Starting phenix.real_space_refine on Mon Sep 14 11:20:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.map" model { file = "/net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5c_26346/09_2026/7u5c_26346.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Fe 4 7.16 5 Zn 4 6.06 5 P 4 5.49 5 S 164 5.16 5 C 19222 2.51 5 N 5167 2.21 5 O 5512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30077 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3243 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 16, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain: "C" Number of atoms: 8546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8546 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1003} Chain breaks: 4 Chain: "D" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "E" Number of atoms: 8966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8966 Classifications: {'peptide': 1147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 85, 'TRANS': 1057} Chain breaks: 4 Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1282 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1054 SG CYS A 122 147.918 103.766 173.053 1.00164.53 S ATOM 1093 SG CYS A 128 148.383 106.803 170.627 1.00133.60 S ATOM 14497 SG CYS C1353 83.618 48.265 116.130 1.00 51.91 S ATOM 14647 SG CYS C1371 82.179 51.385 118.366 1.00 40.69 S ATOM 14665 SG CYS C1374 85.454 49.975 118.388 1.00 59.31 S ATOM 13939 SG CYS C1283 81.004 70.826 75.241 1.00 29.87 S ATOM 13959 SG CYS C1286 81.758 68.041 73.680 1.00 31.59 S ATOM 14145 SG CYS C1310 84.483 69.766 74.489 1.00 35.59 S ATOM 26489 SG CYS E1050 51.656 60.994 65.433 1.00153.28 S ATOM 26528 SG CYS E1055 51.829 56.837 64.037 1.00155.72 S Time building chain proxies: 6.29, per 1000 atoms: 0.21 Number of scatterers: 30077 At special positions: 0 Unit cell: (182.52, 158.76, 198.72, 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 4 29.99 Fe 4 26.01 S 164 16.00 P 4 15.00 O 5512 8.00 N 5167 7.00 C 19222 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 424 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 287 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 122 " pdb=" ZN C1501 " pdb="ZN ZN C1501 " - pdb=" SG CYS C1374 " pdb="ZN ZN C1501 " - pdb=" SG CYS C1371 " pdb="ZN ZN C1501 " - pdb=" SG CYS C1353 " pdb=" ZN C1502 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1286 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1283 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1310 " pdb=" ZN E1301 " pdb="ZN ZN E1301 " - pdb=" SG CYS E1050 " pdb="ZN ZN E1301 " - pdb=" SG CYS E1055 " 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7088 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 35.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.699A pdb=" N ARG A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.084A pdb=" N ASP A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 removed outlier: 4.004A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 209 through 231 removed outlier: 4.208A pdb=" N LYS A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.783A pdb=" N TRP A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.545A pdb=" N LEU A 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 247' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.994A pdb=" N ASP A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 387 through 406 removed outlier: 3.955A pdb=" N VAL A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 63 removed outlier: 3.532A pdb=" N TYR B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 81 removed outlier: 4.037A pdb=" N LEU B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 113 through 133 removed outlier: 3.685A pdb=" N ARG B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 148 Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.672A pdb=" N THR B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 210 through 235 removed outlier: 3.576A pdb=" N ILE B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.335A pdb=" N GLN B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.857A pdb=" N ASN B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 removed outlier: 4.408A pdb=" N LEU B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 299 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.661A pdb=" N TYR B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.986A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.717A pdb=" N ASN B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.632A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'B' and resid 443 through 454 Processing helix chain 'C' and resid 409 through 425 removed outlier: 3.670A pdb=" N ALA C 422 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 597 through 603 Processing helix chain 'C' and resid 614 through 630 Processing helix chain 'C' and resid 638 through 643 Processing helix chain 'C' and resid 643 through 655 Processing helix chain 'C' and resid 658 through 663 Processing helix chain 'C' and resid 681 through 685 removed outlier: 3.825A pdb=" N ALA C 684 " --> pdb=" O GLU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.534A pdb=" N LEU C 700 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 removed outlier: 3.640A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 727 through 733 Processing helix chain 'C' and resid 735 through 760 removed outlier: 3.707A pdb=" N MET C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 773 Processing helix chain 'C' and resid 775 through 779 Processing helix chain 'C' and resid 785 through 797 removed outlier: 5.305A pdb=" N LEU C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS C 794 " --> pdb=" O PHE C 790 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 873 Processing helix chain 'C' and resid 875 through 879 removed outlier: 3.784A pdb=" N VAL C 879 " --> pdb=" O PHE C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 930 removed outlier: 4.008A pdb=" N LYS C 930 " --> pdb=" O LYS C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 956 Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.764A pdb=" N GLY C 961 " --> pdb=" O TYR C 957 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 962 " --> pdb=" O GLY C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 962' Processing helix chain 'C' and resid 970 through 994 removed outlier: 3.581A pdb=" N MET C 994 " --> pdb=" O MET C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1033 removed outlier: 4.157A pdb=" N PHE C1019 " --> pdb=" O LEU C1015 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1100 removed outlier: 3.872A pdb=" N ILE C1099 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C1100 " --> pdb=" O ILE C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1125 removed outlier: 4.552A pdb=" N LEU C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL C1123 " --> pdb=" O ILE C1119 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1134 removed outlier: 3.862A pdb=" N GLU C1134 " --> pdb=" O SER C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1165 removed outlier: 4.180A pdb=" N GLY C1165 " --> pdb=" O ILE C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1199 removed outlier: 3.785A pdb=" N LEU C1198 " --> pdb=" O ALA C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1209 through 1214 removed outlier: 3.801A pdb=" N ALA C1213 " --> pdb=" O GLN C1209 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1225 removed outlier: 3.683A pdb=" N VAL C1219 " --> pdb=" O GLN C1215 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C1223 " --> pdb=" O VAL C1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1240 Processing helix chain 'C' and resid 1242 through 1248 removed outlier: 3.752A pdb=" N VAL C1248 " --> pdb=" O THR C1244 " (cutoff:3.500A) Processing helix chain 'C' and resid 1269 through 1273 Processing helix chain 'C' and resid 1299 through 1303 Processing helix chain 'C' and resid 1318 through 1321 Processing helix chain 'C' and resid 1322 through 1343 removed outlier: 4.911A pdb=" N ARG C1336 " --> pdb=" O MET C1332 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C1337 " --> pdb=" O ASP C1333 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS C1339 " --> pdb=" O ARG C1335 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C1343 " --> pdb=" O LYS C1339 " (cutoff:3.500A) Processing helix chain 'C' and resid 1384 through 1399 removed outlier: 3.651A pdb=" N LEU C1388 " --> pdb=" O SER C1384 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C1398 " --> pdb=" O PHE C1394 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C1399 " --> pdb=" O TYR C1395 " (cutoff:3.500A) Processing helix chain 'C' and resid 1400 through 1407 removed outlier: 4.373A pdb=" N ALA C1404 " --> pdb=" O ASP C1400 " (cutoff:3.500A) Processing helix chain 'C' and resid 1410 through 1422 Processing helix chain 'C' and resid 1423 through 1443 removed outlier: 3.761A pdb=" N LEU C1427 " --> pdb=" O THR C1423 " (cutoff:3.500A) Processing helix chain 'C' and resid 1450 through 1454 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.536A pdb=" N SER D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 236 removed outlier: 3.587A pdb=" N ILE D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 371 Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.772A pdb=" N GLU D 390 " --> pdb=" O HIS D 386 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN D 391 " --> pdb=" O GLU D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 391' Processing helix chain 'D' and resid 398 through 415 removed outlier: 4.691A pdb=" N ILE D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 493 through 505 removed outlier: 3.637A pdb=" N THR D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN D 505 " --> pdb=" O HIS D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 529 removed outlier: 5.767A pdb=" N VAL D 527 " --> pdb=" O GLU D 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 17 removed outlier: 4.530A pdb=" N TRP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 38 through 54 removed outlier: 4.349A pdb=" N LYS E 47 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 71 No H-bonds generated for 'chain 'E' and resid 69 through 71' Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 206 through 210 removed outlier: 3.909A pdb=" N SER E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 273 removed outlier: 3.867A pdb=" N HIS E 272 " --> pdb=" O GLN E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 348 Processing helix chain 'E' and resid 389 through 393 removed outlier: 4.127A pdb=" N ARG E 393 " --> pdb=" O GLY E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 448 removed outlier: 3.987A pdb=" N GLN E 446 " --> pdb=" O HIS E 442 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 451 No H-bonds generated for 'chain 'E' and resid 449 through 451' Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.804A pdb=" N VAL E 457 " --> pdb=" O TYR E 453 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 481 Processing helix chain 'E' and resid 487 through 493 Processing helix chain 'E' and resid 502 through 507 removed outlier: 4.437A pdb=" N LEU E 507 " --> pdb=" O GLY E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 514 Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 551 through 566 Processing helix chain 'E' and resid 569 through 573 Processing helix chain 'E' and resid 576 through 580 Processing helix chain 'E' and resid 584 through 590 Processing helix chain 'E' and resid 786 through 790 removed outlier: 4.113A pdb=" N ASN E 789 " --> pdb=" O PRO E 786 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 808 Processing helix chain 'E' and resid 882 through 887 Processing helix chain 'E' and resid 912 through 916 removed outlier: 3.810A pdb=" N TRP E 916 " --> pdb=" O ALA E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 1093 through 1098 Processing helix chain 'E' and resid 1100 through 1111 Processing helix chain 'E' and resid 1136 through 1147 removed outlier: 3.527A pdb=" N MET E1140 " --> pdb=" O GLU E1136 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 17 Processing helix chain 'F' and resid 30 through 36 Processing helix chain 'F' and resid 109 through 111 No H-bonds generated for 'chain 'F' and resid 109 through 111' Processing helix chain 'F' and resid 112 through 121 removed outlier: 3.844A pdb=" N GLN F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.915A pdb=" N VAL F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 177 Proline residue: F 171 - end of helix removed outlier: 4.464A pdb=" N VAL F 177 " --> pdb=" O ILE F 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 58 removed outlier: 5.423A pdb=" N TYR A 54 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU A 49 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG A 56 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE A 47 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 317 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.506A pdb=" N VAL A 83 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 103 " --> pdb=" O VAL A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 110 removed outlier: 3.907A pdb=" N TRP A 157 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 332 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.506A pdb=" N GLU B 152 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 342 through 344 Processing sheet with id=AA6, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.769A pdb=" N GLY C 363 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS C 376 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA C 518 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS C 377 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA C 520 " --> pdb=" O CYS C 377 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N MET C 379 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 431 through 437 removed outlier: 3.660A pdb=" N LYS C 431 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU C 451 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 581 through 586 removed outlier: 3.748A pdb=" N ALA C 562 " --> pdb=" O PHE C 583 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 558 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS C 545 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N MET C 560 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER C 543 " --> pdb=" O MET C 560 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA C 562 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 541 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL C 564 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 539 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS C 566 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU C 537 " --> pdb=" O HIS C 566 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 633 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 635 " --> pdb=" O MET C 540 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1000 through 1002 removed outlier: 3.767A pdb=" N GLY C1042 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP C 860 " --> pdb=" O ILE C1040 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE C1040 " --> pdb=" O ASP C 860 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE C1044 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C1060 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C1058 " --> pdb=" O SER C1046 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C1056 " --> pdb=" O LEU C1048 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C1050 " --> pdb=" O LYS C1054 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1135 through 1137 Processing sheet with id=AB2, first strand: chain 'C' and resid 1280 through 1282 Processing sheet with id=AB3, first strand: chain 'C' and resid 1356 through 1357 Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 175 removed outlier: 4.069A pdb=" N ALA D 592 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET D 341 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE D 376 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU D 343 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE D 378 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA D 345 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 423 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 420 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.536A pdb=" N VAL D 557 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 283 through 285 removed outlier: 6.030A pdb=" N GLU D 249 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASN D 308 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 251 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU D 305 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 315 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'E' and resid 164 through 166 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 263 removed outlier: 6.034A pdb=" N GLY E 250 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU E 230 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA E 280 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AC3, first strand: chain 'E' and resid 372 through 375 removed outlier: 6.234A pdb=" N LEU E 372 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 407 through 409 Processing sheet with id=AC5, first strand: chain 'E' and resid 592 through 597 removed outlier: 4.256A pdb=" N LYS E 683 " --> pdb=" O ARG E 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 628 through 630 removed outlier: 3.568A pdb=" N CYS E 650 " --> pdb=" O LEU E 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 742 through 744 removed outlier: 5.969A pdb=" N HIS E 797 " --> pdb=" O LEU E 852 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 742 through 744 removed outlier: 5.875A pdb=" N SER E 768 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU E 735 " --> pdb=" O SER E 768 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU E 770 " --> pdb=" O PHE E 733 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE E 733 " --> pdb=" O LEU E 770 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY E 772 " --> pdb=" O ARG E 731 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ARG E 731 " --> pdb=" O GLY E 772 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 776 through 777 removed outlier: 3.530A pdb=" N GLU E 777 " --> pdb=" O GLY E 780 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 905 through 907 removed outlier: 3.596A pdb=" N GLU E 901 " --> pdb=" O ALA E 934 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 899 " --> pdb=" O GLU E 936 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE E 898 " --> pdb=" O SER E 970 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER E 970 " --> pdb=" O PHE E 898 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA E 900 " --> pdb=" O HIS E 968 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS E 968 " --> pdb=" O ALA E 900 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 946 through 950 removed outlier: 3.596A pdb=" N GLU E 901 " --> pdb=" O ALA E 934 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 899 " --> pdb=" O GLU E 936 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE E 898 " --> pdb=" O SER E 970 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER E 970 " --> pdb=" O PHE E 898 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA E 900 " --> pdb=" O HIS E 968 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS E 968 " --> pdb=" O ALA E 900 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG E 966 " --> pdb=" O LEU E 995 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1024 through 1028 removed outlier: 7.256A pdb=" N VAL E1156 " --> pdb=" O ILE E1201 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE E1201 " --> pdb=" O VAL E1156 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER E1158 " --> pdb=" O LEU E1199 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1030 through 1034 removed outlier: 4.742A pdb=" N ILE E1031 " --> pdb=" O GLU E1078 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU E1078 " --> pdb=" O ILE E1031 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 1030 through 1034 removed outlier: 4.742A pdb=" N ILE E1031 " --> pdb=" O GLU E1078 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU E1078 " --> pdb=" O ILE E1031 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E1036 " --> pdb=" O ARG E1074 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1050 through 1051 Processing sheet with id=AD7, first strand: chain 'E' and resid 1179 through 1180 removed outlier: 4.264A pdb=" N PHE E1179 " --> pdb=" O PHE E1186 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.322A pdb=" N ALA F 27 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU F 60 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N THR F 131 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS F 154 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG F 133 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR F 152 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG F 135 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG F 145 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN F 85 " --> pdb=" O ARG F 145 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TRP F 89 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR F 151 " --> pdb=" O TRP F 89 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 25 through 31 removed outlier: 7.172A pdb=" N LEU G 72 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS G 96 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE G 74 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 94 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU G 76 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG G 92 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU G 78 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL G 89 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU G 56 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA G 91 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N CYS G 58 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL G 93 " --> pdb=" O CYS G 58 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.06 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 12785 1.43 - 1.64: 17773 1.64 - 1.85: 218 1.85 - 2.06: 0 2.06 - 2.27: 12 Bond restraints: 30788 Sorted by residual: bond pdb=" C PRO E 167 " pdb=" N PRO E 168 " ideal model delta sigma weight residual 1.334 1.498 -0.164 2.34e-02 1.83e+03 4.91e+01 bond pdb=" N LEU E 79 " pdb=" CA LEU E 79 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.12e+01 bond pdb=" N LEU E 106 " pdb=" CA LEU E 106 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.16e-02 7.43e+03 9.22e+00 bond pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.16e-02 7.43e+03 8.86e+00 bond pdb=" C3' DG H 3 " pdb=" C2' DG H 3 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.09e+00 ... (remaining 30783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 41236 3.08 - 6.17: 464 6.17 - 9.25: 33 9.25 - 12.34: 4 12.34 - 15.42: 1 Bond angle restraints: 41738 Sorted by residual: angle pdb=" C PRO E 167 " pdb=" N PRO E 168 " pdb=" CA PRO E 168 " ideal model delta sigma weight residual 119.84 135.26 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" N LEU B 250 " pdb=" CA LEU B 250 " pdb=" C LEU B 250 " ideal model delta sigma weight residual 111.36 105.49 5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N ILE B 370 " pdb=" CA ILE B 370 " pdb=" C ILE B 370 " ideal model delta sigma weight residual 112.29 107.23 5.06 9.40e-01 1.13e+00 2.90e+01 angle pdb=" N PRO E 167 " pdb=" CA PRO E 167 " pdb=" C PRO E 167 " ideal model delta sigma weight residual 110.70 104.63 6.07 1.22e+00 6.72e-01 2.47e+01 angle pdb=" N TYR E 92 " pdb=" CA TYR E 92 " pdb=" C TYR E 92 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.21e+01 ... (remaining 41733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 16421 17.53 - 35.06: 1893 35.06 - 52.59: 299 52.59 - 70.12: 54 70.12 - 87.65: 33 Dihedral angle restraints: 18700 sinusoidal: 7748 harmonic: 10952 Sorted by residual: dihedral pdb=" CA VAL D 286 " pdb=" C VAL D 286 " pdb=" N ASP D 287 " pdb=" CA ASP D 287 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA B 191 " pdb=" C ALA B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU E 149 " pdb=" C LEU E 149 " pdb=" N ASP E 150 " pdb=" CA ASP E 150 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 18697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3752 0.062 - 0.123: 795 0.123 - 0.185: 78 0.185 - 0.247: 3 0.247 - 0.308: 2 Chirality restraints: 4630 Sorted by residual: chirality pdb=" CA PRO E 167 " pdb=" N PRO E 167 " pdb=" C PRO E 167 " pdb=" CB PRO E 167 " both_signs ideal model delta sigma weight residual False 2.72 3.03 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LEU B 250 " pdb=" N LEU B 250 " pdb=" C LEU B 250 " pdb=" CB LEU B 250 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ARG E 396 " pdb=" N ARG E 396 " pdb=" C ARG E 396 " pdb=" CB ARG E 396 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4627 not shown) Planarity restraints: 5341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 78 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG E 78 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG E 78 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU E 79 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 423 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO D 424 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 424 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 424 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 432 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO D 433 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 433 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 433 " -0.038 5.00e-02 4.00e+02 ... (remaining 5338 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 458 2.53 - 3.12: 25835 3.12 - 3.71: 47861 3.71 - 4.31: 63903 4.31 - 4.90: 98266 Nonbonded interactions: 236323 Sorted by model distance: nonbonded pdb=" O SER E1048 " pdb="ZN ZN E1301 " model vdw 1.932 2.230 nonbonded pdb=" O ILE E1049 " pdb="ZN ZN E1301 " model vdw 2.010 2.230 nonbonded pdb=" N CYS C1374 " pdb="ZN ZN C1501 " model vdw 2.015 2.310 nonbonded pdb=" CD2 LEU E 142 " pdb=" OH TYR E 165 " model vdw 2.021 3.460 nonbonded pdb=" SG CYS E 81 " pdb=" CZ3 TRP E 163 " model vdw 2.048 3.700 ... (remaining 236318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.500 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.822 30800 Z= 0.357 Angle : 1.014 61.769 41744 Z= 0.480 Chirality : 0.049 0.308 4630 Planarity : 0.006 0.075 5341 Dihedral : 15.091 87.655 11612 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.36 % Favored : 83.56 % Rotamer: Outliers : 0.39 % Allowed : 7.83 % Favored : 91.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.10), residues: 3704 helix: -3.66 (0.10), residues: 1034 sheet: -2.98 (0.20), residues: 517 loop : -4.47 (0.10), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.024 0.002 TYR B 93 PHE 0.027 0.002 PHE E1040 TRP 0.041 0.002 TRP A 240 HIS 0.011 0.002 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (30788) covalent geometry : angle 0.86632 / 0.48 (41738) hydrogen bonds : bond 0.17391 / 11.13 ( 1062) hydrogen bonds : angle 8.83675 / 6.06 ( 2916) metal coordination : bond 0.37297 / 19.82 ( 12) metal coordination : angle 44.00895 / 20.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 356 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8942 (tp) cc_final: 0.8627 (tp) REVERT: B 74 LEU cc_start: 0.8971 (tp) cc_final: 0.8545 (tt) REVERT: B 139 LYS cc_start: 0.9198 (mmpt) cc_final: 0.8698 (ttmt) REVERT: B 324 LEU cc_start: 0.9450 (mt) cc_final: 0.9143 (tp) REVERT: B 328 LYS cc_start: 0.9411 (ttmt) cc_final: 0.9001 (tmtt) REVERT: B 336 MET cc_start: 0.4145 (tmm) cc_final: 0.3756 (tmm) REVERT: C 519 MET cc_start: 0.7547 (ttt) cc_final: 0.7284 (ttt) REVERT: C 740 TYR cc_start: 0.8294 (t80) cc_final: 0.8073 (t80) REVERT: C 756 MET cc_start: 0.7894 (tpt) cc_final: 0.7331 (tpt) REVERT: C 801 TYR cc_start: 0.8685 (m-80) cc_final: 0.8191 (m-80) REVERT: C 989 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7291 (tp30) REVERT: C 996 LEU cc_start: 0.9364 (mt) cc_final: 0.9101 (mt) REVERT: C 1332 MET cc_start: 0.9206 (tpp) cc_final: 0.8924 (tpp) REVERT: C 1376 LYS cc_start: 0.7819 (mttp) cc_final: 0.7095 (mtpp) REVERT: C 1438 GLU cc_start: 0.8700 (tt0) cc_final: 0.8265 (tt0) REVERT: E 166 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7082 (mt) REVERT: E 453 TYR cc_start: 0.7169 (m-80) cc_final: 0.6883 (m-80) REVERT: E 811 LEU cc_start: 0.8178 (tt) cc_final: 0.7930 (tt) REVERT: F 49 TYR cc_start: 0.3025 (t80) cc_final: 0.2184 (t80) outliers start: 13 outliers final: 5 residues processed: 366 average time/residue: 0.2053 time to fit residues: 119.0169 Evaluate side-chains 236 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 230 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 71 GLN A 230 ASN ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS B 267 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 445 ASN B 452 GLN C 342 HIS C 466 GLN C 505 GLN C 565 HIS C 637 HIS C 714 GLN C 727 ASN C 767 GLN C 788 ASN C 870 GLN C 932 GLN C 986 HIS C1154 HIS C1250 HIS C1266 GLN C1420 GLN D 262 ASN D 419 HIS ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 217 ASN E 241 GLN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 HIS ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 ASN E 626 GLN ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1038 GLN E1177 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084655 restraints weight = 125850.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.084420 restraints weight = 153209.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.085368 restraints weight = 118198.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.085325 restraints weight = 81539.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085893 restraints weight = 73325.354| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30800 Z= 0.167 Angle : 0.846 36.651 41744 Z= 0.402 Chirality : 0.048 0.247 4630 Planarity : 0.006 0.067 5341 Dihedral : 7.398 56.486 4110 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.18 % Favored : 87.80 % Rotamer: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.12), residues: 3704 helix: -2.07 (0.13), residues: 1060 sheet: -2.74 (0.19), residues: 569 loop : -3.70 (0.12), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 396 TYR 0.043 0.002 TYR C 732 PHE 0.043 0.002 PHE A 259 TRP 0.020 0.002 TRP E 15 HIS 0.012 0.002 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (30788) covalent geometry : angle 0.77956 / 0.40 (41738) hydrogen bonds : bond 0.05533 / 3.60 ( 1062) hydrogen bonds : angle 7.22215 / 4.99 ( 2916) metal coordination : bond 0.02769 / 1.41 ( 12) metal coordination : angle 27.37685 / 12.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 367 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 LEU cc_start: 0.8451 (mt) cc_final: 0.8237 (mt) REVERT: A 260 GLN cc_start: 0.5437 (mm-40) cc_final: 0.5136 (mm110) REVERT: B 74 LEU cc_start: 0.9089 (tp) cc_final: 0.8621 (tt) REVERT: B 125 MET cc_start: 0.8809 (ttm) cc_final: 0.8344 (tpp) REVERT: B 139 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8599 (ttmt) REVERT: B 307 MET cc_start: 0.8036 (mtp) cc_final: 0.7368 (tpp) REVERT: B 324 LEU cc_start: 0.9281 (mt) cc_final: 0.8827 (tp) REVERT: B 328 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8872 (tmtt) REVERT: B 336 MET cc_start: 0.3739 (tmm) cc_final: 0.3146 (tmm) REVERT: B 429 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7612 (tp30) REVERT: C 394 MET cc_start: 0.5200 (tpp) cc_final: 0.4878 (tpp) REVERT: C 519 MET cc_start: 0.7556 (ttt) cc_final: 0.7238 (tmm) REVERT: C 650 ARG cc_start: 0.7318 (mmp-170) cc_final: 0.7097 (mmm160) REVERT: C 731 MET cc_start: 0.6683 (mpp) cc_final: 0.6476 (mpp) REVERT: C 801 TYR cc_start: 0.8599 (m-80) cc_final: 0.8172 (m-80) REVERT: C 908 MET cc_start: 0.8019 (mtt) cc_final: 0.7498 (ppp) REVERT: C 982 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8483 (mm-30) REVERT: C 989 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7375 (tp30) REVERT: C 990 MET cc_start: 0.9217 (tmm) cc_final: 0.8852 (tmm) REVERT: C 1052 LYS cc_start: 0.7716 (tptp) cc_final: 0.7482 (tptp) REVERT: C 1216 ILE cc_start: 0.9390 (mm) cc_final: 0.8970 (tp) REVERT: C 1332 MET cc_start: 0.9187 (tpp) cc_final: 0.8749 (tpp) REVERT: C 1438 GLU cc_start: 0.8710 (tt0) cc_final: 0.8291 (tm-30) REVERT: D 196 LEU cc_start: 0.9202 (pt) cc_final: 0.8896 (pp) REVERT: D 442 TYR cc_start: 0.7487 (t80) cc_final: 0.6995 (t80) REVERT: E 663 ARG cc_start: 0.8224 (mtm180) cc_final: 0.7658 (mtm180) REVERT: E 677 MET cc_start: 0.8320 (mmp) cc_final: 0.8083 (mmm) REVERT: E 811 LEU cc_start: 0.8030 (tt) cc_final: 0.7628 (tt) REVERT: E 925 MET cc_start: 0.2199 (tpp) cc_final: 0.1763 (tpp) REVERT: E 1104 TRP cc_start: 0.7915 (t-100) cc_final: 0.7482 (t-100) REVERT: E 1160 GLU cc_start: 0.8309 (pt0) cc_final: 0.8090 (tm-30) REVERT: F 49 TYR cc_start: 0.2869 (t80) cc_final: 0.1851 (t80) outliers start: 6 outliers final: 2 residues processed: 373 average time/residue: 0.1755 time to fit residues: 106.8340 Evaluate side-chains 242 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 284 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 305 optimal weight: 40.0000 chunk 178 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 297 optimal weight: 0.0370 chunk 294 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 314 optimal weight: 30.0000 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 HIS A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS C 986 HIS D 248 GLN D 262 ASN D 404 GLN ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.106921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.085714 restraints weight = 125537.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.083231 restraints weight = 114475.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084078 restraints weight = 105147.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.084798 restraints weight = 70515.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084873 restraints weight = 66549.989| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30800 Z= 0.147 Angle : 0.773 34.676 41744 Z= 0.365 Chirality : 0.045 0.187 4630 Planarity : 0.005 0.057 5341 Dihedral : 7.056 55.317 4110 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.12), residues: 3704 helix: -1.28 (0.14), residues: 1056 sheet: -2.39 (0.20), residues: 575 loop : -3.41 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 92 TYR 0.037 0.002 TYR C 732 PHE 0.038 0.002 PHE E1040 TRP 0.016 0.002 TRP E 15 HIS 0.009 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (30788) covalent geometry : angle 0.71170 / 0.36 (41738) hydrogen bonds : bond 0.04998 / 3.25 ( 1062) hydrogen bonds : angle 6.88262 / 4.77 ( 2916) metal coordination : bond 0.02701 / 1.35 ( 12) metal coordination : angle 25.15325 / 11.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7926 (mtm-85) REVERT: A 102 GLN cc_start: 0.8402 (mt0) cc_final: 0.8194 (tm-30) REVERT: A 260 GLN cc_start: 0.5462 (mm-40) cc_final: 0.5139 (tp-100) REVERT: B 74 LEU cc_start: 0.9107 (tp) cc_final: 0.8874 (tp) REVERT: B 307 MET cc_start: 0.8155 (mtp) cc_final: 0.7488 (tpp) REVERT: B 324 LEU cc_start: 0.9316 (mt) cc_final: 0.8944 (tp) REVERT: B 328 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8896 (tmtt) REVERT: B 429 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7606 (tp30) REVERT: C 394 MET cc_start: 0.6195 (tpp) cc_final: 0.5604 (tpp) REVERT: C 519 MET cc_start: 0.7451 (ttt) cc_final: 0.7026 (tmm) REVERT: C 570 LEU cc_start: 0.8381 (mp) cc_final: 0.7978 (pp) REVERT: C 695 ILE cc_start: 0.8667 (mt) cc_final: 0.8397 (mp) REVERT: C 801 TYR cc_start: 0.8765 (m-80) cc_final: 0.8551 (m-80) REVERT: C 982 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8295 (mm-30) REVERT: C 990 MET cc_start: 0.9275 (tmm) cc_final: 0.8985 (tmm) REVERT: C 1216 ILE cc_start: 0.9435 (mm) cc_final: 0.9131 (tp) REVERT: C 1434 LYS cc_start: 0.8170 (tmmt) cc_final: 0.7915 (tttt) REVERT: C 1438 GLU cc_start: 0.8823 (tt0) cc_final: 0.8265 (tm-30) REVERT: D 196 LEU cc_start: 0.9273 (pt) cc_final: 0.8913 (pp) REVERT: D 207 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8360 (mmmt) REVERT: D 442 TYR cc_start: 0.7481 (t80) cc_final: 0.7064 (t80) REVERT: E 379 LEU cc_start: 0.7689 (mt) cc_final: 0.7321 (mt) REVERT: E 811 LEU cc_start: 0.8060 (tt) cc_final: 0.7756 (tt) REVERT: E 845 LEU cc_start: 0.6065 (mm) cc_final: 0.5070 (tp) REVERT: E 925 MET cc_start: 0.2520 (tpp) cc_final: 0.2184 (tpp) REVERT: E 959 LEU cc_start: 0.9042 (mt) cc_final: 0.7863 (tp) REVERT: E 1104 TRP cc_start: 0.8199 (t-100) cc_final: 0.7758 (t-100) REVERT: E 1160 GLU cc_start: 0.8466 (pt0) cc_final: 0.8082 (tm-30) REVERT: F 49 TYR cc_start: 0.2370 (t80) cc_final: 0.1448 (t80) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.1737 time to fit residues: 100.6024 Evaluate side-chains 235 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 118 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 334 optimal weight: 8.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 553 HIS C 627 HIS C 986 HIS C1067 ASN C1325 GLN D 262 ASN D 369 HIS ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 HIS ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.104483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.083321 restraints weight = 125967.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081853 restraints weight = 156145.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.082969 restraints weight = 120048.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083526 restraints weight = 79675.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083908 restraints weight = 77837.130| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30800 Z= 0.215 Angle : 0.817 35.189 41744 Z= 0.385 Chirality : 0.047 0.173 4630 Planarity : 0.006 0.057 5341 Dihedral : 7.070 55.931 4110 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.13), residues: 3704 helix: -1.17 (0.14), residues: 1071 sheet: -2.38 (0.19), residues: 612 loop : -3.29 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 926 TYR 0.038 0.002 TYR C 732 PHE 0.037 0.002 PHE E1040 TRP 0.014 0.002 TRP A 168 HIS 0.018 0.002 HIS E 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (30788) covalent geometry : angle 0.75343 / 0.38 (41738) hydrogen bonds : bond 0.04882 / 3.18 ( 1062) hydrogen bonds : angle 6.86183 / 4.76 ( 2916) metal coordination : bond 0.00728 / 0.39 ( 12) metal coordination : angle 26.35688 / 12.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8403 (mtp180) cc_final: 0.7879 (mtm110) REVERT: A 106 LEU cc_start: 0.8887 (tp) cc_final: 0.8421 (tt) REVERT: A 255 LEU cc_start: 0.8586 (mt) cc_final: 0.8346 (mt) REVERT: B 74 LEU cc_start: 0.9149 (tp) cc_final: 0.8755 (tp) REVERT: B 307 MET cc_start: 0.8279 (mtp) cc_final: 0.7808 (tpp) REVERT: B 324 LEU cc_start: 0.9359 (mt) cc_final: 0.8984 (tp) REVERT: B 328 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8918 (tmtt) REVERT: B 336 MET cc_start: 0.3809 (tmm) cc_final: 0.3417 (tmm) REVERT: B 429 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7692 (tp30) REVERT: C 394 MET cc_start: 0.6069 (tpp) cc_final: 0.5588 (tpp) REVERT: C 519 MET cc_start: 0.7456 (ttt) cc_final: 0.6904 (tmm) REVERT: C 570 LEU cc_start: 0.8367 (mp) cc_final: 0.7849 (pp) REVERT: C 695 ILE cc_start: 0.8675 (mt) cc_final: 0.8405 (mp) REVERT: C 731 MET cc_start: 0.6960 (mpp) cc_final: 0.6540 (mpp) REVERT: C 982 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8347 (mm-30) REVERT: C 990 MET cc_start: 0.9286 (tmm) cc_final: 0.8600 (tmm) REVERT: C 1216 ILE cc_start: 0.9421 (mm) cc_final: 0.9122 (tp) REVERT: C 1376 LYS cc_start: 0.7722 (mttp) cc_final: 0.6929 (mtpp) REVERT: C 1438 GLU cc_start: 0.8861 (tt0) cc_final: 0.8356 (tm-30) REVERT: D 207 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8445 (mmmt) REVERT: D 442 TYR cc_start: 0.7501 (t80) cc_final: 0.7157 (t80) REVERT: D 575 TYR cc_start: 0.7664 (m-10) cc_final: 0.7016 (m-10) REVERT: E 379 LEU cc_start: 0.7792 (mt) cc_final: 0.7505 (mt) REVERT: E 811 LEU cc_start: 0.8081 (tt) cc_final: 0.7761 (tt) REVERT: E 1160 GLU cc_start: 0.8507 (pt0) cc_final: 0.8143 (tm-30) REVERT: F 49 TYR cc_start: 0.2351 (t80) cc_final: 0.1509 (t80) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.1809 time to fit residues: 92.6020 Evaluate side-chains 216 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 351 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 363 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 355 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS C1325 GLN D 262 ASN D 369 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 GLN F 180 GLN G 52 GLN G 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.104839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.083514 restraints weight = 124573.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.080980 restraints weight = 114457.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081729 restraints weight = 106908.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.081842 restraints weight = 71332.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.082434 restraints weight = 67849.163| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30800 Z= 0.183 Angle : 0.768 28.868 41744 Z= 0.368 Chirality : 0.046 0.168 4630 Planarity : 0.005 0.057 5341 Dihedral : 6.964 54.951 4110 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3704 helix: -0.92 (0.15), residues: 1062 sheet: -2.20 (0.20), residues: 607 loop : -3.16 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 522 TYR 0.043 0.002 TYR C 732 PHE 0.034 0.002 PHE D 240 TRP 0.019 0.002 TRP A 168 HIS 0.009 0.001 HIS D 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (30788) covalent geometry : angle 0.72092 / 0.37 (41738) hydrogen bonds : bond 0.04633 / 3.03 ( 1062) hydrogen bonds : angle 6.73391 / 4.67 ( 2916) metal coordination : bond 0.01260 / 0.64 ( 12) metal coordination : angle 22.18232 / 10.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8330 (mtp180) cc_final: 0.7946 (mtm110) REVERT: A 106 LEU cc_start: 0.8922 (tp) cc_final: 0.8599 (tt) REVERT: A 260 GLN cc_start: 0.5122 (mm-40) cc_final: 0.4731 (tp-100) REVERT: B 74 LEU cc_start: 0.9127 (tp) cc_final: 0.8885 (tp) REVERT: B 307 MET cc_start: 0.8261 (mtp) cc_final: 0.7797 (tpp) REVERT: B 324 LEU cc_start: 0.9396 (mt) cc_final: 0.8997 (tp) REVERT: B 328 LYS cc_start: 0.9309 (ttmt) cc_final: 0.8902 (tmtt) REVERT: B 429 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7746 (tp30) REVERT: C 394 MET cc_start: 0.6184 (tpp) cc_final: 0.5737 (tpp) REVERT: C 519 MET cc_start: 0.7290 (ttt) cc_final: 0.6740 (tmm) REVERT: C 568 PHE cc_start: 0.7372 (t80) cc_final: 0.7131 (t80) REVERT: C 570 LEU cc_start: 0.8487 (mp) cc_final: 0.8007 (pp) REVERT: C 695 ILE cc_start: 0.8664 (mt) cc_final: 0.8437 (mp) REVERT: C 731 MET cc_start: 0.6764 (mpp) cc_final: 0.6276 (mpp) REVERT: C 801 TYR cc_start: 0.8684 (m-80) cc_final: 0.8074 (m-80) REVERT: C 982 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8204 (mm-30) REVERT: C 1084 TRP cc_start: 0.8763 (m100) cc_final: 0.8432 (m100) REVERT: C 1135 ILE cc_start: 0.8572 (mm) cc_final: 0.8240 (mm) REVERT: C 1216 ILE cc_start: 0.9481 (mm) cc_final: 0.9171 (tp) REVERT: C 1376 LYS cc_start: 0.8041 (mttp) cc_final: 0.7220 (mtpp) REVERT: C 1438 GLU cc_start: 0.8894 (tt0) cc_final: 0.8467 (tm-30) REVERT: D 207 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8470 (mmmt) REVERT: D 442 TYR cc_start: 0.7458 (t80) cc_final: 0.7048 (t80) REVERT: D 575 TYR cc_start: 0.7707 (m-10) cc_final: 0.6922 (m-10) REVERT: E 379 LEU cc_start: 0.7759 (mt) cc_final: 0.7436 (mp) REVERT: E 800 PHE cc_start: 0.8841 (m-80) cc_final: 0.8624 (m-80) REVERT: E 927 ARG cc_start: 0.7007 (mtt180) cc_final: 0.6619 (mtt180) REVERT: E 1104 TRP cc_start: 0.8217 (t-100) cc_final: 0.7731 (t-100) REVERT: E 1160 GLU cc_start: 0.8611 (pt0) cc_final: 0.8097 (tm-30) REVERT: F 49 TYR cc_start: 0.2283 (t80) cc_final: 0.1440 (t80) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.1820 time to fit residues: 92.7966 Evaluate side-chains 226 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 336 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 108 optimal weight: 0.0060 chunk 105 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 362 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 986 HIS D 262 ASN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 HIS ** E 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084933 restraints weight = 125769.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.084131 restraints weight = 132160.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.084568 restraints weight = 109665.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085019 restraints weight = 74359.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.085469 restraints weight = 68905.946| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30800 Z= 0.156 Angle : 0.729 26.777 41744 Z= 0.351 Chirality : 0.045 0.157 4630 Planarity : 0.005 0.077 5341 Dihedral : 6.785 53.398 4110 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.13), residues: 3704 helix: -0.73 (0.15), residues: 1065 sheet: -2.06 (0.20), residues: 627 loop : -3.01 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 268 TYR 0.041 0.002 TYR C 732 PHE 0.032 0.002 PHE E1040 TRP 0.045 0.002 TRP A 240 HIS 0.009 0.001 HIS D 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (30788) covalent geometry : angle 0.69058 / 0.35 (41738) hydrogen bonds : bond 0.04398 / 2.88 ( 1062) hydrogen bonds : angle 6.57349 / 4.56 ( 2916) metal coordination : bond 0.00675 / 0.35 ( 12) metal coordination : angle 19.38010 / 8.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7920 (mtm110) REVERT: A 106 LEU cc_start: 0.8911 (tp) cc_final: 0.8530 (tt) REVERT: A 259 PHE cc_start: 0.5818 (m-10) cc_final: 0.5551 (m-10) REVERT: A 260 GLN cc_start: 0.4801 (mm110) cc_final: 0.4555 (tp-100) REVERT: A 304 ARG cc_start: 0.5698 (mpt90) cc_final: 0.4679 (tpt170) REVERT: B 74 LEU cc_start: 0.9092 (tp) cc_final: 0.8862 (tp) REVERT: B 307 MET cc_start: 0.8213 (mtp) cc_final: 0.7646 (tpp) REVERT: B 328 LYS cc_start: 0.9264 (ttmt) cc_final: 0.8898 (tmtt) REVERT: B 336 MET cc_start: 0.3520 (tmm) cc_final: 0.3268 (tmm) REVERT: B 429 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7700 (tp30) REVERT: C 394 MET cc_start: 0.5963 (tpp) cc_final: 0.5591 (tpp) REVERT: C 519 MET cc_start: 0.7393 (ttt) cc_final: 0.6874 (tmm) REVERT: C 544 MET cc_start: 0.7185 (mpp) cc_final: 0.6985 (mpp) REVERT: C 570 LEU cc_start: 0.8310 (mp) cc_final: 0.7850 (pp) REVERT: C 731 MET cc_start: 0.6625 (mpp) cc_final: 0.6118 (mpp) REVERT: C 801 TYR cc_start: 0.8532 (m-80) cc_final: 0.7699 (m-80) REVERT: C 1135 ILE cc_start: 0.8567 (mm) cc_final: 0.8282 (mm) REVERT: C 1216 ILE cc_start: 0.9454 (mm) cc_final: 0.9247 (tp) REVERT: C 1376 LYS cc_start: 0.8284 (mttp) cc_final: 0.7466 (mtpp) REVERT: C 1438 GLU cc_start: 0.8869 (tt0) cc_final: 0.8315 (tm-30) REVERT: D 196 LEU cc_start: 0.9342 (pt) cc_final: 0.8965 (pp) REVERT: D 442 TYR cc_start: 0.7451 (t80) cc_final: 0.7033 (t80) REVERT: D 575 TYR cc_start: 0.7578 (m-10) cc_final: 0.6775 (m-10) REVERT: E 286 LEU cc_start: 0.8038 (mp) cc_final: 0.7675 (mp) REVERT: E 299 TRP cc_start: 0.5128 (m100) cc_final: 0.4071 (m100) REVERT: E 379 LEU cc_start: 0.7718 (mt) cc_final: 0.7506 (mt) REVERT: E 664 ASP cc_start: 0.8173 (m-30) cc_final: 0.7826 (p0) REVERT: E 927 ARG cc_start: 0.6921 (mtt180) cc_final: 0.6487 (mtt180) REVERT: E 1104 TRP cc_start: 0.7965 (t-100) cc_final: 0.7441 (t-100) REVERT: E 1160 GLU cc_start: 0.8563 (pt0) cc_final: 0.8109 (tm-30) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1757 time to fit residues: 90.9941 Evaluate side-chains 226 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 183 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 330 optimal weight: 30.0000 chunk 108 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 HIS E 638 HIS E 855 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.104735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084251 restraints weight = 125451.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083459 restraints weight = 164647.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.084313 restraints weight = 124584.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.085402 restraints weight = 79947.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085616 restraints weight = 70307.609| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30800 Z= 0.196 Angle : 0.766 29.719 41744 Z= 0.368 Chirality : 0.046 0.298 4630 Planarity : 0.006 0.096 5341 Dihedral : 6.815 54.343 4110 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.13), residues: 3704 helix: -0.75 (0.15), residues: 1062 sheet: -2.03 (0.21), residues: 603 loop : -2.92 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG F 133 TYR 0.040 0.002 TYR C 732 PHE 0.033 0.002 PHE D 240 TRP 0.033 0.002 TRP A 240 HIS 0.010 0.001 HIS D 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (30788) covalent geometry : angle 0.72769 / 0.37 (41738) hydrogen bonds : bond 0.04504 / 2.94 ( 1062) hydrogen bonds : angle 6.63087 / 4.59 ( 2916) metal coordination : bond 0.00359 / 0.21 ( 12) metal coordination : angle 20.00322 / 9.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9025 (tp) cc_final: 0.8801 (tt) REVERT: A 260 GLN cc_start: 0.4627 (mm110) cc_final: 0.4369 (tp-100) REVERT: A 304 ARG cc_start: 0.5562 (mpt90) cc_final: 0.4530 (tpt170) REVERT: B 74 LEU cc_start: 0.9085 (tp) cc_final: 0.8843 (tp) REVERT: B 79 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.8314 (mmt-90) REVERT: B 307 MET cc_start: 0.8353 (mtp) cc_final: 0.7810 (tpp) REVERT: B 328 LYS cc_start: 0.9271 (ttmt) cc_final: 0.8899 (tmtt) REVERT: B 429 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7785 (tp30) REVERT: C 394 MET cc_start: 0.5824 (tpp) cc_final: 0.5517 (tpp) REVERT: C 519 MET cc_start: 0.7399 (ttt) cc_final: 0.6881 (tmm) REVERT: C 568 PHE cc_start: 0.6865 (t80) cc_final: 0.6650 (t80) REVERT: C 570 LEU cc_start: 0.8338 (mp) cc_final: 0.7834 (pt) REVERT: C 731 MET cc_start: 0.6762 (mpp) cc_final: 0.6202 (mpp) REVERT: C 1135 ILE cc_start: 0.8520 (mm) cc_final: 0.8229 (mm) REVERT: C 1376 LYS cc_start: 0.8027 (mttp) cc_final: 0.7297 (mtpp) REVERT: C 1438 GLU cc_start: 0.8881 (tt0) cc_final: 0.8343 (tm-30) REVERT: D 442 TYR cc_start: 0.7522 (t80) cc_final: 0.7160 (t80) REVERT: D 575 TYR cc_start: 0.7536 (m-10) cc_final: 0.6770 (m-10) REVERT: E 286 LEU cc_start: 0.8042 (mp) cc_final: 0.7697 (mp) REVERT: E 299 TRP cc_start: 0.4929 (m100) cc_final: 0.4010 (m100) REVERT: E 927 ARG cc_start: 0.6809 (mtt180) cc_final: 0.6449 (mtt180) REVERT: E 1104 TRP cc_start: 0.7722 (t-100) cc_final: 0.7171 (t-100) REVERT: E 1160 GLU cc_start: 0.8444 (pt0) cc_final: 0.7949 (tm-30) REVERT: F 49 TYR cc_start: 0.2227 (t80) cc_final: 0.1213 (t80) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1797 time to fit residues: 92.5236 Evaluate side-chains 217 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 207 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 306 optimal weight: 0.0980 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 364 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 351 HIS B 452 GLN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C 986 HIS ** C1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1290 ASN ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 HIS E1177 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.107737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087163 restraints weight = 123869.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.084452 restraints weight = 133979.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085023 restraints weight = 109619.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085849 restraints weight = 78713.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.086137 restraints weight = 68970.492| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30800 Z= 0.128 Angle : 0.697 13.952 41744 Z= 0.345 Chirality : 0.045 0.217 4630 Planarity : 0.005 0.076 5341 Dihedral : 6.522 53.700 4110 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.03 % Allowed : 1.55 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3704 helix: -0.46 (0.16), residues: 1059 sheet: -1.84 (0.21), residues: 621 loop : -2.78 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 182 TYR 0.041 0.002 TYR C 732 PHE 0.033 0.002 PHE C1421 TRP 0.028 0.002 TRP A 240 HIS 0.009 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (30788) covalent geometry : angle 0.68883 / 0.35 (41738) hydrogen bonds : bond 0.04191 / 2.75 ( 1062) hydrogen bonds : angle 6.33163 / 4.37 ( 2916) metal coordination : bond 0.01277 / 0.64 ( 12) metal coordination : angle 8.68457 / 3.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9009 (tp) cc_final: 0.8766 (tt) REVERT: A 112 MET cc_start: 0.6061 (tmm) cc_final: 0.4924 (mtp) REVERT: A 260 GLN cc_start: 0.4664 (mm110) cc_final: 0.4403 (tp-100) REVERT: B 74 LEU cc_start: 0.9096 (tp) cc_final: 0.8879 (tp) REVERT: B 79 ARG cc_start: 0.8425 (mmt-90) cc_final: 0.8082 (mmt-90) REVERT: B 307 MET cc_start: 0.8201 (mtp) cc_final: 0.7562 (tpp) REVERT: B 324 LEU cc_start: 0.9182 (mm) cc_final: 0.8923 (tp) REVERT: B 328 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8770 (tmtt) REVERT: B 429 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7706 (tp30) REVERT: C 394 MET cc_start: 0.5689 (tpp) cc_final: 0.5294 (tpp) REVERT: C 519 MET cc_start: 0.7303 (ttt) cc_final: 0.6756 (tmm) REVERT: C 542 PHE cc_start: 0.8032 (t80) cc_final: 0.7686 (t80) REVERT: C 731 MET cc_start: 0.6528 (mpp) cc_final: 0.6035 (mpp) REVERT: C 801 TYR cc_start: 0.8225 (m-80) cc_final: 0.7816 (m-80) REVERT: C 1135 ILE cc_start: 0.8507 (mm) cc_final: 0.8262 (mm) REVERT: C 1376 LYS cc_start: 0.7794 (mttp) cc_final: 0.7035 (mtpp) REVERT: C 1438 GLU cc_start: 0.8842 (tt0) cc_final: 0.8326 (tm-30) REVERT: D 196 LEU cc_start: 0.9347 (pt) cc_final: 0.8977 (pp) REVERT: D 207 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8304 (mmmt) REVERT: D 442 TYR cc_start: 0.7268 (t80) cc_final: 0.6903 (t80) REVERT: D 469 PHE cc_start: 0.7793 (m-80) cc_final: 0.7381 (m-10) REVERT: D 484 GLU cc_start: 0.8906 (tt0) cc_final: 0.8683 (tm-30) REVERT: D 575 TYR cc_start: 0.7477 (m-10) cc_final: 0.6554 (m-10) REVERT: E 286 LEU cc_start: 0.8098 (mp) cc_final: 0.7838 (mp) REVERT: E 299 TRP cc_start: 0.5075 (m100) cc_final: 0.4136 (m100) REVERT: E 392 ARG cc_start: 0.6128 (mtt180) cc_final: 0.4122 (tmm160) REVERT: E 800 PHE cc_start: 0.8730 (m-80) cc_final: 0.8528 (m-80) REVERT: E 917 MET cc_start: -0.0367 (mtp) cc_final: -0.0915 (ttm) REVERT: E 1104 TRP cc_start: 0.7904 (t-100) cc_final: 0.7310 (t-100) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.1799 time to fit residues: 100.3173 Evaluate side-chains 231 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 329 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 39 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 chunk 344 optimal weight: 0.7980 chunk 317 optimal weight: 0.9980 chunk 342 optimal weight: 30.0000 overall best weight: 1.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS C1190 GLN ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS E 272 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.108087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086431 restraints weight = 123575.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.084429 restraints weight = 119358.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.085128 restraints weight = 103934.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.085194 restraints weight = 74881.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.086038 restraints weight = 71484.173| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30800 Z= 0.131 Angle : 0.696 19.632 41744 Z= 0.343 Chirality : 0.045 0.280 4630 Planarity : 0.005 0.067 5341 Dihedral : 6.415 54.138 4110 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.14), residues: 3704 helix: -0.41 (0.16), residues: 1063 sheet: -1.86 (0.21), residues: 613 loop : -2.65 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1191 TYR 0.040 0.002 TYR C 732 PHE 0.029 0.002 PHE E1040 TRP 0.030 0.002 TRP A 240 HIS 0.008 0.001 HIS C 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (30788) covalent geometry : angle 0.68554 / 0.34 (41738) hydrogen bonds : bond 0.04117 / 2.72 ( 1062) hydrogen bonds : angle 6.26453 / 4.32 ( 2916) metal coordination : bond 0.01319 / 0.66 ( 12) metal coordination : angle 9.97488 / 4.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8932 (tp) cc_final: 0.8674 (tt) REVERT: A 112 MET cc_start: 0.6228 (tmm) cc_final: 0.5132 (mtp) REVERT: B 74 LEU cc_start: 0.8972 (tp) cc_final: 0.8742 (tp) REVERT: B 79 ARG cc_start: 0.8416 (mmt-90) cc_final: 0.8156 (mmt-90) REVERT: B 307 MET cc_start: 0.8163 (mtp) cc_final: 0.7516 (tpp) REVERT: B 324 LEU cc_start: 0.9163 (mm) cc_final: 0.8929 (tp) REVERT: B 328 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8774 (tmtt) REVERT: B 429 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7778 (tp30) REVERT: C 394 MET cc_start: 0.5740 (tpp) cc_final: 0.5411 (tpp) REVERT: C 519 MET cc_start: 0.7210 (ttt) cc_final: 0.6667 (tmm) REVERT: C 695 ILE cc_start: 0.8619 (mt) cc_final: 0.8385 (mp) REVERT: C 731 MET cc_start: 0.6524 (mpp) cc_final: 0.6026 (mpp) REVERT: C 778 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8470 (ttm-80) REVERT: C 801 TYR cc_start: 0.8193 (m-80) cc_final: 0.7786 (m-80) REVERT: C 1135 ILE cc_start: 0.8462 (mm) cc_final: 0.8224 (mm) REVERT: C 1376 LYS cc_start: 0.8252 (mttp) cc_final: 0.7411 (mtpp) REVERT: C 1438 GLU cc_start: 0.8802 (tt0) cc_final: 0.8253 (tm-30) REVERT: D 161 TYR cc_start: 0.7337 (t80) cc_final: 0.7130 (t80) REVERT: D 196 LEU cc_start: 0.9342 (pt) cc_final: 0.8988 (pp) REVERT: D 296 LEU cc_start: 0.9259 (mt) cc_final: 0.9035 (mt) REVERT: D 442 TYR cc_start: 0.7305 (t80) cc_final: 0.6917 (t80) REVERT: D 469 PHE cc_start: 0.7741 (m-80) cc_final: 0.7284 (m-10) REVERT: D 556 CYS cc_start: 0.7642 (m) cc_final: 0.7435 (m) REVERT: E 300 MET cc_start: 0.7711 (tmm) cc_final: 0.7396 (tmm) REVERT: E 392 ARG cc_start: 0.6158 (mtt180) cc_final: 0.4046 (tmm160) REVERT: E 395 MET cc_start: 0.6525 (tpp) cc_final: 0.5924 (tpp) REVERT: E 917 MET cc_start: -0.0669 (mtp) cc_final: -0.1371 (ttm) REVERT: E 927 ARG cc_start: 0.6956 (mtt180) cc_final: 0.6434 (mtt180) REVERT: E 1104 TRP cc_start: 0.7940 (t-100) cc_final: 0.7344 (t-100) REVERT: G 45 MET cc_start: -0.0824 (tpp) cc_final: -0.1250 (ttt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1750 time to fit residues: 96.4339 Evaluate side-chains 227 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 205 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 198 optimal weight: 0.0370 chunk 159 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 318 optimal weight: 0.0020 chunk 97 optimal weight: 8.9990 overall best weight: 1.0070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 452 GLN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1363 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.108574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.088351 restraints weight = 123979.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.085498 restraints weight = 116117.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.086284 restraints weight = 115724.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086363 restraints weight = 77938.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087109 restraints weight = 74906.405| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30800 Z= 0.122 Angle : 0.687 16.981 41744 Z= 0.339 Chirality : 0.044 0.171 4630 Planarity : 0.005 0.060 5341 Dihedral : 6.263 54.251 4110 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.14), residues: 3704 helix: -0.29 (0.16), residues: 1060 sheet: -1.68 (0.21), residues: 609 loop : -2.60 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 182 TYR 0.044 0.002 TYR C 732 PHE 0.031 0.002 PHE C 542 TRP 0.028 0.002 TRP A 240 HIS 0.009 0.001 HIS C 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (30788) covalent geometry : angle 0.68187 / 0.34 (41738) hydrogen bonds : bond 0.04055 / 2.67 ( 1062) hydrogen bonds : angle 6.15156 / 4.24 ( 2916) metal coordination : bond 0.00711 / 0.36 ( 12) metal coordination : angle 7.24590 / 3.28 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8890 (tp) cc_final: 0.8541 (tt) REVERT: A 297 MET cc_start: 0.8540 (mpp) cc_final: 0.8264 (mpp) REVERT: B 74 LEU cc_start: 0.9019 (tp) cc_final: 0.8763 (tp) REVERT: B 79 ARG cc_start: 0.8348 (mmt-90) cc_final: 0.8042 (mmt-90) REVERT: B 307 MET cc_start: 0.8190 (mtp) cc_final: 0.7564 (tpp) REVERT: B 321 GLU cc_start: 0.7537 (pm20) cc_final: 0.7137 (pm20) REVERT: B 429 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7741 (tp30) REVERT: C 394 MET cc_start: 0.5565 (tpp) cc_final: 0.5226 (tpp) REVERT: C 411 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7812 (tppt) REVERT: C 519 MET cc_start: 0.7191 (ttt) cc_final: 0.6644 (tmm) REVERT: C 542 PHE cc_start: 0.8263 (t80) cc_final: 0.7775 (t80) REVERT: C 762 LEU cc_start: 0.9336 (pp) cc_final: 0.9026 (mp) REVERT: C 778 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8267 (tpt170) REVERT: C 801 TYR cc_start: 0.8294 (m-80) cc_final: 0.7790 (m-80) REVERT: C 1135 ILE cc_start: 0.8474 (mm) cc_final: 0.8235 (mm) REVERT: C 1376 LYS cc_start: 0.8315 (mttp) cc_final: 0.7301 (mtpp) REVERT: C 1438 GLU cc_start: 0.8759 (tt0) cc_final: 0.8349 (tm-30) REVERT: D 161 TYR cc_start: 0.7309 (t80) cc_final: 0.7041 (t80) REVERT: D 442 TYR cc_start: 0.7320 (t80) cc_final: 0.7020 (t80) REVERT: D 469 PHE cc_start: 0.7602 (m-80) cc_final: 0.7135 (m-10) REVERT: E 300 MET cc_start: 0.7498 (tmm) cc_final: 0.7284 (tmm) REVERT: E 392 ARG cc_start: 0.6264 (mtt180) cc_final: 0.4298 (tmm160) REVERT: E 395 MET cc_start: 0.6674 (tpp) cc_final: 0.6109 (tpp) REVERT: E 917 MET cc_start: -0.0949 (mtp) cc_final: -0.1632 (ttm) REVERT: E 927 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6543 (mtt180) REVERT: E 1104 TRP cc_start: 0.7950 (t-100) cc_final: 0.7355 (t-100) REVERT: F 37 MET cc_start: 0.3612 (ptt) cc_final: 0.3027 (ptp) REVERT: G 45 MET cc_start: -0.1072 (tpp) cc_final: -0.1465 (ttt) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1738 time to fit residues: 95.2461 Evaluate side-chains 225 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 110 optimal weight: 0.0970 chunk 159 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 291 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 206 optimal weight: 0.0970 chunk 297 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 986 HIS ** C1328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.109313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.088609 restraints weight = 123667.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086108 restraints weight = 117595.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086958 restraints weight = 111654.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.087472 restraints weight = 75274.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.087578 restraints weight = 75186.625| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30800 Z= 0.117 Angle : 0.664 13.519 41744 Z= 0.328 Chirality : 0.044 0.196 4630 Planarity : 0.005 0.052 5341 Dihedral : 6.110 54.872 4110 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.14), residues: 3704 helix: -0.26 (0.16), residues: 1083 sheet: -1.61 (0.21), residues: 621 loop : -2.53 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 653 TYR 0.044 0.001 TYR C 732 PHE 0.028 0.002 PHE E1040 TRP 0.028 0.002 TRP E 163 HIS 0.009 0.001 HIS C 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (30788) covalent geometry : angle 0.66189 / 0.33 (41738) hydrogen bonds : bond 0.03843 / 2.55 ( 1062) hydrogen bonds : angle 6.05475 / 4.18 ( 2916) metal coordination : bond 0.00632 / 0.33 ( 12) metal coordination : angle 4.74288 / 2.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4345.25 seconds wall clock time: 76 minutes 58.63 seconds (4618.63 seconds total)