Starting phenix.real_space_refine on Fri Aug 7 03:30:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlq_41371/08_2026/8tlq_41371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlq_41371/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tlq_41371/08_2026/8tlq_41371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlq_41371/08_2026/8tlq_41371.map" model { file = "/net/cci-nas-00/data/ceres_data/8tlq_41371/08_2026/8tlq_41371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlq_41371/08_2026/8tlq_41371.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 69 Unusual residues: {' CA': 1, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 3, 'water': 32} Link IDs: {None: 34} 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: 4.07, per 1000 atoms: 0.21 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: 1.71 Conformation dependent library (CDL) restraints added in 785.3 milliseconds 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: 2.35 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: 4.26 Time building geometry restraints manager: 2.20 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 2.510 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 2.510 nonbonded pdb=" O PHE A 976 " pdb="CA CA A1601 " model vdw 2.348 2.510 ... (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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- 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 : 0.703 16.930 26866 Z= 0.407 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 0.65712 / 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 : 0.747 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: 0.1074 time to fit residues: 40.4362 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 : 0.616 ------------------------------------------------------------------------------- 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 E 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095424 restraints weight = 34684.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097918 restraints weight = 20442.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099598 restraints weight = 14514.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100581 restraints weight = 11521.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101442 restraints weight = 9949.294| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.270 19669 Z= 0.270 Angle : 1.398 51.405 26866 Z= 0.794 Chirality : 0.230 6.589 3141 Planarity : 0.004 0.049 3258 Dihedral : 9.533 70.980 2981 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.59 % Allowed : 23.67 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2468 helix: 2.36 (0.17), residues: 941 sheet: 0.12 (0.29), residues: 326 loop : -0.80 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1447 TYR 0.018 0.001 TYR A1201 PHE 0.016 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 1.22732 / 0.79 (26854) hydrogen bonds : bond 0.03979 / 2.70 ( 882) hydrogen bonds : angle 4.74417 / 3.41 ( 2532) metal coordination : bond 0.06409 / 3.28 ( 4) metal coordination : angle 31.69374 / 19.16 ( 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 260 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.741 Fit side-chains REVERT: A 318 MET cc_start: 0.8376 (ttp) cc_final: 0.7881 (ttm) REVERT: G 65 ILE cc_start: 0.9233 (mm) cc_final: 0.8876 (mt) REVERT: B 913 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8429 (ttmm) outliers start: 41 outliers final: 25 residues processed: 248 average time/residue: 0.1092 time to fit residues: 45.1796 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 : 0.704 ------------------------------------------------------------------------------- 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 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 335 ILE 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: 4.9990 chunk 129 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1082 GLN A1348 ASN D 214 GLN G 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092487 restraints weight = 34578.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094845 restraints weight = 20909.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096409 restraints weight = 15116.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097300 restraints weight = 12140.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098132 restraints weight = 10591.351| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.257 19669 Z= 0.271 Angle : 1.390 50.957 26866 Z= 0.793 Chirality : 0.231 6.475 3141 Planarity : 0.004 0.049 3258 Dihedral : 9.751 69.996 2981 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.48 % Allowed : 23.16 % Favored : 73.35 % 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: 0.66 (0.17), residues: 2468 helix: 2.25 (0.17), residues: 936 sheet: -0.31 (0.28), residues: 338 loop : -0.83 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 936 TYR 0.014 0.001 TYR D 16 PHE 0.025 0.002 PHE A 601 TRP 0.015 0.001 TRP F 103 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.27 (19665) covalent geometry : angle 1.22444 / 0.79 (26854) hydrogen bonds : bond 0.04238 / 2.92 ( 882) hydrogen bonds : angle 4.47151 / 3.22 ( 2532) metal coordination : bond 0.05752 / 2.86 ( 4) metal coordination : angle 31.18541 / 19.15 ( 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 275 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.629 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8681 (mm) REVERT: F 399 MET cc_start: 0.8526 (mmt) cc_final: 0.7652 (mtt) REVERT: G 65 ILE cc_start: 0.9268 (mm) cc_final: 0.8875 (mt) outliers start: 55 outliers final: 33 residues processed: 258 average time/residue: 0.1089 time to fit residues: 46.4818 Evaluate side-chains 238 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 807 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 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 134 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 F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL 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 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 6 SER Chi-restraints excluded: chain G residue 67 ILE 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: 4.9990 chunk 20 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 117 optimal weight: 0.0570 chunk 181 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A1082 GLN D 214 GLN E 99 GLN G 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090396 restraints weight = 34473.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092722 restraints weight = 20981.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094245 restraints weight = 15185.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095299 restraints weight = 12253.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095889 restraints weight = 10517.148| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 19669 Z= 0.284 Angle : 1.411 50.647 26866 Z= 0.799 Chirality : 0.229 6.324 3141 Planarity : 0.004 0.053 3258 Dihedral : 9.917 69.996 2981 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.92 % Allowed : 22.66 % Favored : 73.42 % 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: 0.47 (0.17), residues: 2468 helix: 2.13 (0.17), residues: 935 sheet: -0.54 (0.28), residues: 339 loop : -0.92 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.019 0.001 TYR D 34 PHE 0.017 0.002 PHE E 215 TRP 0.015 0.001 TRP F 103 HIS 0.010 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.28 (19665) covalent geometry : angle 1.23922 / 0.80 (26854) hydrogen bonds : bond 0.03927 / 2.73 ( 882) hydrogen bonds : angle 4.44459 / 3.20 ( 2532) metal coordination : bond 0.02024 / 1.00 ( 4) metal coordination : angle 31.98957 / 19.49 ( 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 272 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.817 Fit side-chains REVERT: E 27 TYR cc_start: 0.8795 (m-80) cc_final: 0.8550 (m-10) REVERT: F 399 MET cc_start: 0.8618 (mmt) cc_final: 0.7719 (mtt) REVERT: G 65 ILE cc_start: 0.9281 (mm) cc_final: 0.8937 (mt) outliers start: 62 outliers final: 45 residues processed: 257 average time/residue: 0.1262 time to fit residues: 53.7011 Evaluate side-chains 245 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 717 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 THR 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 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 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 62 ILE 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 150 LEU 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 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 352 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: 1.9990 chunk 92 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 194 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 191 optimal weight: 0.4980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1082 GLN D 214 GLN E 2 ASN B 185 HIS B 948 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093933 restraints weight = 34001.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096352 restraints weight = 20514.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097965 restraints weight = 14675.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098892 restraints weight = 11706.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099747 restraints weight = 10146.555| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2064 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= 0.220 Angle : 1.375 50.490 26866 Z= 0.784 Chirality : 0.229 6.344 3141 Planarity : 0.003 0.045 3258 Dihedral : 9.723 69.550 2981 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.72 % Allowed : 23.86 % Favored : 73.42 % 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: 0.66 (0.18), residues: 2468 helix: 2.40 (0.17), residues: 934 sheet: -0.56 (0.29), residues: 329 loop : -0.88 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 936 TYR 0.014 0.001 TYR E 16 PHE 0.014 0.001 PHE E 215 TRP 0.014 0.001 TRP F 103 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.22 (19665) covalent geometry : angle 1.20603 / 0.78 (26854) hydrogen bonds : bond 0.03331 / 2.33 ( 882) hydrogen bonds : angle 4.22009 / 3.04 ( 2532) metal coordination : bond 0.02964 / 1.48 ( 4) metal coordination : angle 31.31649 / 19.06 ( 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 262 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.940 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (mm) REVERT: D 30 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: E 27 TYR cc_start: 0.8778 (m-80) cc_final: 0.8552 (m-10) REVERT: F 399 MET cc_start: 0.8564 (mmt) cc_final: 0.7897 (mtt) REVERT: F 405 TRP cc_start: 0.8604 (m-10) cc_final: 0.8392 (m-10) REVERT: G 65 ILE cc_start: 0.9265 (mm) cc_final: 0.8886 (mt) outliers start: 43 outliers final: 29 residues processed: 252 average time/residue: 0.1202 time to fit residues: 51.1156 Evaluate side-chains 243 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 807 THR 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 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 30 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE 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 335 ILE 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 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: 10.0000 chunk 122 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 173 optimal weight: 0.0020 chunk 184 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN E 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091572 restraints weight = 34331.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093913 restraints weight = 20801.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095478 restraints weight = 14974.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096383 restraints weight = 12003.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097182 restraints weight = 10440.183| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2218 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= 0.243 Angle : 1.385 50.547 26866 Z= 0.788 Chirality : 0.229 6.336 3141 Planarity : 0.003 0.049 3258 Dihedral : 9.780 69.864 2981 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.35 % Allowed : 23.48 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2468 helix: 2.34 (0.17), residues: 936 sheet: -0.63 (0.28), residues: 337 loop : -0.90 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 240 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 0.004 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.24 (19665) covalent geometry : angle 1.21504 / 0.79 (26854) hydrogen bonds : bond 0.03489 / 2.44 ( 882) hydrogen bonds : angle 4.22226 / 3.04 ( 2532) metal coordination : bond 0.02437 / 1.22 ( 4) metal coordination : angle 31.49317 / 19.21 ( 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 258 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.745 Fit side-chains REVERT: A 984 MET cc_start: 0.8673 (mmm) cc_final: 0.8396 (mmm) REVERT: A 1050 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8680 (mm) REVERT: D 30 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: E 27 TYR cc_start: 0.8862 (m-80) cc_final: 0.8635 (m-80) REVERT: F 399 MET cc_start: 0.8598 (mmt) cc_final: 0.7775 (mtt) REVERT: G 65 ILE cc_start: 0.9280 (mm) cc_final: 0.8921 (mt) outliers start: 53 outliers final: 40 residues processed: 246 average time/residue: 0.1026 time to fit residues: 42.4761 Evaluate side-chains 241 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 760 ASP Chi-restraints excluded: chain A residue 807 THR 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 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 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 E residue 131 LEU Chi-restraints excluded: chain E residue 139 ILE 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 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 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 919 CYS 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: 7.9990 chunk 147 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 169 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.109657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.092997 restraints weight = 34145.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095389 restraints weight = 20546.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096997 restraints weight = 14740.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098060 restraints weight = 11777.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098681 restraints weight = 10102.980| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2235 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= 0.227 Angle : 1.378 50.504 26866 Z= 0.785 Chirality : 0.229 6.342 3141 Planarity : 0.003 0.047 3258 Dihedral : 9.739 69.831 2981 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.29 % Allowed : 23.80 % 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: 0.64 (0.18), residues: 2468 helix: 2.39 (0.17), residues: 937 sheet: -0.64 (0.28), residues: 337 loop : -0.88 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.012 0.001 TYR F 436 PHE 0.014 0.001 PHE E 215 TRP 0.015 0.001 TRP F 103 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.23 (19665) covalent geometry : angle 1.20834 / 0.78 (26854) hydrogen bonds : bond 0.03300 / 2.31 ( 882) hydrogen bonds : angle 4.13710 / 2.98 ( 2532) metal coordination : bond 0.02429 / 1.21 ( 4) metal coordination : angle 31.37461 / 19.12 ( 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 264 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 0.766 Fit side-chains REVERT: A 984 MET cc_start: 0.8645 (mmm) cc_final: 0.8391 (mmm) REVERT: A 1050 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8656 (mm) REVERT: D 30 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: E 27 TYR cc_start: 0.8858 (m-80) cc_final: 0.8642 (m-80) REVERT: F 399 MET cc_start: 0.8599 (mmt) cc_final: 0.7941 (mtt) REVERT: G 65 ILE cc_start: 0.9271 (mm) cc_final: 0.8915 (mt) outliers start: 52 outliers final: 41 residues processed: 255 average time/residue: 0.1285 time to fit residues: 54.5353 Evaluate side-chains 244 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 807 THR 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 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1082 GLN 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 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 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 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 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: 4.9990 chunk 6 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.108770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092212 restraints weight = 34324.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094578 restraints weight = 20817.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096183 restraints weight = 14911.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097226 restraints weight = 11914.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097852 restraints weight = 10221.775| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2274 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= 0.230 Angle : 1.380 50.516 26866 Z= 0.786 Chirality : 0.229 6.336 3141 Planarity : 0.003 0.047 3258 Dihedral : 9.744 70.009 2981 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.29 % Allowed : 24.05 % Favored : 72.66 % 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: 0.64 (0.18), residues: 2468 helix: 2.40 (0.17), residues: 937 sheet: -0.66 (0.28), residues: 337 loop : -0.89 (0.18), residues: 1194 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 0.015 0.001 TRP F 103 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.23 (19665) covalent geometry : angle 1.21064 / 0.78 (26854) hydrogen bonds : bond 0.03307 / 2.31 ( 882) hydrogen bonds : angle 4.12590 / 2.97 ( 2532) metal coordination : bond 0.02318 / 1.16 ( 4) metal coordination : angle 31.39246 / 19.14 ( 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 254 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.655 Fit side-chains REVERT: A 984 MET cc_start: 0.8651 (mmm) cc_final: 0.8391 (mmm) REVERT: A 1050 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8659 (mm) REVERT: D 30 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: E 27 TYR cc_start: 0.8897 (m-80) cc_final: 0.8685 (m-80) REVERT: F 399 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: G 65 ILE cc_start: 0.9272 (mm) cc_final: 0.8916 (mt) outliers start: 52 outliers final: 41 residues processed: 245 average time/residue: 0.1206 time to fit residues: 49.5726 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 238 LEU 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 807 THR 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 1049 MET 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 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 E residue 131 LEU 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 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 919 CYS 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: 8.9990 chunk 201 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.088185 restraints weight = 34346.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090500 restraints weight = 21014.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092032 restraints weight = 15208.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093051 restraints weight = 12292.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093671 restraints weight = 10623.654| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 19669 Z= 0.295 Angle : 1.422 50.638 26866 Z= 0.804 Chirality : 0.229 6.318 3141 Planarity : 0.004 0.055 3258 Dihedral : 10.064 69.958 2981 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.48 % Allowed : 23.92 % Favored : 72.59 % 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: 0.32 (0.17), residues: 2468 helix: 2.01 (0.17), residues: 944 sheet: -0.85 (0.29), residues: 327 loop : -0.96 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 936 TYR 0.020 0.001 TYR F 436 PHE 0.020 0.002 PHE D 40 TRP 0.017 0.001 TRP F 103 HIS 0.006 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.30 (19665) covalent geometry : angle 1.25136 / 0.80 (26854) hydrogen bonds : bond 0.04154 / 2.89 ( 882) hydrogen bonds : angle 4.37763 / 3.15 ( 2532) metal coordination : bond 0.02433 / 1.22 ( 4) metal coordination : angle 32.01337 / 19.58 ( 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 253 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.805 Fit side-chains REVERT: A 760 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: A 1050 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8744 (mm) REVERT: D 30 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: E 27 TYR cc_start: 0.8932 (m-80) cc_final: 0.8691 (m-80) REVERT: F 399 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: G 65 ILE cc_start: 0.9277 (mm) cc_final: 0.8947 (mt) outliers start: 55 outliers final: 41 residues processed: 241 average time/residue: 0.1197 time to fit residues: 48.3081 Evaluate side-chains 236 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 691 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 THR 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 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1468 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 65 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 188 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 919 CYS 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: 1.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 212 optimal weight: 0.0770 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN E 2 ASN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090256 restraints weight = 34427.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092585 restraints weight = 20911.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094130 restraints weight = 15115.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095101 restraints weight = 12133.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095832 restraints weight = 10488.245| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 19669 Z= 0.233 Angle : 1.390 50.521 26866 Z= 0.790 Chirality : 0.229 6.339 3141 Planarity : 0.003 0.046 3258 Dihedral : 9.911 69.636 2981 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.78 % Allowed : 25.13 % Favored : 72.09 % 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: 2.20 (0.17), residues: 943 sheet: -0.87 (0.29), residues: 321 loop : -0.94 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 936 TYR 0.020 0.001 TYR D 34 PHE 0.015 0.001 PHE E 215 TRP 0.038 0.001 TRP F 103 HIS 0.011 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.23 (19665) covalent geometry : angle 1.21999 / 0.79 (26854) hydrogen bonds : bond 0.03587 / 2.52 ( 882) hydrogen bonds : angle 4.20288 / 3.02 ( 2532) metal coordination : bond 0.02491 / 1.25 ( 4) metal coordination : angle 31.52792 / 19.21 ( 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 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.787 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8685 (mm) REVERT: A 1082 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8687 (pp30) REVERT: D 30 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: E 27 TYR cc_start: 0.8903 (m-80) cc_final: 0.8643 (m-80) REVERT: F 399 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7864 (mtt) REVERT: G 41 PHE cc_start: 0.8064 (t80) cc_final: 0.7758 (t80) REVERT: G 65 ILE cc_start: 0.9283 (mm) cc_final: 0.8937 (mt) outliers start: 44 outliers final: 37 residues processed: 233 average time/residue: 0.1256 time to fit residues: 48.9784 Evaluate side-chains 235 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 592 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 THR 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 1082 GLN Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE 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 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 184 GLU 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 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 919 CYS 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: 0.8980 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 212 optimal weight: 0.3980 chunk 164 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091552 restraints weight = 34359.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093873 restraints weight = 20872.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095481 restraints weight = 15035.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096468 restraints weight = 11985.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097228 restraints weight = 10321.322| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2561 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= 0.223 Angle : 1.384 50.487 26866 Z= 0.788 Chirality : 0.229 6.336 3141 Planarity : 0.003 0.045 3258 Dihedral : 9.829 69.718 2981 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.47 % Allowed : 25.70 % Favored : 71.84 % 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: 0.51 (0.17), residues: 2468 helix: 2.27 (0.17), residues: 944 sheet: -0.84 (0.29), residues: 319 loop : -0.91 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 936 TYR 0.019 0.001 TYR D 34 PHE 0.016 0.001 PHE A 601 TRP 0.033 0.001 TRP F 103 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.22 (19665) covalent geometry : angle 1.21457 / 0.79 (26854) hydrogen bonds : bond 0.03378 / 2.36 ( 882) hydrogen bonds : angle 4.13091 / 2.97 ( 2532) metal coordination : bond 0.02452 / 1.23 ( 4) metal coordination : angle 31.39371 / 19.11 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.00 seconds wall clock time: 47 minutes 38.44 seconds (2858.44 seconds total)