Starting phenix.real_space_refine on Sat Sep 12 03:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3i_27866/09_2026/8e3i_27866.cif" } resolution = 2.53 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= 0.005 sd= 0.176 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 7 5.49 5 S 89 5.16 5 C 8569 2.51 5 N 2333 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 13431 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9344 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 66, 'TRANS': 1111} Chain breaks: 12 Chain: "C" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Classifications: {'DNA': 1, 'RNAv2': 6} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2} Link IDs: {'rna2p': 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3035 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9654 SG CYS C 41 29.749 87.313 95.339 1.00 62.78 S ATOM 9718 SG CYS C 49 26.440 87.944 97.055 1.00 73.55 S ATOM 9753 SG CYS C 55 28.191 84.597 97.489 1.00 69.19 S ATOM 9855 SG CYS C 68 44.819 80.351 107.091 1.00 61.44 S ATOM 9925 SG CYS C 76 41.160 79.397 106.590 1.00 57.31 S ATOM 9970 SG CYS C 82 42.145 83.000 107.592 1.00 65.50 S ATOM 10091 SG CYS C 96 60.844 78.372 110.348 1.00 76.92 S ATOM 10171 SG CYS C 105 63.253 75.414 109.893 1.00 83.85 S ATOM 10209 SG CYS C 110 61.710 77.015 106.792 1.00 82.64 S Time building chain proxies: 2.43, per 1000 atoms: 0.18 Number of scatterers: 13431 At special positions: 0 Unit cell: (87.98, 103.75, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 89 16.00 P 7 15.00 O 2430 8.00 N 2333 7.00 C 8569 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: 0.88 Conformation dependent library (CDL) restraints added in 540.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 68 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 82 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " Number of angles added : 9 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 29 sheets defined 9.9% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.622A pdb=" N ARG A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.574A pdb=" N THR A 304 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1370 Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 3.841A pdb=" N ARG A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1422 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.780A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.511A pdb=" N ARG C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.959A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 101 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315 removed outlier: 4.153A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1339 " --> pdb=" O THR A1310 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 6 " --> pdb=" O LEU A1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 4.191A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 84 removed outlier: 3.651A pdb=" N SER A 80 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 107 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR A 117 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 5.214A pdb=" N CYS A 238 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR A 259 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 240 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 257 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.053A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 7.102A pdb=" N ILE A 344 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS A 364 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 346 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A 362 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 376 removed outlier: 6.356A pdb=" N LYS A 395 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL A 465 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR A 397 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 463 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 477 through 481 removed outlier: 4.058A pdb=" N ASN A 477 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 528 removed outlier: 6.843A pdb=" N ILE A 998 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR A 526 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 996 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.770A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.565A pdb=" N TYR A 617 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 652 Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 removed outlier: 3.759A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 782 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 4.904A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.270A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1021 through 1028 removed outlier: 5.556A pdb=" N ALA A1022 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N SER A1039 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 13.438A pdb=" N GLU A1072 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N GLU A1093 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N PHE A1074 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N ARG A1091 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N ILE A1076 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ASN A1089 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A1078 " --> pdb=" O ILE A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1046 through 1050 Processing sheet with id=AC1, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.501A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 3.707A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1212 through 1218 removed outlier: 3.646A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN A1237 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A1243 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1255 through 1262 removed outlier: 3.974A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A1300 " --> pdb=" O VAL A1280 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET A1282 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARG A1298 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 109 through 115 removed outlier: 5.340A pdb=" N PHE B 110 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR B 403 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 112 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N THR B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 394 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 122 through 127 removed outlier: 4.334A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 155 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN B 147 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 153 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.319A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 205 through 210 removed outlier: 3.824A pdb=" N GLU B 207 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 247 through 252 Processing sheet with id=AD1, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD2, first strand: chain 'B' and resid 334 through 339 438 hydrogen bonds defined for protein. 1158 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: 2.78 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4313 1.34 - 1.46: 2564 1.46 - 1.58: 6737 1.58 - 1.70: 13 1.70 - 1.81: 141 Bond restraints: 13768 Sorted by residual: bond pdb=" N ARG B 70 " pdb=" CA ARG B 70 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.52e+00 bond pdb=" C VAL A 251 " pdb=" N HIS A 252 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.22e-02 6.72e+03 2.03e+00 bond pdb=" CG LEU A 786 " pdb=" CD1 LEU A 786 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" C LYS A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.72e+00 bond pdb=" C ASP A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 18089 1.58 - 3.15: 483 3.15 - 4.73: 90 4.73 - 6.30: 22 6.30 - 7.88: 2 Bond angle restraints: 18686 Sorted by residual: angle pdb=" C TYR A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C LYS A 99 " pdb=" N ASP A 100 " pdb=" CA ASP A 100 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.98e+00 angle pdb=" N LEU A 799 " pdb=" CA LEU A 799 " pdb=" C LEU A 799 " ideal model delta sigma weight residual 109.81 116.00 -6.19 2.21e+00 2.05e-01 7.85e+00 angle pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " pdb=" CG ASP A 333 " ideal model delta sigma weight residual 112.60 115.26 -2.66 1.00e+00 1.00e+00 7.08e+00 angle pdb=" C LEU A1384 " pdb=" N HIS A1385 " pdb=" CA HIS A1385 " ideal model delta sigma weight residual 123.91 128.17 -4.26 1.66e+00 3.63e-01 6.58e+00 ... (remaining 18681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7471 17.75 - 35.49: 560 35.49 - 53.24: 101 53.24 - 70.98: 37 70.98 - 88.73: 16 Dihedral angle restraints: 8185 sinusoidal: 3352 harmonic: 4833 Sorted by residual: dihedral pdb=" C4' A E 4 " pdb=" C3' A E 4 " pdb=" C2' A E 4 " pdb=" C1' A E 4 " ideal model delta sinusoidal sigma weight residual 36.35 -36.83 73.17 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' A E 6 " pdb=" C3' A E 6 " pdb=" C2' A E 6 " pdb=" C1' A E 6 " ideal model delta sinusoidal sigma weight residual 36.34 -36.31 72.66 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' A E 5 " pdb=" C3' A E 5 " pdb=" C2' A E 5 " pdb=" C1' A E 5 " ideal model delta sinusoidal sigma weight residual 36.34 -36.17 72.51 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 8182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1690 0.056 - 0.111: 326 0.111 - 0.167: 42 0.167 - 0.223: 3 0.223 - 0.279: 17 Chirality restraints: 2078 Sorted by residual: chirality pdb=" C2' A E 1 " pdb=" C3' A E 1 " pdb=" O2' A E 1 " pdb=" C1' A E 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' U E 2 " pdb=" C3' U E 2 " pdb=" O2' U E 2 " pdb=" C1' U E 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' A E 4 " pdb=" C3' A E 4 " pdb=" O2' A E 4 " pdb=" C1' A E 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2075 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 252 " 0.025 2.00e-02 2.50e+03 3.17e-02 2.52e+01 pdb=" CG TRP B 252 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP B 252 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 252 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 252 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 252 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 252 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 252 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 252 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 227 " -0.012 2.00e-02 2.50e+03 1.37e-02 4.67e+00 pdb=" CG TRP A 227 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 227 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 227 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 227 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 227 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 227 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 227 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 227 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 332 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C TYR A 332 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR A 332 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 333 " 0.012 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1493 2.75 - 3.29: 12211 3.29 - 3.83: 23160 3.83 - 4.36: 29554 4.36 - 4.90: 50166 Nonbonded interactions: 116584 Sorted by model distance: nonbonded pdb=" OG SER B 170 " pdb=" O ASN B 172 " model vdw 2.215 3.040 nonbonded pdb=" O ASN B 289 " pdb=" OG SER B 307 " model vdw 2.222 3.040 nonbonded pdb=" O2' A E 5 " pdb=" O ARG B 47 " model vdw 2.228 3.040 nonbonded pdb=" NE2 GLN B 325 " pdb=" O VAL B 363 " model vdw 2.233 3.120 nonbonded pdb=" ND1 HIS A1028 " pdb=" O GLU A1030 " model vdw 2.237 3.120 ... (remaining 116579 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13780 Z= 0.176 Angle : 0.649 7.877 18695 Z= 0.344 Chirality : 0.051 0.279 2078 Planarity : 0.004 0.050 2362 Dihedral : 13.970 88.725 5063 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1641 helix: -0.83 (0.47), residues: 123 sheet: 0.73 (0.21), residues: 629 loop : -0.87 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.024 0.001 TYR A1256 PHE 0.028 0.002 PHE A 990 TRP 0.078 0.002 TRP B 252 HIS 0.012 0.001 HIS A 866 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (13768) covalent geometry : angle 0.64750 / 0.34 (18686) hydrogen bonds : bond 0.22946 / 15.36 ( 438) hydrogen bonds : angle 9.14084 / 6.40 ( 1158) metal coordination : bond 0.00909 / 0.58 ( 12) metal coordination : angle 1.76279 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.511 Fit side-chains REVERT: A 63 ARG cc_start: 0.7485 (tpt170) cc_final: 0.7081 (ttm170) REVERT: A 1289 GLU cc_start: 0.7459 (mp0) cc_final: 0.7239 (mp0) REVERT: C 85 LEU cc_start: 0.7659 (tp) cc_final: 0.7384 (tp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.7432 time to fit residues: 169.9330 Evaluate side-chains 160 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 691 HIS A1188 GLN C 21 GLN B 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.101369 restraints weight = 15028.006| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.60 r_work: 0.3078 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13780 Z= 0.271 Angle : 0.810 16.884 18695 Z= 0.407 Chirality : 0.061 0.848 2078 Planarity : 0.005 0.046 2362 Dihedral : 9.125 149.594 1877 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.27 % Rotamer: Outliers : 1.92 % Allowed : 7.21 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1641 helix: -0.86 (0.45), residues: 130 sheet: 0.64 (0.20), residues: 639 loop : -0.90 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 234 TYR 0.014 0.002 TYR A1356 PHE 0.023 0.002 PHE A1160 TRP 0.033 0.002 TRP B 252 HIS 0.013 0.001 HIS A 866 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.27 (13768) covalent geometry : angle 0.80828 / 0.41 (18686) hydrogen bonds : bond 0.05636 / 3.68 ( 438) hydrogen bonds : angle 6.87858 / 4.76 ( 1158) metal coordination : bond 0.00672 / 0.38 ( 12) metal coordination : angle 2.29971 / 1.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.484 Fit side-chains REVERT: A 67 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: A 162 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 591 GLU cc_start: 0.7368 (mp0) cc_final: 0.6851 (pm20) REVERT: A 1050 MET cc_start: 0.7605 (mmm) cc_final: 0.6670 (mtm) REVERT: A 1056 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6178 (tm-30) REVERT: A 1072 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: A 1132 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 1289 GLU cc_start: 0.8021 (mp0) cc_final: 0.7712 (mp0) REVERT: A 1352 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8454 (mt0) REVERT: B 70 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7137 (ptp-170) REVERT: B 173 ASP cc_start: 0.7797 (m-30) cc_final: 0.7512 (m-30) REVERT: B 216 LYS cc_start: 0.8671 (mttp) cc_final: 0.8254 (mtpt) REVERT: B 371 GLU cc_start: 0.8158 (tp30) cc_final: 0.7889 (mm-30) outliers start: 28 outliers final: 11 residues processed: 185 average time/residue: 0.6763 time to fit residues: 135.1265 Evaluate side-chains 177 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 276 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 897 HIS C 21 GLN B 104 ASN B 397 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103445 restraints weight = 15028.308| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.58 r_work: 0.3118 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13780 Z= 0.158 Angle : 0.665 12.769 18695 Z= 0.335 Chirality : 0.049 0.440 2078 Planarity : 0.004 0.046 2362 Dihedral : 9.299 155.868 1877 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.94 % Favored : 94.94 % Rotamer: Outliers : 2.06 % Allowed : 8.72 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1641 helix: -0.78 (0.45), residues: 130 sheet: 0.54 (0.21), residues: 637 loop : -0.92 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.010 0.001 TYR A1356 PHE 0.013 0.002 PHE B 347 TRP 0.019 0.002 TRP B 273 HIS 0.007 0.001 HIS A 866 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (13768) covalent geometry : angle 0.66383 / 0.34 (18686) hydrogen bonds : bond 0.04666 / 3.06 ( 438) hydrogen bonds : angle 6.42326 / 4.42 ( 1158) metal coordination : bond 0.00821 / 0.49 ( 12) metal coordination : angle 1.74992 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.347 Fit side-chains REVERT: A 67 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: A 162 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 591 GLU cc_start: 0.7273 (mp0) cc_final: 0.6775 (pm20) REVERT: A 815 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: A 1050 MET cc_start: 0.7500 (mmm) cc_final: 0.6612 (mtm) REVERT: A 1132 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: A 1289 GLU cc_start: 0.7963 (mp0) cc_final: 0.7631 (mp0) REVERT: C 1 MET cc_start: 0.7372 (tpt) cc_final: 0.7131 (tpp) REVERT: B 70 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7103 (ptp-170) REVERT: B 134 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 174 MET cc_start: 0.8378 (mtp) cc_final: 0.8156 (mtm) REVERT: B 216 LYS cc_start: 0.8606 (mttp) cc_final: 0.8203 (mtpt) REVERT: B 235 HIS cc_start: 0.8183 (t-90) cc_final: 0.7977 (t-90) REVERT: B 279 GLN cc_start: 0.7927 (mm110) cc_final: 0.7267 (pt0) outliers start: 30 outliers final: 10 residues processed: 193 average time/residue: 0.6698 time to fit residues: 139.6530 Evaluate side-chains 186 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 GLN A 680 HIS C 21 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101427 restraints weight = 14870.305| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.58 r_work: 0.3079 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13780 Z= 0.197 Angle : 0.686 12.456 18695 Z= 0.346 Chirality : 0.051 0.383 2078 Planarity : 0.005 0.045 2362 Dihedral : 9.459 154.196 1877 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 2.47 % Allowed : 9.82 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1641 helix: -0.78 (0.45), residues: 130 sheet: 0.44 (0.20), residues: 639 loop : -0.90 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.015 0.002 TYR A 617 PHE 0.013 0.002 PHE A 975 TRP 0.018 0.002 TRP B 273 HIS 0.008 0.001 HIS A 866 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (13768) covalent geometry : angle 0.68537 / 0.35 (18686) hydrogen bonds : bond 0.04622 / 3.01 ( 438) hydrogen bonds : angle 6.31968 / 4.36 ( 1158) metal coordination : bond 0.00786 / 0.51 ( 12) metal coordination : angle 1.81456 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.622 Fit side-chains REVERT: A 67 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 162 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 313 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7518 (mtm-85) REVERT: A 591 GLU cc_start: 0.7270 (mp0) cc_final: 0.6799 (pm20) REVERT: A 815 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: A 872 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8145 (pp) REVERT: A 1050 MET cc_start: 0.7432 (mmm) cc_final: 0.6576 (mtm) REVERT: A 1072 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: A 1132 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: A 1289 GLU cc_start: 0.8005 (mp0) cc_final: 0.7677 (mp0) REVERT: A 1420 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8042 (tppt) REVERT: B 70 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7106 (ptp-170) REVERT: B 134 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8878 (tt) REVERT: B 174 MET cc_start: 0.8458 (mtp) cc_final: 0.8192 (mtm) REVERT: B 216 LYS cc_start: 0.8643 (mttp) cc_final: 0.8254 (mtpt) REVERT: B 237 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: B 288 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7757 (mmtt) outliers start: 36 outliers final: 11 residues processed: 197 average time/residue: 0.7286 time to fit residues: 155.4689 Evaluate side-chains 190 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 0.0050 chunk 163 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 HIS A 680 HIS C 21 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102742 restraints weight = 15000.540| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.59 r_work: 0.3093 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13780 Z= 0.160 Angle : 0.639 12.219 18695 Z= 0.323 Chirality : 0.049 0.293 2078 Planarity : 0.004 0.048 2362 Dihedral : 9.631 151.968 1877 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 2.68 % Allowed : 11.54 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1641 helix: -0.76 (0.45), residues: 130 sheet: 0.40 (0.20), residues: 642 loop : -0.96 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1049 TYR 0.011 0.001 TYR A 288 PHE 0.013 0.001 PHE A1311 TRP 0.018 0.001 TRP B 273 HIS 0.006 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (13768) covalent geometry : angle 0.63807 / 0.32 (18686) hydrogen bonds : bond 0.04223 / 2.76 ( 438) hydrogen bonds : angle 6.14670 / 4.23 ( 1158) metal coordination : bond 0.00823 / 0.51 ( 12) metal coordination : angle 1.66884 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.520 Fit side-chains REVERT: A 67 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: A 162 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 584 MET cc_start: 0.8709 (ttt) cc_final: 0.8274 (ttt) REVERT: A 591 GLU cc_start: 0.7235 (mp0) cc_final: 0.6723 (pm20) REVERT: A 671 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5569 (tmmt) REVERT: A 815 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: A 860 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8234 (mmm-85) REVERT: A 872 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8129 (pp) REVERT: A 1050 MET cc_start: 0.7446 (mmm) cc_final: 0.6583 (mtm) REVERT: A 1132 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 1289 GLU cc_start: 0.7959 (mp0) cc_final: 0.7646 (mp0) REVERT: A 1348 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9105 (mp) REVERT: A 1352 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8477 (mm110) REVERT: A 1420 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8017 (tppt) REVERT: B 70 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7103 (ptp-170) REVERT: B 134 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8846 (tt) REVERT: B 174 MET cc_start: 0.8408 (mtp) cc_final: 0.8139 (mtm) REVERT: B 216 LYS cc_start: 0.8598 (mttp) cc_final: 0.8219 (mtpt) REVERT: B 237 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: B 279 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7284 (pt0) REVERT: B 371 GLU cc_start: 0.8172 (tp30) cc_final: 0.7941 (mm-30) outliers start: 39 outliers final: 14 residues processed: 198 average time/residue: 0.7066 time to fit residues: 151.5218 Evaluate side-chains 197 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS C 21 GLN B 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101378 restraints weight = 14849.058| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.58 r_work: 0.3079 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13780 Z= 0.191 Angle : 0.668 12.129 18695 Z= 0.336 Chirality : 0.050 0.306 2078 Planarity : 0.005 0.048 2362 Dihedral : 9.764 154.343 1877 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 2.40 % Allowed : 12.64 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1641 helix: -0.76 (0.45), residues: 130 sheet: 0.41 (0.20), residues: 637 loop : -0.98 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 702 TYR 0.014 0.001 TYR A 617 PHE 0.013 0.002 PHE A1311 TRP 0.019 0.002 TRP B 273 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (13768) covalent geometry : angle 0.66659 / 0.34 (18686) hydrogen bonds : bond 0.04387 / 2.86 ( 438) hydrogen bonds : angle 6.18803 / 4.27 ( 1158) metal coordination : bond 0.00880 / 0.59 ( 12) metal coordination : angle 1.74114 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.564 Fit side-chains REVERT: A 63 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.4553 (tmt-80) REVERT: A 162 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8469 (tp) REVERT: A 584 MET cc_start: 0.8718 (ttt) cc_final: 0.8318 (ttt) REVERT: A 591 GLU cc_start: 0.7264 (mp0) cc_final: 0.6823 (pm20) REVERT: A 815 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: A 860 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8258 (mmm-85) REVERT: A 872 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 1050 MET cc_start: 0.7447 (mmm) cc_final: 0.6713 (mtm) REVERT: A 1132 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: A 1289 GLU cc_start: 0.7992 (mp0) cc_final: 0.7685 (mp0) REVERT: A 1348 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9124 (mp) REVERT: A 1352 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8480 (mm110) REVERT: A 1420 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8025 (tppt) REVERT: B 70 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7111 (ptp-170) REVERT: B 134 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 174 MET cc_start: 0.8454 (mtp) cc_final: 0.8174 (mtm) REVERT: B 216 LYS cc_start: 0.8629 (mttp) cc_final: 0.8254 (mtpt) REVERT: B 237 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: B 288 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7627 (mmpt) REVERT: B 371 GLU cc_start: 0.8207 (tp30) cc_final: 0.7971 (mm-30) outliers start: 35 outliers final: 15 residues processed: 190 average time/residue: 0.7232 time to fit residues: 148.9980 Evaluate side-chains 195 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 119 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 153 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS C 21 GLN B 181 HIS B 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101400 restraints weight = 14891.702| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.58 r_work: 0.3073 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13780 Z= 0.187 Angle : 0.664 12.038 18695 Z= 0.335 Chirality : 0.049 0.311 2078 Planarity : 0.005 0.047 2362 Dihedral : 9.810 155.632 1877 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.48 % Favored : 94.39 % Rotamer: Outliers : 2.40 % Allowed : 12.98 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1641 helix: -0.78 (0.45), residues: 130 sheet: 0.45 (0.21), residues: 631 loop : -0.97 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 318 TYR 0.012 0.001 TYR A 288 PHE 0.013 0.002 PHE A1311 TRP 0.018 0.002 TRP B 273 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (13768) covalent geometry : angle 0.66329 / 0.33 (18686) hydrogen bonds : bond 0.04329 / 2.82 ( 438) hydrogen bonds : angle 6.17334 / 4.26 ( 1158) metal coordination : bond 0.00908 / 0.61 ( 12) metal coordination : angle 1.72656 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.538 Fit side-chains REVERT: A 63 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.4525 (tmt-80) REVERT: A 162 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 313 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7563 (mtm-85) REVERT: A 591 GLU cc_start: 0.7232 (mp0) cc_final: 0.6812 (pm20) REVERT: A 648 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 698 LEU cc_start: 0.8529 (mp) cc_final: 0.8229 (pp) REVERT: A 798 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7701 (tp-100) REVERT: A 815 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: A 860 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8214 (mmm-85) REVERT: A 872 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8120 (pp) REVERT: A 1050 MET cc_start: 0.7416 (mmm) cc_final: 0.6704 (mtm) REVERT: A 1072 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: A 1132 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: A 1289 GLU cc_start: 0.7999 (mp0) cc_final: 0.7695 (mp0) REVERT: A 1348 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9143 (mp) REVERT: A 1352 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8478 (mm110) REVERT: A 1420 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8033 (tppt) REVERT: B 70 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7121 (ptp-170) REVERT: B 134 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 174 MET cc_start: 0.8461 (mtp) cc_final: 0.8189 (mtm) REVERT: B 216 LYS cc_start: 0.8628 (mttp) cc_final: 0.8256 (mtpt) REVERT: B 237 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: B 288 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7692 (mmtt) outliers start: 35 outliers final: 15 residues processed: 186 average time/residue: 0.7055 time to fit residues: 142.1953 Evaluate side-chains 192 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 798 GLN Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 GLN C 21 GLN B 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101618 restraints weight = 14741.662| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.57 r_work: 0.3079 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13780 Z= 0.178 Angle : 0.655 11.913 18695 Z= 0.330 Chirality : 0.049 0.311 2078 Planarity : 0.004 0.048 2362 Dihedral : 9.788 156.482 1877 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 2.54 % Allowed : 13.05 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1641 helix: -0.76 (0.45), residues: 130 sheet: 0.44 (0.20), residues: 636 loop : -0.95 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.012 0.001 TYR A 288 PHE 0.013 0.002 PHE A1311 TRP 0.019 0.001 TRP B 273 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (13768) covalent geometry : angle 0.65368 / 0.33 (18686) hydrogen bonds : bond 0.04240 / 2.76 ( 438) hydrogen bonds : angle 6.14300 / 4.24 ( 1158) metal coordination : bond 0.00925 / 0.62 ( 12) metal coordination : angle 1.71931 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.529 Fit side-chains REVERT: A 63 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.4405 (tmt-80) REVERT: A 162 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 584 MET cc_start: 0.8672 (ttt) cc_final: 0.8311 (ttt) REVERT: A 593 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7334 (mtt) REVERT: A 798 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7745 (tp-100) REVERT: A 815 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: A 860 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8235 (mmm-85) REVERT: A 872 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8123 (pp) REVERT: A 1050 MET cc_start: 0.7344 (mmm) cc_final: 0.6694 (mtm) REVERT: A 1072 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: A 1132 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 1289 GLU cc_start: 0.7981 (mp0) cc_final: 0.7672 (mp0) REVERT: A 1348 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9149 (mp) REVERT: A 1352 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8485 (mm110) REVERT: A 1420 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8023 (tppt) REVERT: B 70 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7120 (ptp-170) REVERT: B 134 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8897 (tt) REVERT: B 174 MET cc_start: 0.8439 (mtp) cc_final: 0.8179 (mtm) REVERT: B 216 LYS cc_start: 0.8621 (mttp) cc_final: 0.8249 (mtpt) REVERT: B 237 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: B 288 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7714 (mmtm) outliers start: 37 outliers final: 14 residues processed: 189 average time/residue: 0.7055 time to fit residues: 144.5370 Evaluate side-chains 194 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 798 GLN Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 0.0270 chunk 115 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 680 HIS C 21 GLN B 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102255 restraints weight = 14953.614| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.58 r_work: 0.3087 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13780 Z= 0.165 Angle : 0.642 11.854 18695 Z= 0.323 Chirality : 0.048 0.299 2078 Planarity : 0.004 0.048 2362 Dihedral : 9.742 157.000 1877 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 2.27 % Allowed : 13.74 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1641 helix: -0.72 (0.45), residues: 130 sheet: 0.45 (0.20), residues: 635 loop : -0.94 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.014 0.001 TYR A 617 PHE 0.013 0.001 PHE A1311 TRP 0.019 0.001 TRP B 273 HIS 0.006 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (13768) covalent geometry : angle 0.64083 / 0.32 (18686) hydrogen bonds : bond 0.04119 / 2.68 ( 438) hydrogen bonds : angle 6.08235 / 4.20 ( 1158) metal coordination : bond 0.00927 / 0.62 ( 12) metal coordination : angle 1.67028 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.535 Fit side-chains REVERT: A 63 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.4331 (tmt-80) REVERT: A 162 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 584 MET cc_start: 0.8692 (ttt) cc_final: 0.8334 (ttt) REVERT: A 593 MET cc_start: 0.7627 (mtp) cc_final: 0.7341 (mtt) REVERT: A 798 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7614 (tp-100) REVERT: A 815 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: A 860 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8245 (mmm-85) REVERT: A 872 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8119 (pp) REVERT: A 1050 MET cc_start: 0.7357 (mmm) cc_final: 0.6699 (mtm) REVERT: A 1072 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: A 1289 GLU cc_start: 0.7948 (mp0) cc_final: 0.7722 (mp0) REVERT: A 1352 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8484 (mm110) REVERT: A 1420 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8026 (tppt) REVERT: B 70 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7112 (ptp-170) REVERT: B 134 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8895 (tt) REVERT: B 174 MET cc_start: 0.8393 (mtp) cc_final: 0.8145 (mtm) REVERT: B 216 LYS cc_start: 0.8615 (mttp) cc_final: 0.8244 (mtpt) REVERT: B 237 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: B 288 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7715 (mmtm) REVERT: B 371 GLU cc_start: 0.8340 (tp30) cc_final: 0.8110 (mm-30) outliers start: 33 outliers final: 13 residues processed: 186 average time/residue: 0.6979 time to fit residues: 140.9445 Evaluate side-chains 190 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 798 GLN Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 152 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 21 GLN B 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101293 restraints weight = 14825.162| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.57 r_work: 0.3075 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13780 Z= 0.190 Angle : 0.670 11.805 18695 Z= 0.336 Chirality : 0.049 0.318 2078 Planarity : 0.005 0.047 2362 Dihedral : 9.832 157.520 1877 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 1.99 % Allowed : 13.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1641 helix: -0.71 (0.45), residues: 130 sheet: 0.46 (0.20), residues: 634 loop : -0.96 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 958 TYR 0.012 0.001 TYR A 288 PHE 0.013 0.002 PHE A1311 TRP 0.018 0.002 TRP B 273 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (13768) covalent geometry : angle 0.66908 / 0.34 (18686) hydrogen bonds : bond 0.04287 / 2.79 ( 438) hydrogen bonds : angle 6.12991 / 4.23 ( 1158) metal coordination : bond 0.00930 / 0.64 ( 12) metal coordination : angle 1.77658 / 0.83 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.539 Fit side-chains REVERT: A 63 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.4321 (tmt-80) REVERT: A 162 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 584 MET cc_start: 0.8682 (ttt) cc_final: 0.8219 (ttt) REVERT: A 593 MET cc_start: 0.7650 (mtp) cc_final: 0.7368 (mtt) REVERT: A 798 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7653 (tp-100) REVERT: A 815 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: A 860 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8279 (mmm-85) REVERT: A 872 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8129 (pp) REVERT: A 1050 MET cc_start: 0.7364 (mmm) cc_final: 0.6703 (mtm) REVERT: A 1072 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: A 1289 GLU cc_start: 0.7978 (mp0) cc_final: 0.7752 (mp0) REVERT: A 1352 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8478 (mm110) REVERT: A 1420 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8045 (tppt) REVERT: B 70 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.7122 (ptp-170) REVERT: B 134 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8889 (tt) REVERT: B 174 MET cc_start: 0.8443 (mtp) cc_final: 0.8164 (mtm) REVERT: B 216 LYS cc_start: 0.8637 (mttp) cc_final: 0.8270 (mtpt) REVERT: B 237 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: B 288 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7701 (mmtt) REVERT: B 371 GLU cc_start: 0.8334 (tp30) cc_final: 0.8104 (mm-30) outliers start: 29 outliers final: 14 residues processed: 178 average time/residue: 0.7044 time to fit residues: 136.0250 Evaluate side-chains 186 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 798 GLN Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1352 GLN Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 66 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 21 GLN B 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101489 restraints weight = 14927.624| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.58 r_work: 0.3074 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13780 Z= 0.184 Angle : 0.662 11.922 18695 Z= 0.333 Chirality : 0.049 0.320 2078 Planarity : 0.004 0.044 2362 Dihedral : 9.825 157.583 1877 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 2.06 % Allowed : 13.94 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1641 helix: -0.73 (0.45), residues: 130 sheet: 0.44 (0.20), residues: 634 loop : -0.95 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 958 TYR 0.012 0.001 TYR A 288 PHE 0.013 0.002 PHE A1311 TRP 0.018 0.002 TRP B 273 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (13768) covalent geometry : angle 0.66092 / 0.33 (18686) hydrogen bonds : bond 0.04244 / 2.77 ( 438) hydrogen bonds : angle 6.11207 / 4.22 ( 1158) metal coordination : bond 0.00974 / 0.66 ( 12) metal coordination : angle 1.73737 / 0.81 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.58 seconds wall clock time: 82 minutes 8.60 seconds (4928.60 seconds total)