=" O VAL H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 480 removed outlier: 3.641A pdb=" N ASP H 479 " --> pdb=" O ASP H 476 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 480 " --> pdb=" O ARG H 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 476 through 480' Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 494 through 501 Processing helix chain 'H' and resid 509 through 516 Processing helix chain 'H' and resid 529 through 533 Processing helix chain 'H' and resid 534 through 544 Processing helix chain 'H' and resid 555 through 559 removed outlier: 4.064A pdb=" N ARG H 559 " --> pdb=" O LEU H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 567 through 572 removed outlier: 3.580A pdb=" N MET H 571 " --> pdb=" O SER H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 604 Processing helix chain 'H' and resid 632 through 648 removed outlier: 3.817A pdb=" N ALA H 638 " --> pdb=" O ALA H 634 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 647 " --> pdb=" O GLU H 643 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 648 " --> pdb=" O GLU H 644 " (cutoff:3.500A) Processing helix chain 'H' and resid 664 through 669 removed outlier: 3.541A pdb=" N THR H 668 " --> pdb=" O PRO H 664 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS H 669 " --> pdb=" O PRO H 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 664 through 669' Processing helix chain 'H' and resid 680 through 686 removed outlier: 3.900A pdb=" N ILE H 684 " --> pdb=" O GLU H 680 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 701 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 5.670A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 196 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL A 22 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.325A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 13 removed outlier: 6.402A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.750A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.623A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.341A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.548A pdb=" N SER C 168 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 182 removed outlier: 4.289A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.397A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.578A pdb=" N ASP C 571 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.654A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.340A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC4, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.623A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 756 through 757 removed outlier: 3.741A pdb=" N GLU C 858 " --> pdb=" O ALA C 750 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP C 752 " --> pdb=" O VAL C 856 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL C 856 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS C 867 " --> pdb=" O SER C 835 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N SER C 835 " --> pdb=" O LYS C 867 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC7, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.654A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AC9, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 7.607A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 3.663A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1127 through 1129 Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 102 removed outlier: 4.094A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.861A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 329 through 330 Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD7, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 899 removed outlier: 4.713A pdb=" N THR D 923 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE1, first strand: chain 'D' and resid 928 through 929 removed outlier: 7.114A pdb=" N ALA D 928 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE3, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 5.631A pdb=" N VAL D1077 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE D1067 " --> pdb=" O VAL D1077 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP D1079 " --> pdb=" O ILE D1065 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE D1065 " --> pdb=" O ASP D1079 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D1081 " --> pdb=" O PHE D1063 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 5.715A pdb=" N VAL D1166 " --> pdb=" O VAL D1207 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D1207 " --> pdb=" O VAL D1166 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE D1168 " --> pdb=" O ARG D1205 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG D1205 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE6, first strand: chain 'J' and resid 39 through 42 Processing sheet with id=AE7, first strand: chain 'H' and resid 90 through 91 removed outlier: 6.341A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE H 72 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 125 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ARG H 124 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE H 143 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG H 126 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP H 141 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN H 128 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE H 139 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N HIS H 130 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 254 through 257 Processing sheet with id=AE9, first strand: chain 'H' and resid 304 through 305 Processing sheet with id=AF1, first strand: chain 'H' and resid 624 through 627 removed outlier: 6.772A pdb=" N TRP H 624 " --> pdb=" O VAL H 708 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR H 710 " --> pdb=" O TRP H 624 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG H 626 " --> pdb=" O TYR H 710 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP H 674 " --> pdb=" O ARG H 705 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLY H 707 " --> pdb=" O ASP H 674 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL H 676 " --> pdb=" O GLY H 707 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU H 709 " --> pdb=" O VAL H 676 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL H 678 " --> pdb=" O LEU H 709 " (cutoff:3.500A) 1430 hydrogen bonds defined for protein. 4038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 7.92 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10904 1.34 - 1.46: 4076 1.46 - 1.58: 17845 1.58 - 1.70: 105 1.70 - 1.81: 192 Bond restraints: 33122 Sorted by residual: bond pdb=" C3' DC P 22 " pdb=" C2' DC P 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.07e+00 bond pdb=" C3' DC P 1 " pdb=" C2' DC P 1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" CB PRO D1178 " pdb=" CG PRO D1178 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.91e+00 bond pdb=" C1' DC P 11 " pdb=" N1 DC P 11 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.72e+00 bond pdb=" C3' DC O 2 " pdb=" C2' DC O 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 ... (remaining 33117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 44070 1.42 - 2.85: 760 2.85 - 4.27: 250 4.27 - 5.70: 12 5.70 - 7.12: 3 Bond angle restraints: 45095 Sorted by residual: angle pdb=" O4' DG P 21 " pdb=" C1' DG P 21 " pdb=" N9 DG P 21 " ideal model delta sigma weight residual 108.00 111.78 -3.78 7.00e-01 2.04e+00 2.91e+01 angle pdb=" CA PRO D1178 " pdb=" N PRO D1178 " pdb=" CD PRO D1178 " ideal model delta sigma weight residual 112.00 105.19 6.81 1.40e+00 5.10e-01 2.36e+01 angle pdb=" N GLY C 365 " pdb=" CA GLY C 365 " pdb=" C GLY C 365 " ideal model delta sigma weight residual 115.32 109.19 6.13 1.31e+00 5.83e-01 2.19e+01 angle pdb=" N3 DT O 4 " pdb=" C4 DT O 4 " pdb=" O4 DT O 4 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT O 15 " pdb=" C4 DT O 15 " pdb=" O4 DT O 15 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 ... (remaining 45090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.67: 19426 31.67 - 63.34: 668 63.34 - 95.01: 68 95.01 - 126.69: 0 126.69 - 158.36: 1 Dihedral angle restraints: 20163 sinusoidal: 8615 harmonic: 11548 Sorted by residual: dihedral pdb=" CA ARG D 412 " pdb=" C ARG D 412 " pdb=" N PHE D 413 " pdb=" CA PHE D 413 " ideal model delta harmonic sigma weight residual -180.00 -158.82 -21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DA P 7 " pdb=" C3' DA P 7 " pdb=" O3' DA P 7 " pdb=" P DA P 8 " ideal model delta sinusoidal sigma weight residual 220.00 61.64 158.36 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CA PHE C 291 " pdb=" C PHE C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta harmonic sigma weight residual 180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 20160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3545 0.033 - 0.066: 991 0.066 - 0.099: 317 0.099 - 0.132: 207 0.132 - 0.165: 52 Chirality restraints: 5112 Sorted by residual: chirality pdb=" C3' DG O 22 " pdb=" C4' DG O 22 " pdb=" O3' DG O 22 " pdb=" C2' DG O 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" C3' DA P 20 " pdb=" C4' DA P 20 " pdb=" O3' DA P 20 " pdb=" C2' DA P 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" C3' DG O 5 " pdb=" C4' DG O 5 " pdb=" O3' DG O 5 " pdb=" C2' DG O 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 5109 not shown) Planarity restraints: 5772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1177 " 0.047 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO D1178 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D1178 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D1178 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 42 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO J 43 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 43 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 43 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 782 " -0.145 9.50e-02 1.11e+02 6.50e-02 2.86e+00 pdb=" NE ARG C 782 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 782 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 782 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 782 " -0.002 2.00e-02 2.50e+03 ... (remaining 5769 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 249 2.62 - 3.19: 29226 3.19 - 3.76: 47802 3.76 - 4.33: 67345 4.33 - 4.90: 112692 Nonbonded interactions: 257314 Sorted by model distance: nonbonded pdb=" OH TYR C1040 " pdb=" OD2 ASP D 423 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR F 426 " pdb=" OP2 DG P 16 " model vdw 2.076 3.040 nonbonded pdb=" OG SER D1220 " pdb=" OE1 GLU D1251 " model vdw 2.085 3.040 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2003 " model vdw 2.133 2.170 nonbonded pdb=" OH TYR D 599 " pdb=" OE1 GLU D 608 " model vdw 2.149 3.040 ... (remaining 257309 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 'A' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.384 33130 Z= 0.186 Angle : 0.523 10.864 45107 Z= 0.324 Chirality : 0.042 0.165 5112 Planarity : 0.004 0.069 5772 Dihedral : 15.171 158.357 12723 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 4003 helix: 1.56 (0.14), residues: 1588 sheet: 0.29 (0.23), residues: 462 loop : 0.22 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 782 TYR 0.009 0.001 TYR H 582 PHE 0.022 0.001 PHE C 500 TRP 0.019 0.001 TRP F 221 HIS 0.008 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.17 (33122) covalent geometry : angle 0.51683 / 0.32 (45095) hydrogen bonds : bond 0.14969 / 10.28 ( 1479) hydrogen bonds : angle 5.74976 / 4.04 ( 4140) metal coordination : bond 0.15270 / 7.56 ( 8) metal coordination : angle 4.76932 / 2.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.2437 time to fit residues: 131.7541 Evaluate side-chains 191 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 146 ASN D 349 ASN D1092 HIS F 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047547 restraints weight = 109746.747| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.18 r_work: 0.2670 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33130 Z= 0.238 Angle : 0.625 14.138 45107 Z= 0.328 Chirality : 0.045 0.181 5112 Planarity : 0.005 0.050 5772 Dihedral : 11.634 161.347 5018 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.57 % Allowed : 6.34 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4003 helix: 1.44 (0.13), residues: 1607 sheet: 0.39 (0.25), residues: 437 loop : 0.13 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG J 31 TYR 0.028 0.002 TYR J 32 PHE 0.022 0.002 PHE C 364 TRP 0.024 0.001 TRP H 424 HIS 0.022 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (33122) covalent geometry : angle 0.61721 / 0.33 (45095) hydrogen bonds : bond 0.05082 / 3.46 ( 1479) hydrogen bonds : angle 4.76668 / 3.36 ( 4140) metal coordination : bond 0.02096 / 1.01 ( 8) metal coordination : angle 6.07923 / 3.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 1129 LEU cc_start: 0.7795 (mt) cc_final: 0.7587 (mt) REVERT: D 8 ASP cc_start: 0.8234 (t0) cc_final: 0.7855 (t0) REVERT: D 205 MET cc_start: 0.7168 (tmm) cc_final: 0.6635 (ptp) REVERT: D 269 ASP cc_start: 0.8554 (t0) cc_final: 0.8302 (t0) REVERT: D 1092 HIS cc_start: 0.7744 (t-90) cc_final: 0.7542 (t-90) REVERT: D 1113 MET cc_start: 0.9546 (mmm) cc_final: 0.9148 (mmm) REVERT: J 33 ARG cc_start: 0.9276 (ptm160) cc_final: 0.9066 (ttm-80) REVERT: J 46 ASP cc_start: 0.7926 (m-30) cc_final: 0.7646 (m-30) REVERT: F 183 GLU cc_start: 0.8842 (mp0) cc_final: 0.8613 (mp0) REVERT: F 196 TYR cc_start: 0.9316 (t80) cc_final: 0.9099 (t80) REVERT: F 310 MET cc_start: 0.9455 (tpp) cc_final: 0.9235 (tpp) REVERT: F 425 ARG cc_start: 0.6317 (mmm160) cc_final: 0.6056 (mmm160) REVERT: H 371 GLU cc_start: 0.8649 (mp0) cc_final: 0.8404 (mp0) REVERT: H 571 MET cc_start: 0.9453 (mmm) cc_final: 0.9252 (mmm) outliers start: 19 outliers final: 13 residues processed: 216 average time/residue: 0.2112 time to fit residues: 74.3489 Evaluate side-chains 196 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 27 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 272 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 354 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 709 ASN D 686 GLN F 454 HIS H 411 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048677 restraints weight = 109016.646| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.12 r_work: 0.2686 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33130 Z= 0.185 Angle : 0.551 13.512 45107 Z= 0.292 Chirality : 0.043 0.203 5112 Planarity : 0.004 0.048 5772 Dihedral : 11.769 162.995 5018 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.31 % Allowed : 7.44 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.13), residues: 4003 helix: 1.51 (0.13), residues: 1608 sheet: 0.39 (0.25), residues: 447 loop : 0.08 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 209 TYR 0.020 0.001 TYR C 269 PHE 0.018 0.001 PHE D1062 TRP 0.011 0.001 TRP D1221 HIS 0.006 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (33122) covalent geometry : angle 0.54335 / 0.29 (45095) hydrogen bonds : bond 0.04461 / 3.03 ( 1479) hydrogen bonds : angle 4.51857 / 3.19 ( 4140) metal coordination : bond 0.01272 / 0.62 ( 8) metal coordination : angle 5.47572 / 3.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.364 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 5 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8481 (tm-30) REVERT: B 131 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8638 (tptp) REVERT: C 346 MET cc_start: 0.8828 (ttp) cc_final: 0.8593 (ptm) REVERT: D 8 ASP cc_start: 0.8260 (t0) cc_final: 0.7767 (t0) REVERT: D 143 MET cc_start: 0.8038 (mtp) cc_final: 0.7431 (ttm) REVERT: D 205 MET cc_start: 0.7309 (tmm) cc_final: 0.6746 (ptp) REVERT: D 269 ASP cc_start: 0.8517 (t0) cc_final: 0.8126 (t0) REVERT: D 1061 LYS cc_start: 0.8884 (tptp) cc_final: 0.8632 (mttt) REVERT: D 1092 HIS cc_start: 0.8013 (t-90) cc_final: 0.7731 (t-90) REVERT: F 183 GLU cc_start: 0.8909 (mp0) cc_final: 0.8569 (mp0) REVERT: F 310 MET cc_start: 0.9481 (tpp) cc_final: 0.9191 (tpp) REVERT: H 571 MET cc_start: 0.9301 (mmm) cc_final: 0.9093 (mmm) REVERT: H 680 GLU cc_start: 0.7905 (tp30) cc_final: 0.7391 (tm-30) outliers start: 44 outliers final: 21 residues processed: 223 average time/residue: 0.2057 time to fit residues: 76.2543 Evaluate side-chains 196 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 1043 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 352 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 328 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 350 optimal weight: 1.9990 chunk 285 optimal weight: 0.0050 chunk 48 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 GLN C 534 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.047632 restraints weight = 108345.360| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.08 r_work: 0.2654 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33130 Z= 0.154 Angle : 0.531 12.793 45107 Z= 0.279 Chirality : 0.042 0.207 5112 Planarity : 0.004 0.052 5772 Dihedral : 11.787 163.022 5018 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.25 % Allowed : 8.78 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.13), residues: 4003 helix: 1.60 (0.13), residues: 1618 sheet: 0.40 (0.25), residues: 447 loop : 0.10 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 214 TYR 0.014 0.001 TYR J 32 PHE 0.011 0.001 PHE C 897 TRP 0.014 0.001 TRP H 370 HIS 0.005 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (33122) covalent geometry : angle 0.52432 / 0.28 (45095) hydrogen bonds : bond 0.04098 / 2.78 ( 1479) hydrogen bonds : angle 4.36901 / 3.08 ( 4140) metal coordination : bond 0.01080 / 0.52 ( 8) metal coordination : angle 5.11692 / 2.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 131 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8634 (tptp) REVERT: D 8 ASP cc_start: 0.8324 (t0) cc_final: 0.7834 (t0) REVERT: D 143 MET cc_start: 0.7974 (mtp) cc_final: 0.7345 (ttm) REVERT: D 165 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 269 ASP cc_start: 0.8490 (t0) cc_final: 0.8062 (t0) REVERT: J 31 ARG cc_start: 0.8620 (mmt180) cc_final: 0.8287 (mmm160) REVERT: J 102 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8723 (mm) REVERT: F 183 GLU cc_start: 0.8982 (mp0) cc_final: 0.8624 (mp0) REVERT: F 219 MET cc_start: 0.9474 (mmp) cc_final: 0.9156 (mmm) REVERT: F 310 MET cc_start: 0.9464 (tpp) cc_final: 0.9229 (tpp) REVERT: H 356 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8759 (ttp-170) REVERT: H 571 MET cc_start: 0.9268 (mmm) cc_final: 0.8671 (mmm) REVERT: H 680 GLU cc_start: 0.8048 (tp30) cc_final: 0.7714 (tp30) outliers start: 42 outliers final: 27 residues processed: 212 average time/residue: 0.2014 time to fit residues: 71.6984 Evaluate side-chains 202 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 208 optimal weight: 0.0060 chunk 92 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 377 GLN C 601 ASN C 709 ASN C 926 HIS D 881 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.048924 restraints weight = 108696.600| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.04 r_work: 0.2700 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33130 Z= 0.128 Angle : 0.515 14.982 45107 Z= 0.269 Chirality : 0.041 0.220 5112 Planarity : 0.004 0.055 5772 Dihedral : 11.809 163.845 5018 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.43 % Allowed : 9.58 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 4003 helix: 1.66 (0.13), residues: 1626 sheet: 0.44 (0.25), residues: 447 loop : 0.12 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 77 TYR 0.011 0.001 TYR J 32 PHE 0.011 0.001 PHE C 897 TRP 0.009 0.001 TRP D 722 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33122) covalent geometry : angle 0.50926 / 0.27 (45095) hydrogen bonds : bond 0.03852 / 2.61 ( 1479) hydrogen bonds : angle 4.27444 / 3.00 ( 4140) metal coordination : bond 0.01962 / 0.97 ( 8) metal coordination : angle 4.91504 / 2.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9098 (m-30) cc_final: 0.8896 (t0) REVERT: B 131 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8711 (tptp) REVERT: C 94 MET cc_start: 0.8734 (ttp) cc_final: 0.8473 (ptm) REVERT: C 523 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8992 (p) REVERT: D 8 ASP cc_start: 0.8339 (t0) cc_final: 0.7829 (t0) REVERT: D 143 MET cc_start: 0.7981 (mtp) cc_final: 0.7372 (ttm) REVERT: D 165 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 205 MET cc_start: 0.7757 (tmm) cc_final: 0.6777 (ptp) REVERT: D 269 ASP cc_start: 0.8534 (t0) cc_final: 0.8078 (t0) REVERT: J 31 ARG cc_start: 0.8592 (mmt180) cc_final: 0.8030 (mmm-85) REVERT: J 102 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8851 (mm) REVERT: F 196 TYR cc_start: 0.9365 (t80) cc_final: 0.9067 (t80) REVERT: F 219 MET cc_start: 0.9437 (mmp) cc_final: 0.9113 (mmm) REVERT: F 310 MET cc_start: 0.9449 (tpp) cc_final: 0.9243 (tpp) REVERT: H 356 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8789 (ttp-170) REVERT: H 571 MET cc_start: 0.9254 (mmm) cc_final: 0.8685 (mmm) REVERT: H 680 GLU cc_start: 0.8140 (tp30) cc_final: 0.7854 (tp30) outliers start: 48 outliers final: 29 residues processed: 218 average time/residue: 0.1977 time to fit residues: 71.8461 Evaluate side-chains 203 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 231 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 383 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 386 optimal weight: 7.9990 chunk 399 optimal weight: 40.0000 chunk 288 optimal weight: 0.0170 chunk 389 optimal weight: 6.9990 overall best weight: 3.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS C 601 ASN D 765 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.046643 restraints weight = 108988.463| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.16 r_work: 0.2642 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33130 Z= 0.186 Angle : 0.548 14.919 45107 Z= 0.283 Chirality : 0.042 0.219 5112 Planarity : 0.004 0.057 5772 Dihedral : 11.875 163.960 5018 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.64 % Allowed : 10.29 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.13), residues: 4003 helix: 1.57 (0.13), residues: 1638 sheet: 0.36 (0.25), residues: 433 loop : 0.04 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 77 TYR 0.012 0.001 TYR H 696 PHE 0.012 0.001 PHE C 364 TRP 0.009 0.001 TRP D 722 HIS 0.006 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (33122) covalent geometry : angle 0.54131 / 0.28 (45095) hydrogen bonds : bond 0.04086 / 2.77 ( 1479) hydrogen bonds : angle 4.31370 / 3.02 ( 4140) metal coordination : bond 0.01266 / 0.62 ( 8) metal coordination : angle 5.13515 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9177 (m-30) cc_final: 0.8935 (t0) REVERT: B 131 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8739 (tptp) REVERT: C 94 MET cc_start: 0.8740 (ttp) cc_final: 0.8540 (ptm) REVERT: C 341 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: C 523 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8958 (p) REVERT: D 8 ASP cc_start: 0.8344 (t0) cc_final: 0.7820 (t0) REVERT: D 143 MET cc_start: 0.8055 (mtp) cc_final: 0.7442 (ttm) REVERT: D 165 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7807 (tm-30) REVERT: D 269 ASP cc_start: 0.8514 (t0) cc_final: 0.8096 (t0) REVERT: J 31 ARG cc_start: 0.8541 (mmt180) cc_final: 0.8164 (mmm-85) REVERT: J 102 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8827 (mm) REVERT: F 183 GLU cc_start: 0.8971 (mp0) cc_final: 0.8691 (mp0) REVERT: F 310 MET cc_start: 0.9460 (tpp) cc_final: 0.9247 (tpp) REVERT: H 302 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8334 (pm20) REVERT: H 356 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8800 (ttp-170) REVERT: H 371 GLU cc_start: 0.8648 (mp0) cc_final: 0.8390 (mp0) REVERT: H 571 MET cc_start: 0.9291 (mmm) cc_final: 0.8668 (mmm) REVERT: H 680 GLU cc_start: 0.8159 (tp30) cc_final: 0.7795 (tp30) outliers start: 55 outliers final: 38 residues processed: 223 average time/residue: 0.1948 time to fit residues: 73.1726 Evaluate side-chains 216 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1129 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 631 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 679 VAL Chi-restraints excluded: chain H residue 695 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046702 restraints weight = 109126.741| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.29 r_work: 0.2641 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33130 Z= 0.159 Angle : 0.533 15.260 45107 Z= 0.274 Chirality : 0.042 0.228 5112 Planarity : 0.004 0.057 5772 Dihedral : 11.895 164.075 5018 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.52 % Allowed : 11.19 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4003 helix: 1.61 (0.13), residues: 1635 sheet: 0.35 (0.25), residues: 433 loop : 0.05 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 364 TYR 0.011 0.001 TYR D 586 PHE 0.011 0.001 PHE C 897 TRP 0.020 0.001 TRP F 221 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (33122) covalent geometry : angle 0.52641 / 0.27 (45095) hydrogen bonds : bond 0.03935 / 2.67 ( 1479) hydrogen bonds : angle 4.26512 / 2.99 ( 4140) metal coordination : bond 0.00895 / 0.43 ( 8) metal coordination : angle 5.01863 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9175 (m-30) cc_final: 0.8925 (t0) REVERT: B 131 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8738 (tptp) REVERT: C 94 MET cc_start: 0.8776 (ttp) cc_final: 0.8565 (ptm) REVERT: C 341 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: C 523 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8932 (p) REVERT: C 1129 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7833 (mt) REVERT: D 8 ASP cc_start: 0.8353 (t0) cc_final: 0.7832 (t0) REVERT: D 143 MET cc_start: 0.8093 (mtp) cc_final: 0.7452 (ttm) REVERT: D 165 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 205 MET cc_start: 0.7615 (tmm) cc_final: 0.7067 (ptp) REVERT: D 269 ASP cc_start: 0.8572 (t0) cc_final: 0.8175 (t0) REVERT: J 31 ARG cc_start: 0.8503 (mmt180) cc_final: 0.8141 (mmm-85) REVERT: J 102 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8829 (mm) REVERT: F 183 GLU cc_start: 0.8985 (mp0) cc_final: 0.8721 (mp0) REVERT: F 219 MET cc_start: 0.9442 (mmp) cc_final: 0.9137 (mmm) REVERT: F 310 MET cc_start: 0.9441 (tpp) cc_final: 0.9238 (tpp) REVERT: H 302 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8343 (pm20) REVERT: H 356 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8813 (ttp-170) REVERT: H 371 GLU cc_start: 0.8670 (mp0) cc_final: 0.8463 (mp0) REVERT: H 680 GLU cc_start: 0.8225 (tp30) cc_final: 0.7838 (tp30) outliers start: 51 outliers final: 36 residues processed: 220 average time/residue: 0.1880 time to fit residues: 69.6447 Evaluate side-chains 218 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1129 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 631 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 332 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 399 optimal weight: 50.0000 chunk 307 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 314 ASN C 601 ASN C 857 ASN D 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.044660 restraints weight = 111480.211| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.14 r_work: 0.2588 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 33130 Z= 0.263 Angle : 0.612 13.905 45107 Z= 0.315 Chirality : 0.044 0.250 5112 Planarity : 0.004 0.058 5772 Dihedral : 12.043 163.893 5018 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.67 % Allowed : 11.16 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4003 helix: 1.45 (0.13), residues: 1637 sheet: 0.14 (0.25), residues: 449 loop : -0.06 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 364 TYR 0.015 0.001 TYR H 696 PHE 0.014 0.002 PHE H 97 TRP 0.012 0.001 TRP F 221 HIS 0.008 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.26 (33122) covalent geometry : angle 0.60568 / 0.31 (45095) hydrogen bonds : bond 0.04553 / 3.09 ( 1479) hydrogen bonds : angle 4.47627 / 3.14 ( 4140) metal coordination : bond 0.01321 / 0.64 ( 8) metal coordination : angle 5.43342 / 3.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9221 (m-30) cc_final: 0.8982 (t0) REVERT: B 131 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8740 (tptp) REVERT: C 341 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: C 523 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 1129 LEU cc_start: 0.8260 (mt) cc_final: 0.7916 (mt) REVERT: D 8 ASP cc_start: 0.8405 (t0) cc_final: 0.7901 (t0) REVERT: D 143 MET cc_start: 0.8071 (mtp) cc_final: 0.7377 (ttm) REVERT: D 165 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 202 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7955 (mm-30) REVERT: D 269 ASP cc_start: 0.8556 (t0) cc_final: 0.8186 (t0) REVERT: J 46 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: J 102 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8889 (mm) REVERT: F 219 MET cc_start: 0.9474 (mmp) cc_final: 0.9203 (mmm) REVERT: F 449 MET cc_start: 0.8700 (tpp) cc_final: 0.8498 (tmm) REVERT: H 302 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8468 (pm20) REVERT: H 356 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8713 (ttp-170) REVERT: H 371 GLU cc_start: 0.8751 (mp0) cc_final: 0.8481 (mp0) REVERT: H 454 GLU cc_start: 0.8574 (tp30) cc_final: 0.8182 (tm-30) REVERT: H 680 GLU cc_start: 0.8216 (tp30) cc_final: 0.7809 (tp30) outliers start: 56 outliers final: 41 residues processed: 225 average time/residue: 0.1895 time to fit residues: 71.9924 Evaluate side-chains 217 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 46 ASP Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 361 TRP Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 631 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 678 VAL Chi-restraints excluded: chain H residue 679 VAL Chi-restraints excluded: chain H residue 695 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 21 optimal weight: 7.9990 chunk 399 optimal weight: 40.0000 chunk 368 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 330 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.063805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.046040 restraints weight = 108421.126| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.06 r_work: 0.2607 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33130 Z= 0.140 Angle : 0.544 15.852 45107 Z= 0.278 Chirality : 0.042 0.260 5112 Planarity : 0.004 0.059 5772 Dihedral : 12.024 164.741 5018 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.34 % Allowed : 11.93 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 4003 helix: 1.61 (0.13), residues: 1630 sheet: 0.28 (0.25), residues: 444 loop : -0.02 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 364 TYR 0.028 0.001 TYR D 248 PHE 0.012 0.001 PHE C 897 TRP 0.015 0.001 TRP F 221 HIS 0.004 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (33122) covalent geometry : angle 0.53920 / 0.28 (45095) hydrogen bonds : bond 0.03917 / 2.65 ( 1479) hydrogen bonds : angle 4.28557 / 3.00 ( 4140) metal coordination : bond 0.00851 / 0.41 ( 8) metal coordination : angle 4.58889 / 2.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9196 (m-30) cc_final: 0.8903 (t0) REVERT: B 131 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8750 (tptp) REVERT: C 94 MET cc_start: 0.8741 (ptm) cc_final: 0.8283 (ptm) REVERT: C 296 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8032 (mtt180) REVERT: C 523 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8956 (p) REVERT: C 1129 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7849 (mt) REVERT: D 8 ASP cc_start: 0.8385 (t0) cc_final: 0.7879 (t0) REVERT: D 77 ARG cc_start: 0.8594 (ptt-90) cc_final: 0.8259 (ptt-90) REVERT: D 143 MET cc_start: 0.8078 (mtp) cc_final: 0.7380 (ttm) REVERT: D 205 MET cc_start: 0.7541 (tmm) cc_final: 0.6856 (ptp) REVERT: D 269 ASP cc_start: 0.8567 (t0) cc_final: 0.8217 (t70) REVERT: J 46 ASP cc_start: 0.8127 (m-30) cc_final: 0.7854 (m-30) REVERT: J 102 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8887 (mm) REVERT: F 183 GLU cc_start: 0.9073 (mp0) cc_final: 0.8836 (mp0) REVERT: F 219 MET cc_start: 0.9448 (mmp) cc_final: 0.9175 (mmm) REVERT: F 445 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8134 (mm-30) REVERT: H 302 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8361 (pm20) REVERT: H 356 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8729 (ttp-170) REVERT: H 371 GLU cc_start: 0.8729 (mp0) cc_final: 0.8513 (mp0) REVERT: H 422 CYS cc_start: 0.9263 (p) cc_final: 0.8996 (p) REVERT: H 571 MET cc_start: 0.9161 (mmm) cc_final: 0.8553 (mmm) REVERT: H 596 MET cc_start: 0.6985 (tpt) cc_final: 0.6708 (tpp) REVERT: H 680 GLU cc_start: 0.8271 (tp30) cc_final: 0.7844 (tp30) outliers start: 45 outliers final: 34 residues processed: 215 average time/residue: 0.1936 time to fit residues: 69.8351 Evaluate side-chains 212 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1129 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 361 TRP Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 678 VAL Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 323 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 314 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 359 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.045763 restraints weight = 109983.050| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.07 r_work: 0.2602 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33130 Z= 0.163 Angle : 0.551 15.302 45107 Z= 0.281 Chirality : 0.042 0.307 5112 Planarity : 0.004 0.059 5772 Dihedral : 12.041 165.968 5018 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.25 % Allowed : 12.14 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4003 helix: 1.63 (0.13), residues: 1638 sheet: 0.24 (0.25), residues: 438 loop : 0.01 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 440 TYR 0.023 0.001 TYR D 248 PHE 0.014 0.001 PHE D1227 TRP 0.016 0.001 TRP F 221 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (33122) covalent geometry : angle 0.54620 / 0.28 (45095) hydrogen bonds : bond 0.03925 / 2.66 ( 1479) hydrogen bonds : angle 4.27867 / 2.99 ( 4140) metal coordination : bond 0.00927 / 0.45 ( 8) metal coordination : angle 4.65875 / 2.75 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9205 (m-30) cc_final: 0.8957 (t0) REVERT: B 131 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8745 (tptp) REVERT: C 94 MET cc_start: 0.8879 (ptm) cc_final: 0.8456 (ptm) REVERT: C 523 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8958 (p) REVERT: C 992 MET cc_start: 0.9203 (mmp) cc_final: 0.8587 (mmm) REVERT: C 1129 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7881 (mt) REVERT: D 8 ASP cc_start: 0.8404 (t0) cc_final: 0.7903 (t0) REVERT: D 77 ARG cc_start: 0.8582 (ptt-90) cc_final: 0.8215 (ptt-90) REVERT: D 143 MET cc_start: 0.8087 (mtp) cc_final: 0.7384 (ttm) REVERT: D 269 ASP cc_start: 0.8561 (t0) cc_final: 0.8226 (t70) REVERT: J 31 ARG cc_start: 0.8583 (mmt180) cc_final: 0.8076 (mmm160) REVERT: J 46 ASP cc_start: 0.8183 (m-30) cc_final: 0.7915 (m-30) REVERT: J 102 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8906 (mm) REVERT: F 183 GLU cc_start: 0.9093 (mp0) cc_final: 0.8840 (mp0) REVERT: F 219 MET cc_start: 0.9461 (mmp) cc_final: 0.9194 (mmm) REVERT: H 356 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8676 (ttp-170) REVERT: H 371 GLU cc_start: 0.8747 (mp0) cc_final: 0.8511 (mp0) REVERT: H 454 GLU cc_start: 0.8504 (tp30) cc_final: 0.8182 (tm-30) REVERT: H 596 MET cc_start: 0.7011 (tpt) cc_final: 0.6735 (tpp) REVERT: H 680 GLU cc_start: 0.8247 (tp30) cc_final: 0.7815 (tp30) outliers start: 42 outliers final: 34 residues processed: 213 average time/residue: 0.1915 time to fit residues: 69.1906 Evaluate side-chains 212 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 802 GLU Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1129 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 941 HIS Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 356 ARG Chi-restraints excluded: chain H residue 361 TRP Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 678 VAL Chi-restraints excluded: chain H residue 679 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 141 optimal weight: 7.9990 chunk 351 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 186 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 369 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN C 926 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.046779 restraints weight = 109775.742| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.18 r_work: 0.2639 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33130 Z= 0.110 Angle : 0.527 16.038 45107 Z= 0.269 Chirality : 0.041 0.302 5112 Planarity : 0.004 0.061 5772 Dihedral : 12.009 166.834 5018 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.34 % Allowed : 12.11 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 4003 helix: 1.69 (0.13), residues: 1642 sheet: 0.23 (0.25), residues: 455 loop : 0.06 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 364 TYR 0.017 0.001 TYR D 248 PHE 0.010 0.001 PHE C 897 TRP 0.017 0.001 TRP F 221 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (33122) covalent geometry : angle 0.52239 / 0.27 (45095) hydrogen bonds : bond 0.03547 / 2.40 ( 1479) hydrogen bonds : angle 4.16008 / 2.91 ( 4140) metal coordination : bond 0.00693 / 0.34 ( 8) metal coordination : angle 4.12623 / 2.44 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6288.38 seconds wall clock time: 108 minutes 53.57 seconds (6533.57 seconds total)