Starting phenix.real_space_refine on Mon Jul 6 02:53:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qu6_18656/07_2026/8qu6_18656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qu6_18656/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qu6_18656/07_2026/8qu6_18656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qu6_18656/07_2026/8qu6_18656.map" model { file = "/net/cci-nas-00/data/ceres_data/8qu6_18656/07_2026/8qu6_18656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qu6_18656/07_2026/8qu6_18656.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 6.25, per 1000 atoms: 0.19 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 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: 4.08 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: 8.44 Time building geometry restraints manager: 3.59 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: 44071 1.42 - 2.85: 759 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.200 Find NCS groups from input model: 0.250 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- 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 : 0.522 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 0.51631 / 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 : 1.205 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: 0.2379 time to fit residues: 127.9743 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 : 1.501 ------------------------------------------------------------------------------- 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 = 0.065832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.047593 restraints weight = 109783.551| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.15 r_work: 0.2672 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 33130 Z= 0.234 Angle : 0.619 14.232 45107 Z= 0.325 Chirality : 0.044 0.185 5112 Planarity : 0.005 0.051 5772 Dihedral : 11.631 162.595 5018 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.60 % Allowed : 6.34 % Favored : 93.07 % 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: 0.97 (0.13), residues: 4003 helix: 1.44 (0.13), residues: 1608 sheet: 0.39 (0.25), residues: 437 loop : 0.13 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 209 TYR 0.025 0.002 TYR J 32 PHE 0.021 0.002 PHE C 364 TRP 0.026 0.002 TRP H 424 HIS 0.015 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (33122) covalent geometry : angle 0.61119 / 0.32 (45095) hydrogen bonds : bond 0.05072 / 3.45 ( 1479) hydrogen bonds : angle 4.76778 / 3.36 ( 4140) metal coordination : bond 0.01914 / 0.92 ( 8) metal coordination : angle 6.10364 / 3.53 ( 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 221 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8379 (tm-30) REVERT: C 1129 LEU cc_start: 0.7806 (mt) cc_final: 0.7598 (mt) REVERT: D 8 ASP cc_start: 0.8228 (t0) cc_final: 0.7856 (t0) REVERT: D 205 MET cc_start: 0.7172 (tmm) cc_final: 0.6652 (ptp) REVERT: D 269 ASP cc_start: 0.8549 (t0) cc_final: 0.8316 (t0) REVERT: D 1092 HIS cc_start: 0.7660 (t-90) cc_final: 0.7459 (t-90) REVERT: D 1113 MET cc_start: 0.9542 (mmm) cc_final: 0.9158 (mmm) REVERT: J 33 ARG cc_start: 0.9271 (ptm160) cc_final: 0.9060 (ttm-80) REVERT: J 46 ASP cc_start: 0.7919 (m-30) cc_final: 0.7646 (m-30) REVERT: F 183 GLU cc_start: 0.8841 (mp0) cc_final: 0.8626 (mp0) REVERT: F 196 TYR cc_start: 0.9312 (t80) cc_final: 0.9098 (t80) REVERT: F 310 MET cc_start: 0.9459 (tpp) cc_final: 0.9232 (tpp) REVERT: F 425 ARG cc_start: 0.6323 (mmm160) cc_final: 0.6065 (mmm160) REVERT: H 371 GLU cc_start: 0.8624 (mp0) cc_final: 0.8398 (mp0) outliers start: 20 outliers final: 13 residues processed: 217 average time/residue: 0.2070 time to fit residues: 72.7396 Evaluate side-chains 195 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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: 9.9990 chunk 280 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 272 optimal weight: 0.0010 chunk 255 optimal weight: 0.5980 chunk 181 optimal weight: 7.9990 chunk 354 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS B 200 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 709 ASN D 686 GLN H 411 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.048502 restraints weight = 109182.793| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.04 r_work: 0.2685 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33130 Z= 0.195 Angle : 0.558 13.432 45107 Z= 0.295 Chirality : 0.043 0.193 5112 Planarity : 0.004 0.052 5772 Dihedral : 11.793 164.896 5018 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.34 % Allowed : 7.68 % Favored : 90.98 % 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: 0.95 (0.13), residues: 4003 helix: 1.48 (0.13), residues: 1612 sheet: 0.37 (0.25), residues: 445 loop : 0.07 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 282 TYR 0.021 0.001 TYR C 269 PHE 0.019 0.001 PHE C 364 TRP 0.010 0.001 TRP D1221 HIS 0.007 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (33122) covalent geometry : angle 0.55089 / 0.29 (45095) hydrogen bonds : bond 0.04506 / 3.06 ( 1479) hydrogen bonds : angle 4.52737 / 3.19 ( 4140) metal coordination : bond 0.01298 / 0.63 ( 8) metal coordination : angle 5.46878 / 3.14 ( 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 234 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 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: 0.8795 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 131 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8650 (tptp) REVERT: C 346 MET cc_start: 0.8847 (ttp) cc_final: 0.8589 (ptm) REVERT: D 8 ASP cc_start: 0.8257 (t0) cc_final: 0.7729 (t0) REVERT: D 143 MET cc_start: 0.8032 (mtp) cc_final: 0.6923 (ttm) REVERT: D 147 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7854 (mp0) REVERT: D 205 MET cc_start: 0.7266 (tmm) cc_final: 0.6709 (ptp) REVERT: D 269 ASP cc_start: 0.8511 (t0) cc_final: 0.8115 (t0) REVERT: D 1061 LYS cc_start: 0.8856 (tptp) cc_final: 0.8656 (mttt) REVERT: D 1092 HIS cc_start: 0.8137 (t-90) cc_final: 0.7872 (t-90) REVERT: J 104 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9289 (mt) REVERT: F 183 GLU cc_start: 0.8882 (mp0) cc_final: 0.8544 (mp0) REVERT: F 219 MET cc_start: 0.9406 (mmp) cc_final: 0.9102 (mmm) REVERT: F 310 MET cc_start: 0.9484 (tpp) cc_final: 0.9254 (tpp) REVERT: H 680 GLU cc_start: 0.7957 (tp30) cc_final: 0.7070 (tm-30) outliers start: 45 outliers final: 20 residues processed: 222 average time/residue: 0.1863 time to fit residues: 69.6150 Evaluate side-chains 195 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 J residue 104 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 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: 3.9990 chunk 309 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 328 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 350 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.046986 restraints weight = 110022.241| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.14 r_work: 0.2659 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33130 Z= 0.172 Angle : 0.540 13.112 45107 Z= 0.284 Chirality : 0.042 0.194 5112 Planarity : 0.004 0.052 5772 Dihedral : 11.798 164.759 5018 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.46 % Allowed : 8.99 % Favored : 89.56 % 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: 1612 sheet: 0.33 (0.25), residues: 447 loop : 0.07 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 364 TYR 0.012 0.001 TYR D 586 PHE 0.012 0.001 PHE C 897 TRP 0.012 0.001 TRP H 370 HIS 0.006 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (33122) covalent geometry : angle 0.53317 / 0.28 (45095) hydrogen bonds : bond 0.04220 / 2.86 ( 1479) hydrogen bonds : angle 4.41595 / 3.11 ( 4140) metal coordination : bond 0.01127 / 0.55 ( 8) metal coordination : angle 5.33330 / 3.05 ( 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 227 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 131 LYS cc_start: 0.8888 (mmmm) cc_final: 0.8651 (tptp) REVERT: D 8 ASP cc_start: 0.8332 (t0) cc_final: 0.7856 (t0) REVERT: D 143 MET cc_start: 0.8010 (mtp) cc_final: 0.7375 (ttm) REVERT: D 205 MET cc_start: 0.7203 (tmm) cc_final: 0.6732 (ptp) REVERT: D 269 ASP cc_start: 0.8444 (t0) cc_final: 0.8027 (t0) REVERT: F 183 GLU cc_start: 0.8983 (mp0) cc_final: 0.8615 (mp0) REVERT: F 223 CYS cc_start: 0.9313 (t) cc_final: 0.9056 (m) REVERT: F 310 MET cc_start: 0.9459 (tpp) cc_final: 0.9228 (tpp) REVERT: H 302 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8375 (pm20) REVERT: H 356 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8778 (ttp-170) REVERT: H 371 GLU cc_start: 0.8652 (mp0) cc_final: 0.8446 (mp0) REVERT: H 422 CYS cc_start: 0.9281 (p) cc_final: 0.9080 (p) REVERT: H 680 GLU cc_start: 0.8152 (tp30) cc_final: 0.7773 (tp30) outliers start: 49 outliers final: 30 residues processed: 217 average time/residue: 0.1904 time to fit residues: 69.2046 Evaluate side-chains 204 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 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 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 581 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 E residue 45 SER Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 425 ARG 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: 5.9990 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 GLN C 377 GLN C 534 GLN C 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.047642 restraints weight = 109120.751| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.25 r_work: 0.2670 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33130 Z= 0.125 Angle : 0.515 15.979 45107 Z= 0.268 Chirality : 0.041 0.212 5112 Planarity : 0.004 0.056 5772 Dihedral : 11.823 165.819 5018 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.40 % Allowed : 9.88 % Favored : 88.72 % 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 (0.13), residues: 4003 helix: 1.60 (0.13), residues: 1641 sheet: 0.38 (0.25), residues: 444 loop : 0.10 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 364 TYR 0.011 0.001 TYR D 586 PHE 0.011 0.001 PHE C 897 TRP 0.010 0.001 TRP D 722 HIS 0.004 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (33122) covalent geometry : angle 0.50889 / 0.27 (45095) hydrogen bonds : bond 0.03847 / 2.61 ( 1479) hydrogen bonds : angle 4.28368 / 3.01 ( 4140) metal coordination : bond 0.00950 / 0.46 ( 8) metal coordination : angle 4.78347 / 2.75 ( 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 227 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9126 (m-30) cc_final: 0.8893 (t0) REVERT: B 131 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8736 (tptp) REVERT: D 8 ASP cc_start: 0.8348 (t0) cc_final: 0.7826 (t0) REVERT: D 143 MET cc_start: 0.8000 (mtp) cc_final: 0.7386 (ttm) REVERT: D 269 ASP cc_start: 0.8466 (t0) cc_final: 0.8025 (t0) REVERT: J 31 ARG cc_start: 0.7995 (mmt180) cc_final: 0.7480 (mmm-85) REVERT: J 102 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8774 (mm) REVERT: F 183 GLU cc_start: 0.8997 (mp0) cc_final: 0.8794 (mp0) REVERT: F 219 MET cc_start: 0.9452 (mmp) cc_final: 0.9135 (mmm) REVERT: F 223 CYS cc_start: 0.9268 (t) cc_final: 0.9054 (m) REVERT: F 310 MET cc_start: 0.9460 (tpp) cc_final: 0.9251 (tpp) REVERT: H 356 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8827 (ttp-170) REVERT: H 422 CYS cc_start: 0.9318 (p) cc_final: 0.9081 (p) REVERT: H 571 MET cc_start: 0.9206 (mmm) cc_final: 0.8614 (mmm) REVERT: H 680 GLU cc_start: 0.8178 (tp30) cc_final: 0.7853 (tp30) outliers start: 47 outliers final: 31 residues processed: 216 average time/residue: 0.1850 time to fit residues: 67.2850 Evaluate side-chains 203 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 279 THR 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 843 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1088 VAL 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 581 MET 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 46 ASP 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 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: 4.9990 chunk 61 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 390 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 386 optimal weight: 5.9990 chunk 399 optimal weight: 40.0000 chunk 288 optimal weight: 10.0000 chunk 389 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 314 ASN 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 = 0.3216 r_free = 0.3216 target = 0.062679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.044599 restraints weight = 111367.011| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.12 r_work: 0.2601 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 33130 Z= 0.307 Angle : 0.644 15.973 45107 Z= 0.331 Chirality : 0.045 0.299 5112 Planarity : 0.005 0.056 5772 Dihedral : 11.990 165.167 5018 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.93 % Allowed : 10.71 % Favored : 87.35 % 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: 0.73 (0.13), residues: 4003 helix: 1.39 (0.13), residues: 1620 sheet: 0.10 (0.24), residues: 462 loop : -0.11 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 330 TYR 0.016 0.002 TYR H 696 PHE 0.017 0.002 PHE C 364 TRP 0.009 0.001 TRP H 370 HIS 0.009 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.31 (33122) covalent geometry : angle 0.63619 / 0.33 (45095) hydrogen bonds : bond 0.04768 / 3.23 ( 1479) hydrogen bonds : angle 4.55212 / 3.20 ( 4140) metal coordination : bond 0.01887 / 0.91 ( 8) metal coordination : angle 6.08685 / 3.53 ( 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 238 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.9200 (m-30) cc_final: 0.8971 (t0) REVERT: B 131 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8719 (tptp) REVERT: C 341 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: C 523 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8994 (p) REVERT: D 8 ASP cc_start: 0.8366 (t0) cc_final: 0.7836 (t0) REVERT: D 143 MET cc_start: 0.8039 (mtp) cc_final: 0.7405 (ttm) REVERT: D 205 MET cc_start: 0.7715 (tmm) cc_final: 0.7124 (ptp) REVERT: D 248 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: D 269 ASP cc_start: 0.8511 (t0) cc_final: 0.8132 (t0) REVERT: J 102 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8822 (mm) REVERT: F 183 GLU cc_start: 0.9060 (mp0) cc_final: 0.8860 (mp0) REVERT: F 223 CYS cc_start: 0.9288 (t) cc_final: 0.9082 (m) REVERT: H 302 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8459 (pm20) REVERT: H 356 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8802 (ttp-170) REVERT: H 680 GLU cc_start: 0.8280 (tp30) cc_final: 0.7906 (tp30) outliers start: 65 outliers final: 40 residues processed: 228 average time/residue: 0.2058 time to fit residues: 78.2490 Evaluate side-chains 211 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 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 248 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 1025 ILE Chi-restraints excluded: chain D residue 1026 VAL 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 F residue 221 TRP 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 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: 7.9990 chunk 129 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 49 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 360 optimal weight: 0.0970 chunk 263 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN F 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.046302 restraints weight = 110135.822| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.11 r_work: 0.2651 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33130 Z= 0.127 Angle : 0.533 15.748 45107 Z= 0.275 Chirality : 0.042 0.334 5112 Planarity : 0.004 0.057 5772 Dihedral : 11.967 165.863 5018 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.22 % Allowed : 11.63 % Favored : 87.15 % 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: 0.97 (0.13), residues: 4003 helix: 1.57 (0.13), residues: 1638 sheet: 0.28 (0.25), residues: 436 loop : 0.01 (0.14), residues: 1929 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 0.013 0.001 PHE C 897 TRP 0.011 0.001 TRP D 722 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (33122) covalent geometry : angle 0.52773 / 0.27 (45095) hydrogen bonds : bond 0.03885 / 2.63 ( 1479) hydrogen bonds : angle 4.28321 / 3.00 ( 4140) metal coordination : bond 0.01506 / 0.73 ( 8) metal coordination : angle 4.51897 / 2.72 ( 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 216 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.350 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: 0.9149 (m-30) cc_final: 0.8937 (t0) REVERT: B 131 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8741 (tptp) REVERT: C 523 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8922 (p) REVERT: C 1129 LEU cc_start: 0.8219 (mt) cc_final: 0.7868 (mt) REVERT: D 8 ASP cc_start: 0.8380 (t0) cc_final: 0.7864 (t0) REVERT: D 77 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8390 (ptt-90) REVERT: D 143 MET cc_start: 0.8076 (mtp) cc_final: 0.7467 (ttm) REVERT: D 205 MET cc_start: 0.7755 (tmm) cc_final: 0.7054 (ptp) REVERT: D 269 ASP cc_start: 0.8512 (t0) cc_final: 0.8121 (t0) REVERT: J 102 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8845 (mm) REVERT: F 183 GLU cc_start: 0.9121 (mp0) cc_final: 0.8857 (mp0) REVERT: F 219 MET cc_start: 0.9463 (mmp) cc_final: 0.9155 (mmm) REVERT: F 223 CYS cc_start: 0.9250 (t) cc_final: 0.9035 (m) REVERT: H 302 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8378 (pm20) REVERT: H 356 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8760 (ttp-170) REVERT: H 680 GLU cc_start: 0.8295 (tp30) cc_final: 0.7891 (tp30) outliers start: 41 outliers final: 31 residues processed: 208 average time/residue: 0.2066 time to fit residues: 71.8144 Evaluate side-chains 204 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 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 261 ILE Chi-restraints excluded: chain D residue 581 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 46 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 332 optimal weight: 10.0000 chunk 388 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 189 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 399 optimal weight: 40.0000 chunk 307 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 289 ASN C 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.046045 restraints weight = 110417.886| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.15 r_work: 0.2645 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33130 Z= 0.142 Angle : 0.532 15.610 45107 Z= 0.272 Chirality : 0.042 0.355 5112 Planarity : 0.004 0.060 5772 Dihedral : 11.984 167.496 5018 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.37 % Allowed : 11.99 % Favored : 86.64 % 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: 1.02 (0.13), residues: 4003 helix: 1.61 (0.13), residues: 1643 sheet: 0.30 (0.25), residues: 436 loop : 0.04 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 330 TYR 0.012 0.001 TYR J 32 PHE 0.012 0.001 PHE D1227 TRP 0.010 0.001 TRP D 722 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (33122) covalent geometry : angle 0.52604 / 0.27 (45095) hydrogen bonds : bond 0.03847 / 2.60 ( 1479) hydrogen bonds : angle 4.26083 / 2.98 ( 4140) metal coordination : bond 0.00899 / 0.43 ( 8) metal coordination : angle 4.78110 / 2.81 ( 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 222 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.458 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: 0.9164 (m-30) cc_final: 0.8947 (t0) REVERT: B 131 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8778 (tptp) REVERT: C 523 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8966 (p) REVERT: C 992 MET cc_start: 0.9194 (mmp) cc_final: 0.8583 (mmm) REVERT: C 1129 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7868 (mt) REVERT: D 8 ASP cc_start: 0.8367 (t0) cc_final: 0.7847 (t0) REVERT: D 143 MET cc_start: 0.8082 (mtp) cc_final: 0.7459 (ttm) REVERT: D 248 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: D 269 ASP cc_start: 0.8531 (t0) cc_final: 0.8132 (t0) REVERT: J 31 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7833 (mmm-85) REVERT: J 102 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8882 (mm) REVERT: F 183 GLU cc_start: 0.9110 (mp0) cc_final: 0.8823 (mp0) REVERT: F 219 MET cc_start: 0.9454 (mmp) cc_final: 0.9147 (mmm) REVERT: H 302 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8386 (pm20) REVERT: H 356 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8756 (ttp-170) REVERT: H 371 GLU cc_start: 0.8622 (mp0) cc_final: 0.8387 (mp0) REVERT: H 596 MET cc_start: 0.6965 (tpt) cc_final: 0.6685 (tpp) REVERT: H 680 GLU cc_start: 0.8283 (tp30) cc_final: 0.7845 (tp30) outliers start: 46 outliers final: 34 residues processed: 213 average time/residue: 0.2026 time to fit residues: 72.4753 Evaluate side-chains 211 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 248 TYR 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 581 MET Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 1025 ILE 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 F residue 221 TRP Chi-restraints excluded: chain H residue 224 MET 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 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: 9.9990 chunk 399 optimal weight: 40.0000 chunk 368 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN C 857 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.044693 restraints weight = 109639.898| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.04 r_work: 0.2575 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 33130 Z= 0.281 Angle : 0.626 14.547 45107 Z= 0.321 Chirality : 0.045 0.356 5112 Planarity : 0.005 0.060 5772 Dihedral : 12.141 166.709 5018 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.52 % Allowed : 12.05 % Favored : 86.43 % 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: 0.77 (0.13), residues: 4003 helix: 1.45 (0.13), residues: 1625 sheet: 0.11 (0.25), residues: 444 loop : -0.12 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 364 TYR 0.015 0.001 TYR H 696 PHE 0.014 0.002 PHE H 97 TRP 0.010 0.001 TRP F 221 HIS 0.009 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.28 (33122) covalent geometry : angle 0.61964 / 0.32 (45095) hydrogen bonds : bond 0.04608 / 3.12 ( 1479) hydrogen bonds : angle 4.49337 / 3.15 ( 4140) metal coordination : bond 0.01503 / 0.73 ( 8) metal coordination : angle 5.43584 / 3.23 ( 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 224 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 1.344 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: 0.9217 (m-30) cc_final: 0.8980 (t0) REVERT: B 131 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8744 (tptp) REVERT: C 523 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8999 (p) REVERT: C 1129 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7889 (mt) REVERT: D 8 ASP cc_start: 0.8414 (t0) cc_final: 0.7899 (t0) REVERT: D 77 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8094 (ptt-90) REVERT: D 143 MET cc_start: 0.8071 (mtp) cc_final: 0.7414 (ttm) REVERT: D 269 ASP cc_start: 0.8548 (t0) cc_final: 0.8208 (t70) REVERT: J 28 GLN cc_start: 0.8085 (tt0) cc_final: 0.7820 (tp-100) REVERT: J 102 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8893 (mm) REVERT: F 183 GLU cc_start: 0.9182 (mp0) cc_final: 0.8886 (mp0) REVERT: H 302 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8459 (pm20) REVERT: H 356 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8738 (ttp-170) REVERT: H 596 MET cc_start: 0.7122 (tpt) cc_final: 0.6846 (tpp) REVERT: H 680 GLU cc_start: 0.8307 (tp30) cc_final: 0.7870 (tp30) outliers start: 51 outliers final: 37 residues processed: 214 average time/residue: 0.2019 time to fit residues: 72.8417 Evaluate side-chains 213 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 285 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 581 MET Chi-restraints excluded: chain D residue 737 VAL 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 221 TRP Chi-restraints excluded: chain H residue 224 MET 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 679 VAL Chi-restraints excluded: chain H residue 695 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 323 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 314 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 311 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 chunk 359 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 601 ASN C 709 ASN D 499 ASN D 564 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.046593 restraints weight = 109324.987| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.08 r_work: 0.2623 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33130 Z= 0.106 Angle : 0.536 16.244 45107 Z= 0.275 Chirality : 0.042 0.371 5112 Planarity : 0.004 0.061 5772 Dihedral : 12.076 168.521 5018 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.31 % Allowed : 12.44 % Favored : 86.25 % 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: 1.02 (0.13), residues: 4003 helix: 1.65 (0.13), residues: 1635 sheet: 0.23 (0.25), residues: 443 loop : 0.02 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 77 TYR 0.025 0.001 TYR D 248 PHE 0.011 0.001 PHE C 897 TRP 0.013 0.001 TRP D 722 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (33122) covalent geometry : angle 0.53171 / 0.27 (45095) hydrogen bonds : bond 0.03664 / 2.48 ( 1479) hydrogen bonds : angle 4.20916 / 2.94 ( 4140) metal coordination : bond 0.00641 / 0.31 ( 8) metal coordination : angle 4.33047 / 2.58 ( 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 226 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 1.325 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: 0.9183 (m-30) cc_final: 0.8942 (t0) REVERT: B 131 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8775 (tptp) REVERT: C 523 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8932 (p) REVERT: C 1129 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7856 (mt) REVERT: D 8 ASP cc_start: 0.8406 (t0) cc_final: 0.7915 (t0) REVERT: D 77 ARG cc_start: 0.8570 (ptt-90) cc_final: 0.8153 (ptt-90) REVERT: D 143 MET cc_start: 0.8084 (mtp) cc_final: 0.7448 (ttm) REVERT: D 269 ASP cc_start: 0.8548 (t0) cc_final: 0.8203 (t70) REVERT: J 102 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8897 (mm) REVERT: F 183 GLU cc_start: 0.9216 (mp0) cc_final: 0.8925 (mp0) REVERT: F 219 MET cc_start: 0.9432 (mmp) cc_final: 0.9169 (mmm) REVERT: H 242 ILE cc_start: 0.8477 (mm) cc_final: 0.8251 (tt) REVERT: H 302 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8385 (pm20) REVERT: H 371 GLU cc_start: 0.8672 (mp0) cc_final: 0.8445 (mp0) REVERT: H 596 MET cc_start: 0.7007 (tpt) cc_final: 0.6738 (tpp) REVERT: H 680 GLU cc_start: 0.8289 (tp30) cc_final: 0.7843 (tp30) outliers start: 44 outliers final: 30 residues processed: 218 average time/residue: 0.2056 time to fit residues: 75.1286 Evaluate side-chains 207 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 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 110 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 737 VAL 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 221 TRP Chi-restraints excluded: chain H residue 224 MET 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: 8.9990 chunk 351 optimal weight: 6.9990 chunk 108 optimal weight: 0.0370 chunk 186 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 0.0570 chunk 54 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 369 optimal weight: 10.0000 overall best weight: 3.6182 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.063008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.045641 restraints weight = 109818.055| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.04 r_work: 0.2589 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33130 Z= 0.206 Angle : 0.569 14.752 45107 Z= 0.291 Chirality : 0.043 0.337 5112 Planarity : 0.004 0.062 5772 Dihedral : 12.122 168.983 5018 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.19 % Allowed : 12.73 % Favored : 86.08 % 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: 0.95 (0.13), residues: 4003 helix: 1.62 (0.13), residues: 1644 sheet: 0.10 (0.24), residues: 459 loop : -0.04 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 364 TYR 0.023 0.001 TYR D 248 PHE 0.011 0.001 PHE C 897 TRP 0.009 0.001 TRP C 202 HIS 0.006 0.001 HIS C 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (33122) covalent geometry : angle 0.56367 / 0.29 (45095) hydrogen bonds : bond 0.04091 / 2.77 ( 1479) hydrogen bonds : angle 4.31236 / 3.02 ( 4140) metal coordination : bond 0.01064 / 0.51 ( 8) metal coordination : angle 4.82693 / 2.84 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.29 seconds wall clock time: 106 minutes 3.86 seconds (6363.86 seconds total)