Starting phenix.real_space_refine on Mon May 19 22:53:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlq_41371/05_2025/8tlq_41371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlq_41371/05_2025/8tlq_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_41371/05_2025/8tlq_41371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlq_41371/05_2025/8tlq_41371.map" model { file = "/net/cci-nas-00/data/ceres_data/8tlq_41371/05_2025/8tlq_41371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlq_41371/05_2025/8tlq_41371.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 18, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 18, 'ASP:plan': 50, 'PHE:plan': 3, 'GLU:plan': 58, 'ARG:plan': 17} 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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG: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: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} 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: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 4} 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, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9} 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: {'GLN:plan1': 9, 'ARG:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 11} 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: 12.23, per 1000 atoms: 0.64 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: 5.27 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1603 " pdb="FE3 SF4 A1603 " - pdb=" SG CYS A1468 " pdb="FE2 SF4 A1603 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1603 " - pdb=" SG CYS A1446 " pdb="FE1 SF4 A1603 " - pdb=" SG CYS A1473 " Number of angles added : 12 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 21 sheets defined 40.2% alpha, 14.0% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 6.69 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: 8.26 Time building geometry restraints manager: 6.22 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=" 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 bond pdb=" S4 SF4 A1603 " pdb="FE2 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 ... (remaining 19660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 26784 3.38 - 6.77: 44 6.77 - 10.15: 1 10.15 - 13.54: 1 13.54 - 16.92: 24 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: 9999 17.80 - 35.61: 1127 35.61 - 53.41: 399 53.41 - 71.21: 67 71.21 - 89.02: 13 Dihedral angle restraints: 11605 sinusoidal: 4185 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 11602 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 58.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 19669 Z= 0.159 Angle : 0.682 16.930 26866 Z= 0.385 Chirality : 0.720 20.237 3141 Planarity : 0.003 0.062 3258 Dihedral : 17.379 89.016 6777 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP F 103 HIS 0.002 0.000 HIS A 669 PHE 0.009 0.001 PHE A 39 TYR 0.018 0.001 TYR B 973 ARG 0.003 0.000 ARG A 884 Details of bonding type rmsd hydrogen bonds : bond 0.17135 ( 882) hydrogen bonds : angle 6.29789 ( 2532) metal coordination : bond 0.00061 ( 4) metal coordination : angle 11.78462 ( 12) covalent geometry : bond 0.00423 (19665) covalent geometry : angle 0.63452 (26854) *********************** 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 : 2.335 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: 0.2515 time to fit residues: 93.9520 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 : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 103 GLN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN D 214 GLN E 99 GLN F 117 ASN F 316 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089387 restraints weight = 34582.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091644 restraints weight = 21269.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093154 restraints weight = 15540.541| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.274 19669 Z= 0.396 Angle : 1.476 51.152 26866 Z= 0.831 Chirality : 0.226 6.434 3141 Planarity : 0.005 0.063 3258 Dihedral : 10.148 83.473 2974 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 3.80 % Allowed : 21.90 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2468 helix: 1.83 (0.17), residues: 936 sheet: -0.24 (0.29), residues: 335 loop : -0.89 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 604 HIS 0.008 0.002 HIS A 74 PHE 0.028 0.002 PHE F 345 TYR 0.021 0.002 TYR D 16 ARG 0.006 0.001 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 882) hydrogen bonds : angle 4.90371 ( 2532) metal coordination : bond 0.03038 ( 4) metal coordination : angle 32.27829 ( 12) covalent geometry : bond 0.01011 (19665) covalent geometry : angle 1.30930 (26854) *********************** 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 273 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 2.186 Fit side-chains REVERT: A 760 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: E 184 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: G 65 ILE cc_start: 0.9265 (mm) cc_final: 0.8880 (mt) REVERT: B 913 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8413 (ttmm) outliers start: 60 outliers final: 35 residues processed: 259 average time/residue: 0.2635 time to fit residues: 111.5425 Evaluate side-chains 233 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 213 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 760 ASP 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 1197 VAL 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 131 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 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 133 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL 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 912 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 177 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN D 214 GLN E 214 GLN B 948 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.092350 restraints weight = 34110.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094725 restraints weight = 20813.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096297 restraints weight = 15017.793| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 19669 Z= 0.239 Angle : 1.380 50.492 26866 Z= 0.787 Chirality : 0.229 6.350 3141 Planarity : 0.004 0.051 3258 Dihedral : 9.905 88.652 2974 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.04 % Allowed : 23.04 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2468 helix: 2.23 (0.17), residues: 933 sheet: -0.37 (0.29), residues: 331 loop : -0.87 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 103 HIS 0.014 0.001 HIS F 316 PHE 0.016 0.001 PHE E 215 TYR 0.019 0.001 TYR A 353 ARG 0.003 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 882) hydrogen bonds : angle 4.43991 ( 2532) metal coordination : bond 0.03505 ( 4) metal coordination : angle 31.17094 ( 12) covalent geometry : bond 0.00664 (19665) covalent geometry : angle 1.21284 (26854) *********************** 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 265 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 2.158 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8689 (mm) REVERT: E 27 TYR cc_start: 0.8783 (m-80) cc_final: 0.8542 (m-10) REVERT: F 399 MET cc_start: 0.8497 (mmt) cc_final: 0.7568 (mtt) REVERT: G 65 ILE cc_start: 0.9282 (mm) cc_final: 0.8917 (mt) REVERT: B 913 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8398 (ttmm) outliers start: 48 outliers final: 25 residues processed: 252 average time/residue: 0.2680 time to fit residues: 110.4153 Evaluate side-chains 230 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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 807 THR 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 1047 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 A residue 1480 VAL 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 F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 136 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 HIS G 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088326 restraints weight = 34355.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.090604 restraints weight = 21252.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092120 restraints weight = 15471.513| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 19669 Z= 0.290 Angle : 1.415 50.501 26866 Z= 0.800 Chirality : 0.230 6.378 3141 Planarity : 0.004 0.054 3258 Dihedral : 10.105 81.459 2974 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.37 % Allowed : 22.53 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2468 helix: 1.86 (0.17), residues: 949 sheet: -0.66 (0.29), residues: 325 loop : -0.96 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 103 HIS 0.008 0.001 HIS F 316 PHE 0.018 0.002 PHE E 215 TYR 0.019 0.001 TYR D 34 ARG 0.003 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 882) hydrogen bonds : angle 4.47020 ( 2532) metal coordination : bond 0.02797 ( 4) metal coordination : angle 31.86374 ( 12) covalent geometry : bond 0.00772 (19665) covalent geometry : angle 1.24423 (26854) *********************** 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 273 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 2.046 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8746 (mm) REVERT: E 27 TYR cc_start: 0.8928 (m-80) cc_final: 0.8676 (m-80) REVERT: F 103 TRP cc_start: 0.8875 (p-90) cc_final: 0.8665 (p-90) REVERT: F 399 MET cc_start: 0.8662 (mmt) cc_final: 0.7800 (mtt) REVERT: G 65 ILE cc_start: 0.9275 (mm) cc_final: 0.8931 (mt) REVERT: B 913 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8510 (ttmm) outliers start: 69 outliers final: 48 residues processed: 256 average time/residue: 0.2624 time to fit residues: 110.0209 Evaluate side-chains 239 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 583 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 861 LEU 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 1047 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain 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 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 13 LEU 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 976 VAL Chi-restraints excluded: chain B residue 979 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 192 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 107 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN B 948 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090451 restraints weight = 34506.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.092762 restraints weight = 20996.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094335 restraints weight = 15203.589| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2466 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= 0.236 Angle : 1.382 50.502 26866 Z= 0.787 Chirality : 0.229 6.335 3141 Planarity : 0.003 0.046 3258 Dihedral : 9.950 77.783 2974 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.86 % Allowed : 23.10 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2468 helix: 2.08 (0.17), residues: 949 sheet: -0.77 (0.29), residues: 332 loop : -0.97 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 103 HIS 0.004 0.001 HIS D 51 PHE 0.015 0.001 PHE E 215 TYR 0.019 0.001 TYR A 353 ARG 0.004 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 882) hydrogen bonds : angle 4.26544 ( 2532) metal coordination : bond 0.02521 ( 4) metal coordination : angle 31.39012 ( 12) covalent geometry : bond 0.00659 (19665) covalent geometry : angle 1.21288 (26854) *********************** 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 264 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 2.304 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8696 (mm) REVERT: D 30 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: E 27 TYR cc_start: 0.8899 (m-80) cc_final: 0.8650 (m-80) REVERT: F 399 MET cc_start: 0.8579 (mmt) cc_final: 0.7857 (mtt) REVERT: G 65 ILE cc_start: 0.9266 (mm) cc_final: 0.8898 (mt) REVERT: B 913 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8462 (ttmm) outliers start: 61 outliers final: 42 residues processed: 255 average time/residue: 0.2691 time to fit residues: 113.7887 Evaluate side-chains 239 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 385 THR 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 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 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN Chi-restraints excluded: chain A residue 1499 ILE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER 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 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 128 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 167 optimal weight: 0.0970 chunk 190 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN G 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089476 restraints weight = 34529.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091790 restraints weight = 21117.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093328 restraints weight = 15339.849| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2610 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= 0.254 Angle : 1.391 50.538 26866 Z= 0.790 Chirality : 0.229 6.334 3141 Planarity : 0.004 0.049 3258 Dihedral : 9.984 75.687 2974 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.11 % Allowed : 23.54 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2468 helix: 2.03 (0.17), residues: 951 sheet: -0.85 (0.28), residues: 332 loop : -0.99 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 103 HIS 0.019 0.001 HIS F 316 PHE 0.016 0.001 PHE E 215 TYR 0.019 0.001 TYR A 353 ARG 0.005 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 882) hydrogen bonds : angle 4.25634 ( 2532) metal coordination : bond 0.02415 ( 4) metal coordination : angle 31.58819 ( 12) covalent geometry : bond 0.00695 (19665) covalent geometry : angle 1.22088 (26854) *********************** 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 255 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 2.051 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 1082 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8734 (tm-30) REVERT: A 1303 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: D 30 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: E 27 TYR cc_start: 0.8937 (m-80) cc_final: 0.8726 (m-80) REVERT: F 298 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8708 (mm) REVERT: F 399 MET cc_start: 0.8692 (mmt) cc_final: 0.7987 (mtt) REVERT: G 65 ILE cc_start: 0.9265 (mm) cc_final: 0.8911 (mt) REVERT: B 913 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8486 (ttmm) outliers start: 65 outliers final: 46 residues processed: 244 average time/residue: 0.2573 time to fit residues: 104.8897 Evaluate side-chains 242 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 1082 GLN Chi-restraints excluded: chain A residue 1143 THR 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 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN 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 185 ASN Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER 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 298 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 68 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089380 restraints weight = 34142.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091682 restraints weight = 20930.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093189 restraints weight = 15205.415| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2680 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= 0.256 Angle : 1.392 50.555 26866 Z= 0.791 Chirality : 0.229 6.334 3141 Planarity : 0.004 0.049 3258 Dihedral : 10.007 75.221 2974 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.05 % Allowed : 23.92 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2468 helix: 2.02 (0.17), residues: 949 sheet: -0.90 (0.28), residues: 332 loop : -0.98 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 103 HIS 0.014 0.001 HIS F 316 PHE 0.016 0.001 PHE E 215 TYR 0.020 0.001 TYR A 353 ARG 0.005 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 882) hydrogen bonds : angle 4.25524 ( 2532) metal coordination : bond 0.02369 ( 4) metal coordination : angle 31.61231 ( 12) covalent geometry : bond 0.00700 (19665) covalent geometry : angle 1.22169 (26854) *********************** 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 261 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 2.185 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8696 (mm) REVERT: A 1303 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: D 30 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: E 27 TYR cc_start: 0.8943 (m-80) cc_final: 0.8719 (m-80) REVERT: F 298 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8724 (mm) REVERT: F 399 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7885 (mtt) REVERT: F 403 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7283 (mpp) REVERT: G 65 ILE cc_start: 0.9268 (mm) cc_final: 0.8916 (mt) REVERT: B 913 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8499 (ttmm) outliers start: 64 outliers final: 50 residues processed: 249 average time/residue: 0.2588 time to fit residues: 106.8795 Evaluate side-chains 245 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 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 1143 THR Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN 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 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 403 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 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 13 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 ASN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN G 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091399 restraints weight = 34114.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093765 restraints weight = 20720.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095337 restraints weight = 14943.419| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2644 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= 0.226 Angle : 1.376 50.496 26866 Z= 0.784 Chirality : 0.229 6.336 3141 Planarity : 0.003 0.045 3258 Dihedral : 9.860 73.461 2974 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.48 % Allowed : 24.75 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2468 helix: 2.20 (0.17), residues: 949 sheet: -0.82 (0.29), residues: 321 loop : -0.94 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 103 HIS 0.011 0.001 HIS F 316 PHE 0.014 0.001 PHE E 215 TYR 0.020 0.001 TYR A 353 ARG 0.006 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 882) hydrogen bonds : angle 4.11571 ( 2532) metal coordination : bond 0.02277 ( 4) metal coordination : angle 31.33511 ( 12) covalent geometry : bond 0.00638 (19665) covalent geometry : angle 1.20635 (26854) *********************** 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 262 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 2.181 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 1303 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: D 30 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: E 27 TYR cc_start: 0.8902 (m-80) cc_final: 0.8660 (m-80) REVERT: F 103 TRP cc_start: 0.8863 (p-90) cc_final: 0.8578 (p-90) REVERT: F 298 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8706 (mm) REVERT: F 399 MET cc_start: 0.8634 (mmt) cc_final: 0.7828 (mtt) REVERT: G 65 ILE cc_start: 0.9267 (mm) cc_final: 0.8913 (mt) REVERT: B 913 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8491 (ttmm) outliers start: 55 outliers final: 41 residues processed: 252 average time/residue: 0.2603 time to fit residues: 108.8391 Evaluate side-chains 240 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 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 1184 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN 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 F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU 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 217 VAL Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.087001 restraints weight = 34541.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089213 restraints weight = 21101.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.090661 restraints weight = 15376.874| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 19669 Z= 0.316 Angle : 1.424 50.609 26866 Z= 0.804 Chirality : 0.230 6.365 3141 Planarity : 0.004 0.053 3258 Dihedral : 10.171 74.551 2974 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.99 % Allowed : 24.68 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2468 helix: 1.88 (0.17), residues: 949 sheet: -1.01 (0.29), residues: 321 loop : -1.06 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 103 HIS 0.011 0.001 HIS F 316 PHE 0.020 0.002 PHE D 40 TYR 0.022 0.001 TYR A 353 ARG 0.006 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 882) hydrogen bonds : angle 4.40290 ( 2532) metal coordination : bond 0.02320 ( 4) metal coordination : angle 32.06911 ( 12) covalent geometry : bond 0.00826 (19665) covalent geometry : angle 1.25270 (26854) *********************** 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 247 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 2.082 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8747 (mm) REVERT: D 30 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: F 315 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: F 399 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: G 65 ILE cc_start: 0.9263 (mm) cc_final: 0.8935 (mt) outliers start: 63 outliers final: 47 residues processed: 234 average time/residue: 0.2609 time to fit residues: 100.9282 Evaluate side-chains 232 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL 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 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 1263 VAL Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN 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 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 315 PHE 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 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 80 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 245 optimal weight: 0.0000 chunk 210 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.090851 restraints weight = 34039.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093202 restraints weight = 20774.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094752 restraints weight = 14986.973| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 19669 Z= 0.224 Angle : 1.381 50.498 26866 Z= 0.786 Chirality : 0.229 6.340 3141 Planarity : 0.003 0.045 3258 Dihedral : 9.951 74.543 2974 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.97 % Allowed : 25.82 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2468 helix: 2.13 (0.17), residues: 951 sheet: -0.89 (0.29), residues: 321 loop : -0.99 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 103 HIS 0.005 0.001 HIS D 51 PHE 0.017 0.001 PHE A 741 TYR 0.022 0.001 TYR A 353 ARG 0.006 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 882) hydrogen bonds : angle 4.17062 ( 2532) metal coordination : bond 0.02450 ( 4) metal coordination : angle 31.37617 ( 12) covalent geometry : bond 0.00634 (19665) covalent geometry : angle 1.21210 (26854) ********************** 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: 47 poor density : 195 time to evaluate : 2.308 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8677 (mm) REVERT: D 30 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: D 90 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8209 (tttm) REVERT: F 315 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: F 399 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7817 (mtt) REVERT: G 65 ILE cc_start: 0.9260 (mm) cc_final: 0.8918 (mt) outliers start: 47 outliers final: 40 residues processed: 235 average time/residue: 0.2650 time to fit residues: 103.1340 Evaluate side-chains 236 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL 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 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 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN 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 F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 315 PHE 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 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 15 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 0.0040 chunk 204 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087628 restraints weight = 34726.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089924 restraints weight = 21054.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091453 restraints weight = 15231.390| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 19669 Z= 0.274 Angle : 1.405 50.548 26866 Z= 0.796 Chirality : 0.230 6.346 3141 Planarity : 0.004 0.050 3258 Dihedral : 10.070 73.872 2974 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.29 % Allowed : 25.57 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2468 helix: 2.01 (0.17), residues: 949 sheet: -0.97 (0.29), residues: 321 loop : -1.05 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 103 HIS 0.005 0.001 HIS D 51 PHE 0.018 0.001 PHE A 741 TYR 0.023 0.001 TYR A 353 ARG 0.005 0.000 ARG B 936 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 882) hydrogen bonds : angle 4.29265 ( 2532) metal coordination : bond 0.02265 ( 4) metal coordination : angle 31.77661 ( 12) covalent geometry : bond 0.00737 (19665) covalent geometry : angle 1.23483 (26854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5060.26 seconds wall clock time: 89 minutes 46.88 seconds (5386.88 seconds total)