Starting phenix.real_space_refine on Sat Jul 4 07:02:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlq_41371/07_2026/8tlq_41371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlq_41371/07_2026/8tlq_41371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tlq_41371/07_2026/8tlq_41371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlq_41371/07_2026/8tlq_41371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tlq_41371/07_2026/8tlq_41371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlq_41371/07_2026/8tlq_41371.map" } resolution = 3.53 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= 0.004 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 29 5.49 5 S 82 5.16 5 C 12496 2.51 5 N 3256 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19219 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 9541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1283, 9541 Classifications: {'peptide': 1283} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 59, 'TRANS': 1223} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 934 Unresolved non-hydrogen angles: 1190 Unresolved non-hydrogen dihedrals: 708 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'ASP:plan': 50, 'GLU:plan': 58, 'GLN:plan1': 18, 'ASN:plan1': 18, 'PHE:plan': 3, 'ARG:plan': 17, 'TYR:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 537 Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1399 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 5 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 11, 'ASN:plan1': 6, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1705 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 7, 'GLN:plan1': 5, 'ASP:plan': 15, 'GLU:plan': 11, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 146 Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3260 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 24, 'ASN:plan1': 11, 'GLU:plan': 19, 'GLN:plan1': 8, 'ARG:plan': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 260 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 882 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1818 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 11, 'GLN:plan1': 9, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 135 Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 212 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 322 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 68 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 2, 'water': 32} Link IDs: {None: 33} Chain breaks: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9297 SG CYS A1473 40.113 60.169 92.457 1.00 56.04 S ATOM 9119 SG CYS A1449 43.892 54.936 92.487 1.00 53.21 S ATOM 9257 SG CYS A1468 37.481 54.051 94.304 1.00 49.71 S ATOM 9097 SG CYS A1446 38.578 55.227 88.079 1.00 52.81 S Time building chain proxies: 4.47, per 1000 atoms: 0.23 Number of scatterers: 19219 At special positions: 0 Unit cell: (87.658, 143.246, 180.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 82 16.00 P 29 15.00 O 3351 8.00 N 3256 7.00 C 12496 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1603 " pdb="FE3 SF4 A1603 " - pdb=" SG CYS A1468 " pdb="FE2 SF4 A1603 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1603 " - pdb=" SG CYS A1446 " pdb="FE1 SF4 A1603 " - pdb=" SG CYS A1473 " Number of angles added : 12 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 21 sheets defined 40.2% alpha, 14.0% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 95 through 117 removed outlier: 3.521A pdb=" N GLN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 306 through 322 removed outlier: 4.215A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 531 through 541 removed outlier: 4.146A pdb=" N ASN A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.527A pdb=" N ASP A 557 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.570A pdb=" N GLU A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 870 through 896 removed outlier: 3.569A pdb=" N LEU A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.758A pdb=" N VAL A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR A 916 " --> pdb=" O PHE A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 3.888A pdb=" N LYS A 923 " --> pdb=" O GLY A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 990 through 992 No H-bonds generated for 'chain 'A' and resid 990 through 992' Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1044 through 1067 Processing helix chain 'A' and resid 1071 through 1095 Processing helix chain 'A' and resid 1106 through 1131 removed outlier: 3.593A pdb=" N ASP A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1173 removed outlier: 4.259A pdb=" N SER A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 Processing helix chain 'A' and resid 1243 through 1261 removed outlier: 3.651A pdb=" N ILE A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1299 removed outlier: 3.635A pdb=" N VAL A1290 " --> pdb=" O PRO A1286 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1327 removed outlier: 3.913A pdb=" N ARG A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A1327 " --> pdb=" O LEU A1323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1327' Processing helix chain 'A' and resid 1329 through 1336 Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.651A pdb=" N LEU A1351 " --> pdb=" O ILE A1347 " (cutoff:3.500A) Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 4.386A pdb=" N TRP A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1373 " --> pdb=" O TRP A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1455 removed outlier: 3.877A pdb=" N LEU A1426 " --> pdb=" O SER A1422 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1468 Processing helix chain 'A' and resid 1473 through 1488 removed outlier: 3.791A pdb=" N TYR A1477 " --> pdb=" O CYS A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1502 removed outlier: 3.585A pdb=" N VAL A1492 " --> pdb=" O ASP A1488 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 removed outlier: 3.800A pdb=" N VAL D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.525A pdb=" N LYS D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.610A pdb=" N VAL D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 4.124A pdb=" N SER D 243 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.593A pdb=" N LYS E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.522A pdb=" N LYS E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 3.832A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.794A pdb=" N ASP E 157 " --> pdb=" O HIS E 154 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG E 158 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN E 159 " --> pdb=" O LEU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 159' Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.590A pdb=" N SER E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 0 through 9 Processing helix chain 'F' and resid 53 through 76 Processing helix chain 'F' and resid 92 through 96 removed outlier: 4.118A pdb=" N ILE F 96 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 227 through 241 Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.631A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 291 removed outlier: 3.602A pdb=" N LEU F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 325 Processing helix chain 'F' and resid 357 through 365 Processing helix chain 'F' and resid 391 through 405 Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.751A pdb=" N LYS G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 removed outlier: 3.535A pdb=" N PHE B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 229 through 239 removed outlier: 4.273A pdb=" N VAL B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 899 removed outlier: 4.398A pdb=" N GLY B 899 " --> pdb=" O ALA B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 921 Processing helix chain 'B' and resid 923 through 941 Processing helix chain 'B' and resid 950 through 961 Processing helix chain 'B' and resid 962 through 967 removed outlier: 4.411A pdb=" N ASN B 967 " --> pdb=" O ILE B 963 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.117A pdb=" N LEU A 27 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA A 64 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 70 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 268 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 72 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A 270 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A 74 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 removed outlier: 7.362A pdb=" N ILE A 938 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 146 " --> pdb=" O ILE A 938 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 177 through 179 removed outlier: 5.963A pdb=" N ALA D 143 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 140 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE D 79 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU D 142 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE D 77 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL D 144 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE D 75 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN D 146 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.274A pdb=" N TYR A 563 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA6, first strand: chain 'E' and resid 177 through 179 removed outlier: 5.861A pdb=" N ALA E 143 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.152A pdb=" N MET A 740 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 714 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR A 742 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 716 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER A 692 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS A 675 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 694 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU A 673 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP A 696 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A 671 " --> pdb=" O TRP A 696 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 670 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 965 through 967 removed outlier: 3.611A pdb=" N ALA A 965 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1190 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 975 " --> pdb=" O LYS A1180 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1180 " --> pdb=" O ASP A 975 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1138 through 1141 removed outlier: 6.239A pdb=" N VAL A1138 " --> pdb=" O TYR A1149 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1149 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1140 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A1185 " --> pdb=" O TYR A1201 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR A1201 " --> pdb=" O TYR A1185 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ARG A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.811A pdb=" N MET A 994 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A1037 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 996 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1006 through 1008 removed outlier: 3.606A pdb=" N ASN A1006 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A1013 " --> pdb=" O ASN A1006 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A1011 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 4.305A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A1308 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AB6, first strand: chain 'F' and resid 23 through 24 removed outlier: 5.934A pdb=" N ARG F 23 " --> pdb=" O LYS G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 88 through 89 removed outlier: 8.529A pdb=" N PHE F 185 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 156 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 88 through 89 removed outlier: 3.667A pdb=" N GLY F 106 " --> pdb=" O VAL F 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC1, first strand: chain 'F' and resid 336 through 338 removed outlier: 3.552A pdb=" N ASN F 337 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER F 295 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS F 213 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU F 258 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 215 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 20 " --> pdb=" O PHE G 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 343 through 347 removed outlier: 3.526A pdb=" N TYR F 343 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP F 351 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE F 437 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU F 353 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA F 439 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL F 355 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLN F 441 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN F 440 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.475A pdb=" N ILE B 171 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 210 " --> pdb=" O VAL B 227 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 5.95 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 7977 1.40 - 1.59: 11515 1.59 - 1.77: 54 1.77 - 1.96: 107 1.96 - 2.14: 12 Bond restraints: 19665 Sorted by residual: bond pdb=" O3B DCP A1602 " pdb=" PG DCP A1602 " ideal model delta sigma weight residual 1.746 1.600 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" S1 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.104 0.176 3.00e-02 1.11e+03 3.45e+01 bond pdb=" S1 SF4 A1603 " pdb="FE3 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.124 0.156 3.00e-02 1.11e+03 2.69e+01 bond pdb=" S3 SF4 A1603 " pdb="FE2 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.68e+01 bond pdb=" S2 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.68e+01 ... (remaining 19660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 26780 3.38 - 6.77: 45 6.77 - 10.15: 3 10.15 - 13.54: 1 13.54 - 16.92: 25 Bond angle restraints: 26854 Sorted by residual: angle pdb="FE3 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.62 -16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE2 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.49 -16.79 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE1 SF4 A1603 " pdb=" S2 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.43 -16.73 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1603 " pdb=" S3 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.39 -16.69 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1603 " pdb=" S4 SF4 A1603 " pdb="FE3 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.34 -16.64 1.50e+00 4.44e-01 1.23e+02 ... (remaining 26849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10002 17.80 - 35.61: 1135 35.61 - 53.41: 399 53.41 - 71.21: 63 71.21 - 89.02: 13 Dihedral angle restraints: 11612 sinusoidal: 4192 harmonic: 7420 Sorted by residual: dihedral pdb=" CG ARG A1324 " pdb=" CD ARG A1324 " pdb=" NE ARG A1324 " pdb=" CZ ARG A1324 " ideal model delta sinusoidal sigma weight residual 180.00 -135.95 -44.05 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU E 6 " pdb=" CG GLU E 6 " pdb=" CD GLU E 6 " pdb=" OE1 GLU E 6 " ideal model delta sinusoidal sigma weight residual 0.00 87.23 -87.23 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA HIS F 316 " pdb=" C HIS F 316 " pdb=" N LYS F 317 " pdb=" CA LYS F 317 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 11609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.047: 3137 4.047 - 8.095: 0 8.095 - 12.142: 0 12.142 - 16.190: 0 16.190 - 20.237: 4 Chirality restraints: 3141 Sorted by residual: chirality pdb="FE3 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb=" S2 SF4 A1603 " pdb=" S4 SF4 A1603 " both_signs ideal model delta sigma weight residual False -10.55 9.68 -20.24 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE1 SF4 A1603 " pdb=" S2 SF4 A1603 " pdb=" S3 SF4 A1603 " pdb=" S4 SF4 A1603 " both_signs ideal model delta sigma weight residual False -10.55 9.61 -20.16 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE2 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb=" S3 SF4 A1603 " pdb=" S4 SF4 A1603 " both_signs ideal model delta sigma weight residual False 10.55 -9.60 20.15 2.00e-01 2.50e+01 1.02e+04 ... (remaining 3138 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 28 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO D 29 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 922 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ASN B 922 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN B 922 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 923 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1352 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A1353 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1353 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1353 " -0.021 5.00e-02 4.00e+02 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4072 2.78 - 3.31: 17544 3.31 - 3.84: 31863 3.84 - 4.37: 34104 4.37 - 4.90: 61923 Nonbonded interactions: 149506 Sorted by model distance: nonbonded pdb=" OH TYR A 613 " pdb=" OD1 ASP E 136 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP A1144 " pdb="CA CA A1601 " model vdw 2.307 3.250 nonbonded pdb=" OH TYR B 130 " pdb=" OE1 GLU B 138 " model vdw 2.331 3.040 nonbonded pdb="CA CA A1601 " pdb=" O2G DCP A1602 " model vdw 2.343 3.250 nonbonded pdb=" O PHE A 976 " pdb="CA CA A1601 " model vdw 2.348 3.250 ... (remaining 149501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 27.780 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.005 0.176 19669 Z= 0.209 Angle : 0.702 16.930 26866 Z= 0.406 Chirality : 0.720 20.237 3141 Planarity : 0.003 0.062 3258 Dihedral : 17.339 89.016 6784 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.13 % Allowed : 24.43 % Favored : 75.44 % 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: 1.03 (0.18), residues: 2468 helix: 2.54 (0.17), residues: 933 sheet: 0.45 (0.30), residues: 324 loop : -0.78 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 884 TYR 0.018 0.001 TYR B 973 PHE 0.009 0.001 PHE A 39 TRP 0.017 0.001 TRP F 103 HIS 0.002 0.000 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (19665) covalent geometry : angle 0.65689 / 0.41 (26854) hydrogen bonds : bond 0.17135 / 11.33 ( 882) hydrogen bonds : angle 6.29789 / 4.55 ( 2532) metal coordination : bond 0.00061 / 0.03 ( 4) metal coordination : angle 11.78462 / 6.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.752 Fit side-chains REVERT: G 12 LYS cc_start: 0.8567 (tptm) cc_final: 0.8063 (tppt) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1083 time to fit residues: 40.7671 Evaluate side-chains 217 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN A1082 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095667 restraints weight = 34733.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098235 restraints weight = 20248.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099957 restraints weight = 14202.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101117 restraints weight = 11213.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101666 restraints weight = 9517.575| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.269 19669 Z= 0.270 Angle : 1.396 51.652 26866 Z= 0.795 Chirality : 0.229 6.539 3141 Planarity : 0.004 0.050 3258 Dihedral : 9.831 71.182 2981 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.47 % Allowed : 23.61 % Favored : 73.92 % 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: 0.88 (0.17), residues: 2468 helix: 2.40 (0.17), residues: 941 sheet: 0.17 (0.29), residues: 326 loop : -0.81 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 118 TYR 0.016 0.001 TYR A1201 PHE 0.014 0.001 PHE E 215 TRP 0.014 0.001 TRP F 103 HIS 0.006 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.27 (19665) covalent geometry : angle 1.22720 / 0.79 (26854) hydrogen bonds : bond 0.03959 / 2.69 ( 882) hydrogen bonds : angle 4.77851 / 3.43 ( 2532) metal coordination : bond 0.06221 / 3.19 ( 4) metal coordination : angle 31.55736 / 19.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.773 Fit side-chains REVERT: A 601 PHE cc_start: 0.8473 (m-80) cc_final: 0.8271 (m-80) REVERT: G 65 ILE cc_start: 0.9230 (mm) cc_final: 0.8873 (mt) REVERT: B 913 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8415 (ttmm) outliers start: 39 outliers final: 25 residues processed: 246 average time/residue: 0.1103 time to fit residues: 45.2739 Evaluate side-chains 232 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1082 GLN Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 912 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 247 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1348 ASN D 214 GLN E 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094894 restraints weight = 34563.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097481 restraints weight = 19953.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099221 restraints weight = 13935.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100369 restraints weight = 10937.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101156 restraints weight = 9252.074| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 19669 Z= 0.251 Angle : 1.381 50.745 26866 Z= 0.787 Chirality : 0.230 6.436 3141 Planarity : 0.003 0.048 3258 Dihedral : 9.834 70.575 2981 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.91 % Allowed : 23.48 % Favored : 73.61 % 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: 0.78 (0.17), residues: 2468 helix: 2.36 (0.17), residues: 939 sheet: -0.14 (0.29), residues: 333 loop : -0.82 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 181 TYR 0.012 0.001 TYR D 16 PHE 0.014 0.001 PHE E 215 TRP 0.014 0.001 TRP F 103 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.25 (19665) covalent geometry : angle 1.21389 / 0.79 (26854) hydrogen bonds : bond 0.03871 / 2.65 ( 882) hydrogen bonds : angle 4.46398 / 3.21 ( 2532) metal coordination : bond 0.04888 / 2.44 ( 4) metal coordination : angle 31.16895 / 19.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.727 Fit side-chains REVERT: A 601 PHE cc_start: 0.8561 (m-80) cc_final: 0.8360 (m-80) REVERT: A 1050 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8603 (mm) REVERT: F 399 MET cc_start: 0.8586 (mmt) cc_final: 0.7676 (mtt) REVERT: G 65 ILE cc_start: 0.9218 (mm) cc_final: 0.8867 (mt) outliers start: 46 outliers final: 26 residues processed: 254 average time/residue: 0.1171 time to fit residues: 49.4807 Evaluate side-chains 235 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 98 optimal weight: 0.0010 chunk 20 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN D 214 GLN G 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091628 restraints weight = 34389.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093946 restraints weight = 20791.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095508 restraints weight = 14992.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096409 restraints weight = 12041.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097224 restraints weight = 10476.736| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 19669 Z= 0.271 Angle : 1.403 50.615 26866 Z= 0.796 Chirality : 0.229 6.342 3141 Planarity : 0.004 0.050 3258 Dihedral : 9.987 70.380 2981 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.05 % Allowed : 22.41 % Favored : 73.54 % 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 (0.17), residues: 2468 helix: 2.20 (0.17), residues: 936 sheet: -0.43 (0.28), residues: 339 loop : -0.87 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 118 TYR 0.017 0.001 TYR D 34 PHE 0.017 0.002 PHE A 528 TRP 0.015 0.001 TRP F 103 HIS 0.008 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.27 (19665) covalent geometry : angle 1.23193 / 0.79 (26854) hydrogen bonds : bond 0.03877 / 2.69 ( 882) hydrogen bonds : angle 4.39305 / 3.16 ( 2532) metal coordination : bond 0.02298 / 1.14 ( 4) metal coordination : angle 31.78609 / 19.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 0.744 Fit side-chains REVERT: D 30 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: F 399 MET cc_start: 0.8606 (mmt) cc_final: 0.7706 (mtt) REVERT: G 65 ILE cc_start: 0.9281 (mm) cc_final: 0.8919 (mt) outliers start: 64 outliers final: 45 residues processed: 263 average time/residue: 0.1135 time to fit residues: 49.2157 Evaluate side-chains 249 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1499 ILE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 152 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 214 GLN G 53 ASN B 183 GLN B 185 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093329 restraints weight = 34209.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095853 restraints weight = 19770.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097541 restraints weight = 13899.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098555 restraints weight = 10959.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099426 restraints weight = 9399.406| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 19669 Z= 0.222 Angle : 1.373 50.480 26866 Z= 0.784 Chirality : 0.229 6.341 3141 Planarity : 0.003 0.045 3258 Dihedral : 9.841 70.110 2981 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.53 % Allowed : 24.56 % Favored : 72.91 % 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: 0.69 (0.18), residues: 2468 helix: 2.37 (0.17), residues: 939 sheet: -0.49 (0.29), residues: 331 loop : -0.84 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 118 TYR 0.014 0.001 TYR E 16 PHE 0.015 0.001 PHE E 215 TRP 0.013 0.001 TRP F 103 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.22 (19665) covalent geometry : angle 1.20391 / 0.78 (26854) hydrogen bonds : bond 0.03344 / 2.34 ( 882) hydrogen bonds : angle 4.19534 / 3.02 ( 2532) metal coordination : bond 0.02794 / 1.39 ( 4) metal coordination : angle 31.30362 / 19.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.742 Fit side-chains REVERT: A 984 MET cc_start: 0.8587 (mmm) cc_final: 0.8328 (mmm) REVERT: A 1050 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (mm) REVERT: E 27 TYR cc_start: 0.8830 (m-80) cc_final: 0.8541 (m-10) REVERT: F 399 MET cc_start: 0.8576 (mmt) cc_final: 0.7765 (mtt) REVERT: F 405 TRP cc_start: 0.8615 (m-10) cc_final: 0.8365 (m-10) REVERT: G 65 ILE cc_start: 0.9233 (mm) cc_final: 0.8891 (mt) outliers start: 40 outliers final: 28 residues processed: 251 average time/residue: 0.1102 time to fit residues: 46.0806 Evaluate side-chains 236 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 228 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093258 restraints weight = 34127.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095615 restraints weight = 20580.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097175 restraints weight = 14769.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098252 restraints weight = 11824.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098808 restraints weight = 10104.186| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 19669 Z= 0.230 Angle : 1.377 50.522 26866 Z= 0.785 Chirality : 0.229 6.337 3141 Planarity : 0.003 0.047 3258 Dihedral : 9.824 70.322 2981 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.59 % Allowed : 24.49 % Favored : 72.91 % 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: 0.68 (0.18), residues: 2468 helix: 2.41 (0.17), residues: 935 sheet: -0.50 (0.28), residues: 337 loop : -0.87 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.016 0.001 TYR D 34 PHE 0.014 0.001 PHE E 215 TRP 0.014 0.001 TRP F 103 HIS 0.005 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.23 (19665) covalent geometry : angle 1.20694 / 0.78 (26854) hydrogen bonds : bond 0.03341 / 2.33 ( 882) hydrogen bonds : angle 4.16973 / 3.00 ( 2532) metal coordination : bond 0.02446 / 1.22 ( 4) metal coordination : angle 31.36138 / 19.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.660 Fit side-chains REVERT: A 984 MET cc_start: 0.8629 (mmm) cc_final: 0.8386 (mmm) REVERT: A 1050 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8662 (mm) REVERT: E 27 TYR cc_start: 0.8814 (m-80) cc_final: 0.8598 (m-80) REVERT: F 399 MET cc_start: 0.8572 (mmt) cc_final: 0.7733 (mtt) REVERT: F 405 TRP cc_start: 0.8599 (m-10) cc_final: 0.8366 (m-10) REVERT: G 65 ILE cc_start: 0.9267 (mm) cc_final: 0.8904 (mt) outliers start: 41 outliers final: 34 residues processed: 242 average time/residue: 0.1066 time to fit residues: 42.7586 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 52 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 99 GLN B 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091537 restraints weight = 34540.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093894 restraints weight = 21066.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095477 restraints weight = 15200.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096534 restraints weight = 12203.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097130 restraints weight = 10487.907| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 19669 Z= 0.245 Angle : 1.386 50.544 26866 Z= 0.789 Chirality : 0.229 6.333 3141 Planarity : 0.003 0.049 3258 Dihedral : 9.903 70.318 2981 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.67 % Allowed : 23.54 % Favored : 72.78 % 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: 0.58 (0.17), residues: 2468 helix: 2.32 (0.17), residues: 937 sheet: -0.65 (0.29), residues: 331 loop : -0.91 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 240 TYR 0.015 0.001 TYR F 436 PHE 0.014 0.001 PHE E 215 TRP 0.016 0.001 TRP F 103 HIS 0.005 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.24 (19665) covalent geometry : angle 1.21648 / 0.79 (26854) hydrogen bonds : bond 0.03499 / 2.44 ( 882) hydrogen bonds : angle 4.19152 / 3.02 ( 2532) metal coordination : bond 0.02385 / 1.19 ( 4) metal coordination : angle 31.48070 / 19.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.589 Fit side-chains REVERT: A 984 MET cc_start: 0.8677 (mmm) cc_final: 0.8431 (mmm) REVERT: A 1050 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8696 (mm) REVERT: E 27 TYR cc_start: 0.8883 (m-80) cc_final: 0.8661 (m-80) REVERT: F 399 MET cc_start: 0.8614 (mmt) cc_final: 0.7773 (mtt) REVERT: G 65 ILE cc_start: 0.9276 (mm) cc_final: 0.8922 (mt) outliers start: 58 outliers final: 45 residues processed: 249 average time/residue: 0.1031 time to fit residues: 42.8791 Evaluate side-chains 243 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 131 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 233 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 145 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090252 restraints weight = 34409.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092551 restraints weight = 21108.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094109 restraints weight = 15322.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095157 restraints weight = 12334.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095575 restraints weight = 10614.896| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 19669 Z= 0.261 Angle : 1.395 50.565 26866 Z= 0.793 Chirality : 0.229 6.337 3141 Planarity : 0.004 0.051 3258 Dihedral : 10.002 70.424 2981 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.35 % Allowed : 23.73 % Favored : 72.91 % 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: 0.46 (0.17), residues: 2468 helix: 2.22 (0.17), residues: 939 sheet: -0.78 (0.29), residues: 320 loop : -0.96 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.013 0.001 TYR D 16 PHE 0.015 0.001 PHE E 215 TRP 0.016 0.001 TRP F 103 HIS 0.014 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.26 (19665) covalent geometry : angle 1.22518 / 0.79 (26854) hydrogen bonds : bond 0.03732 / 2.61 ( 882) hydrogen bonds : angle 4.24972 / 3.06 ( 2532) metal coordination : bond 0.02413 / 1.21 ( 4) metal coordination : angle 31.63183 / 19.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.604 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8746 (mm) REVERT: E 27 TYR cc_start: 0.8957 (m-80) cc_final: 0.8738 (m-80) REVERT: F 103 TRP cc_start: 0.8872 (p-90) cc_final: 0.8641 (p-90) REVERT: F 399 MET cc_start: 0.8664 (mmt) cc_final: 0.7759 (mtt) REVERT: G 65 ILE cc_start: 0.9268 (mm) cc_final: 0.8929 (mt) outliers start: 53 outliers final: 44 residues processed: 242 average time/residue: 0.1033 time to fit residues: 41.7141 Evaluate side-chains 239 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 243 optimal weight: 7.9990 chunk 201 optimal weight: 0.2980 chunk 249 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN G 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090335 restraints weight = 34094.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092617 restraints weight = 20858.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094161 restraints weight = 15167.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095210 restraints weight = 12230.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095790 restraints weight = 10533.578| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 19669 Z= 0.251 Angle : 1.391 50.551 26866 Z= 0.791 Chirality : 0.229 6.338 3141 Planarity : 0.003 0.049 3258 Dihedral : 10.005 70.181 2981 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.91 % Allowed : 24.87 % Favored : 72.22 % 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: 0.45 (0.17), residues: 2468 helix: 2.18 (0.17), residues: 944 sheet: -0.85 (0.29), residues: 321 loop : -0.93 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.014 0.001 TYR F 436 PHE 0.015 0.001 PHE E 215 TRP 0.016 0.001 TRP F 103 HIS 0.010 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.25 (19665) covalent geometry : angle 1.22133 / 0.79 (26854) hydrogen bonds : bond 0.03628 / 2.54 ( 882) hydrogen bonds : angle 4.22638 / 3.04 ( 2532) metal coordination : bond 0.02380 / 1.19 ( 4) metal coordination : angle 31.56315 / 19.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.674 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8724 (mm) REVERT: D 30 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: E 27 TYR cc_start: 0.8929 (m-80) cc_final: 0.8661 (m-80) REVERT: F 103 TRP cc_start: 0.8870 (p-90) cc_final: 0.8649 (p-90) REVERT: F 399 MET cc_start: 0.8675 (mmt) cc_final: 0.7764 (mtt) REVERT: G 65 ILE cc_start: 0.9278 (mm) cc_final: 0.8934 (mt) outliers start: 46 outliers final: 39 residues processed: 235 average time/residue: 0.1040 time to fit residues: 41.0091 Evaluate side-chains 231 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1499 ILE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088090 restraints weight = 34526.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090348 restraints weight = 21270.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091863 restraints weight = 15521.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092745 restraints weight = 12556.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093526 restraints weight = 10981.778| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 19669 Z= 0.293 Angle : 1.417 50.634 26866 Z= 0.802 Chirality : 0.230 6.340 3141 Planarity : 0.004 0.054 3258 Dihedral : 10.204 69.906 2981 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.10 % Allowed : 24.68 % Favored : 72.22 % 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: 0.23 (0.17), residues: 2468 helix: 1.97 (0.17), residues: 943 sheet: -0.99 (0.29), residues: 323 loop : -1.02 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.014 0.001 TYR D 16 PHE 0.019 0.002 PHE D 40 TRP 0.015 0.001 TRP F 103 HIS 0.013 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.29 (19665) covalent geometry : angle 1.24616 / 0.80 (26854) hydrogen bonds : bond 0.04111 / 2.87 ( 882) hydrogen bonds : angle 4.38972 / 3.16 ( 2532) metal coordination : bond 0.02462 / 1.23 ( 4) metal coordination : angle 31.95887 / 19.54 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.681 Fit side-chains REVERT: A 1050 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 30 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: D 115 ASP cc_start: 0.7702 (m-30) cc_final: 0.7397 (m-30) REVERT: F 103 TRP cc_start: 0.8899 (p-90) cc_final: 0.8679 (p-90) REVERT: F 399 MET cc_start: 0.8717 (mmt) cc_final: 0.7804 (mtt) REVERT: G 65 ILE cc_start: 0.9280 (mm) cc_final: 0.8947 (mt) outliers start: 49 outliers final: 41 residues processed: 239 average time/residue: 0.1033 time to fit residues: 40.9760 Evaluate side-chains 237 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1499 ILE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 133 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090890 restraints weight = 34542.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093239 restraints weight = 20865.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094758 restraints weight = 15010.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095801 restraints weight = 12081.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096442 restraints weight = 10384.218| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 19669 Z= 0.225 Angle : 1.383 50.480 26866 Z= 0.788 Chirality : 0.229 6.339 3141 Planarity : 0.003 0.044 3258 Dihedral : 9.988 69.581 2981 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.34 % Allowed : 25.38 % Favored : 72.28 % 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: 0.42 (0.17), residues: 2468 helix: 2.22 (0.17), residues: 943 sheet: -0.92 (0.29), residues: 321 loop : -0.98 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 936 TYR 0.012 0.001 TYR E 73 PHE 0.015 0.001 PHE E 215 TRP 0.018 0.001 TRP F 103 HIS 0.017 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.22 (19665) covalent geometry : angle 1.21415 / 0.79 (26854) hydrogen bonds : bond 0.03429 / 2.42 ( 882) hydrogen bonds : angle 4.17317 / 3.00 ( 2532) metal coordination : bond 0.02446 / 1.22 ( 4) metal coordination : angle 31.37265 / 19.10 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.77 seconds wall clock time: 44 minutes 34.49 seconds (2674.49 seconds total)