Starting phenix.real_space_refine on Tue Nov 18 07:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bly_7113/11_2025/6bly_7113.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bly_7113/11_2025/6bly_7113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bly_7113/11_2025/6bly_7113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bly_7113/11_2025/6bly_7113.map" model { file = "/net/cci-nas-00/data/ceres_data/6bly_7113/11_2025/6bly_7113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bly_7113/11_2025/6bly_7113.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7853 2.51 5 N 2132 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12263 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9337 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 66, 'TRANS': 1110} Chain breaks: 12 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2926 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 15, 'TRANS': 347} Time building chain proxies: 3.20, per 1000 atoms: 0.26 Number of scatterers: 12263 At special positions: 0 Unit cell: (88.81, 136.96, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2204 8.00 N 2132 7.00 C 7853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 577.4 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 35 sheets defined 6.4% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.747A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1154 through 1156 No H-bonds generated for 'chain 'A' and resid 1154 through 1156' Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.863A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A1365 " --> pdb=" O MET A1361 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 removed outlier: 3.518A pdb=" N GLY A1375 " --> pdb=" O HIS A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.677A pdb=" N ARG A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 3.529A pdb=" N LEU A1408 " --> pdb=" O ASN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.588A pdb=" N SER A1416 " --> pdb=" O THR A1412 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A1419 " --> pdb=" O ARG A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.577A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.734A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.835A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.607A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1312 through 1314 removed outlier: 6.187A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 3.888A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.637A pdb=" N ALA A 93 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.602A pdb=" N ARG A 140 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 189 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 208 removed outlier: 5.392A pdb=" N ILE A 203 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 222 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 260 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 242 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.644A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.880A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 329 removed outlier: 4.666A pdb=" N ILE A 344 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.641A pdb=" N LEU A 392 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.368A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 525 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.666A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 578 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.539A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 651 removed outlier: 7.583A pdb=" N MET A 659 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N CYS A 649 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 657 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AB7, first strand: chain 'A' and resid 695 through 702 removed outlier: 3.620A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 854 removed outlier: 6.529A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AC1, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.645A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER A 941 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 955 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1021 through 1024 removed outlier: 6.598A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1027 through 1028 Processing sheet with id=AC4, first strand: chain 'A' and resid 1046 through 1050 removed outlier: 3.544A pdb=" N GLU A1056 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.627A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1172 through 1177 removed outlier: 4.104A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.630A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1232 through 1237 removed outlier: 7.106A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.802A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.802A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1297 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.656A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE B 389 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TRP B 383 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS B 391 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B 381 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY B 393 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.575A pdb=" N ARG B 126 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 135 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.072A pdb=" N ALA B 166 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 187 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN B 189 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B 194 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.895A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 226 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 239 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 228 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AD7, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD8, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.929A pdb=" N ALA B 336 " --> pdb=" O GLY B 350 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3252 1.33 - 1.45: 2273 1.45 - 1.57: 6918 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12563 Sorted by residual: bond pdb=" C PHE A 811 " pdb=" N PRO A 812 " ideal model delta sigma weight residual 1.337 1.384 -0.047 9.80e-03 1.04e+04 2.32e+01 bond pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 1.528 1.505 0.023 8.80e-03 1.29e+04 6.63e+00 bond pdb=" C ILE A 873 " pdb=" O ILE A 873 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.05e-02 9.07e+03 5.24e+00 bond pdb=" C LEU B 346 " pdb=" O LEU B 346 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.20e-02 6.94e+03 4.65e+00 bond pdb=" C ALA A 242 " pdb=" N ILE A 243 " ideal model delta sigma weight residual 1.333 1.308 0.025 1.20e-02 6.94e+03 4.41e+00 ... (remaining 12558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 16427 2.44 - 4.87: 540 4.87 - 7.31: 60 7.31 - 9.75: 17 9.75 - 12.19: 3 Bond angle restraints: 17047 Sorted by residual: angle pdb=" C ASP A 653 " pdb=" N PRO A 654 " pdb=" CA PRO A 654 " ideal model delta sigma weight residual 119.84 131.80 -11.96 1.25e+00 6.40e-01 9.15e+01 angle pdb=" N PHE B 210 " pdb=" CA PHE B 210 " pdb=" C PHE B 210 " ideal model delta sigma weight residual 108.45 115.91 -7.46 1.26e+00 6.30e-01 3.50e+01 angle pdb=" C PRO A 272 " pdb=" N LYS A 273 " pdb=" CA LYS A 273 " ideal model delta sigma weight residual 120.58 128.05 -7.47 1.32e+00 5.74e-01 3.20e+01 angle pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" O PHE B 151 " ideal model delta sigma weight residual 120.51 113.17 7.34 1.43e+00 4.89e-01 2.64e+01 angle pdb=" C LEU A 201 " pdb=" CA LEU A 201 " pdb=" CB LEU A 201 " ideal model delta sigma weight residual 116.63 111.05 5.58 1.16e+00 7.43e-01 2.31e+01 ... (remaining 17042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 7030 14.79 - 29.58: 376 29.58 - 44.37: 57 44.37 - 59.16: 8 59.16 - 73.95: 7 Dihedral angle restraints: 7478 sinusoidal: 3016 harmonic: 4462 Sorted by residual: dihedral pdb=" C ASP A 333 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual -122.60 -137.32 14.72 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" CA GLY A 211 " pdb=" C GLY A 211 " pdb=" N TYR A 212 " pdb=" CA TYR A 212 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 7475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1771 0.112 - 0.225: 130 0.225 - 0.337: 2 0.337 - 0.450: 0 0.450 - 0.562: 1 Chirality restraints: 1904 Sorted by residual: chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" CA LEU A 200 " pdb=" N LEU A 200 " pdb=" C LEU A 200 " pdb=" CB LEU A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 243 " pdb=" CA ILE A 243 " pdb=" CG1 ILE A 243 " pdb=" CG2 ILE A 243 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1901 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1312 " 0.043 2.00e-02 2.50e+03 2.39e-02 1.42e+01 pdb=" CG TRP A1312 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A1312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1312 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1312 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1312 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1312 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1312 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1312 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 653 " 0.060 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 654 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1074 " 0.016 2.00e-02 2.50e+03 2.38e-02 9.93e+00 pdb=" CG PHE A1074 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A1074 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A1074 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A1074 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A1074 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1074 " 0.004 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1710 2.76 - 3.29: 10398 3.29 - 3.83: 19956 3.83 - 4.36: 23703 4.36 - 4.90: 42357 Nonbonded interactions: 98124 Sorted by model distance: nonbonded pdb=" OG SER A 331 " pdb=" N TYR A 332 " model vdw 2.220 3.120 nonbonded pdb=" OG SER A 17 " pdb=" OG SER A 373 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 221 " pdb=" OD1 ASP B 223 " model vdw 2.279 3.040 nonbonded pdb=" O GLY A 276 " pdb=" OH TYR A 288 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 583 " pdb=" O GLY A 604 " model vdw 2.309 3.040 ... (remaining 98119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.008 0.072 12563 Z= 0.362 Angle : 1.040 12.185 17047 Z= 0.582 Chirality : 0.061 0.562 1904 Planarity : 0.008 0.089 2172 Dihedral : 9.963 73.946 4594 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.66 % Favored : 91.27 % Rotamer: Outliers : 0.89 % Allowed : 1.49 % Favored : 97.62 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.18), residues: 1512 helix: -4.44 (0.26), residues: 80 sheet: -2.21 (0.19), residues: 603 loop : -2.84 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 404 TYR 0.040 0.004 TYR A 2 PHE 0.051 0.005 PHE A1074 TRP 0.059 0.004 TRP A1312 HIS 0.012 0.003 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00838 (12563) covalent geometry : angle 1.04050 (17047) hydrogen bonds : bond 0.24356 ( 326) hydrogen bonds : angle 9.90677 ( 888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 343 time to evaluate : 0.482 Fit side-chains REVERT: A 320 ILE cc_start: 0.7879 (pp) cc_final: 0.7512 (pt) REVERT: A 1208 THR cc_start: 0.7905 (t) cc_final: 0.7654 (p) REVERT: B 176 MET cc_start: 0.8663 (ttp) cc_final: 0.8387 (ttm) outliers start: 12 outliers final: 7 residues processed: 353 average time/residue: 0.1492 time to fit residues: 71.1564 Evaluate side-chains 166 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN A1095 GLN B 69 ASN B 325 GLN B 343 HIS B 405 ASN B 416 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112729 restraints weight = 17416.163| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.12 r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12563 Z= 0.127 Angle : 0.641 8.929 17047 Z= 0.336 Chirality : 0.047 0.223 1904 Planarity : 0.005 0.096 2172 Dihedral : 6.593 58.694 1682 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 2.16 % Allowed : 8.18 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.19), residues: 1512 helix: -3.10 (0.44), residues: 79 sheet: -1.59 (0.19), residues: 619 loop : -2.50 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1274 TYR 0.016 0.001 TYR A 2 PHE 0.020 0.002 PHE B 210 TRP 0.021 0.002 TRP A1337 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00293 (12563) covalent geometry : angle 0.64068 (17047) hydrogen bonds : bond 0.03948 ( 326) hydrogen bonds : angle 6.68027 ( 888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8113 (pt) REVERT: A 496 PRO cc_start: 0.7886 (Cg_exo) cc_final: 0.7684 (Cg_endo) REVERT: A 681 ARG cc_start: 0.6938 (ptm-80) cc_final: 0.5748 (ttm-80) REVERT: A 857 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7727 (mmm-85) REVERT: A 1208 THR cc_start: 0.8576 (t) cc_final: 0.8030 (p) REVERT: A 1393 ASN cc_start: 0.6882 (t0) cc_final: 0.6639 (t0) REVERT: A 1414 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7968 (pt0) REVERT: A 1431 ASP cc_start: 0.9004 (t0) cc_final: 0.8728 (t0) REVERT: B 75 ASP cc_start: 0.7501 (m-30) cc_final: 0.7152 (m-30) REVERT: B 83 GLN cc_start: 0.8193 (mt0) cc_final: 0.7725 (mm-40) REVERT: B 142 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 229 TRP cc_start: 0.8540 (m100) cc_final: 0.8319 (m100) outliers start: 29 outliers final: 12 residues processed: 225 average time/residue: 0.1124 time to fit residues: 36.9720 Evaluate side-chains 180 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 57 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110112 restraints weight = 17587.693| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.15 r_work: 0.3170 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12563 Z= 0.133 Angle : 0.598 7.397 17047 Z= 0.310 Chirality : 0.046 0.212 1904 Planarity : 0.005 0.100 2172 Dihedral : 5.648 41.839 1672 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 2.75 % Allowed : 10.11 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.20), residues: 1512 helix: -2.34 (0.49), residues: 85 sheet: -1.24 (0.19), residues: 634 loop : -2.24 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 308 TYR 0.014 0.001 TYR A 2 PHE 0.014 0.002 PHE B 210 TRP 0.015 0.002 TRP A1312 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00316 (12563) covalent geometry : angle 0.59804 (17047) hydrogen bonds : bond 0.03560 ( 326) hydrogen bonds : angle 5.98597 ( 888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.485 Fit side-chains REVERT: A 857 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7882 (mmm-85) REVERT: A 1208 THR cc_start: 0.8415 (t) cc_final: 0.7994 (m) REVERT: A 1273 ASP cc_start: 0.8638 (p0) cc_final: 0.8422 (p0) REVERT: A 1393 ASN cc_start: 0.6968 (t0) cc_final: 0.6764 (t0) REVERT: A 1414 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7947 (mt-10) REVERT: A 1431 ASP cc_start: 0.9012 (t0) cc_final: 0.8795 (t0) REVERT: B 75 ASP cc_start: 0.7492 (m-30) cc_final: 0.7146 (m-30) REVERT: B 142 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 143 PHE cc_start: 0.9207 (m-10) cc_final: 0.9000 (m-10) outliers start: 37 outliers final: 24 residues processed: 206 average time/residue: 0.1055 time to fit residues: 32.7056 Evaluate side-chains 189 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 65 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112541 restraints weight = 17397.164| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.14 r_work: 0.3200 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 12563 Z= 0.101 Angle : 0.554 6.817 17047 Z= 0.287 Chirality : 0.045 0.208 1904 Planarity : 0.005 0.103 2172 Dihedral : 5.172 33.101 1672 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 2.38 % Allowed : 12.12 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.20), residues: 1512 helix: -1.52 (0.55), residues: 85 sheet: -0.94 (0.20), residues: 616 loop : -2.06 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.011 0.001 TYR A 2 PHE 0.011 0.001 PHE A 708 TRP 0.016 0.001 TRP A1337 HIS 0.005 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00238 (12563) covalent geometry : angle 0.55379 (17047) hydrogen bonds : bond 0.03044 ( 326) hydrogen bonds : angle 5.62917 ( 888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 216 THR cc_start: 0.9419 (m) cc_final: 0.9154 (p) REVERT: A 256 TRP cc_start: 0.8539 (t60) cc_final: 0.8074 (t60) REVERT: A 340 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8153 (pttt) REVERT: A 392 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8674 (pp) REVERT: A 608 PHE cc_start: 0.7454 (t80) cc_final: 0.6984 (t80) REVERT: A 857 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7823 (mmm-85) REVERT: A 1166 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8450 (mtpp) REVERT: A 1208 THR cc_start: 0.8418 (t) cc_final: 0.8015 (m) REVERT: A 1273 ASP cc_start: 0.8694 (p0) cc_final: 0.8462 (p0) REVERT: A 1393 ASN cc_start: 0.7061 (t0) cc_final: 0.6630 (t0) REVERT: A 1414 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 1431 ASP cc_start: 0.8948 (t0) cc_final: 0.8694 (t0) REVERT: B 75 ASP cc_start: 0.7444 (m-30) cc_final: 0.7153 (m-30) REVERT: B 142 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 143 PHE cc_start: 0.9131 (m-10) cc_final: 0.8927 (m-10) outliers start: 32 outliers final: 19 residues processed: 211 average time/residue: 0.1088 time to fit residues: 34.0242 Evaluate side-chains 188 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105759 restraints weight = 17630.263| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.16 r_work: 0.3089 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12563 Z= 0.199 Angle : 0.646 7.466 17047 Z= 0.330 Chirality : 0.047 0.222 1904 Planarity : 0.005 0.106 2172 Dihedral : 5.447 31.212 1671 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.47 % Favored : 92.46 % Rotamer: Outliers : 3.20 % Allowed : 13.01 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.20), residues: 1512 helix: -1.23 (0.58), residues: 85 sheet: -0.92 (0.20), residues: 626 loop : -1.93 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 404 TYR 0.019 0.002 TYR A 345 PHE 0.016 0.002 PHE A 892 TRP 0.020 0.002 TRP A1337 HIS 0.006 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00478 (12563) covalent geometry : angle 0.64568 (17047) hydrogen bonds : bond 0.03425 ( 326) hydrogen bonds : angle 5.64358 ( 888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.499 Fit side-chains REVERT: A 635 LEU cc_start: 0.8412 (tp) cc_final: 0.8080 (tt) REVERT: A 659 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7690 (ttm) REVERT: A 857 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.8016 (mmm-85) REVERT: A 1032 LYS cc_start: 0.9233 (mttt) cc_final: 0.8985 (mttp) REVERT: A 1208 THR cc_start: 0.8393 (t) cc_final: 0.8107 (m) REVERT: A 1291 PHE cc_start: 0.7228 (m-10) cc_final: 0.7027 (m-10) REVERT: A 1393 ASN cc_start: 0.6843 (t0) cc_final: 0.6523 (t0) REVERT: A 1414 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 1421 LYS cc_start: 0.7972 (tmtt) cc_final: 0.7758 (ttmt) REVERT: B 75 ASP cc_start: 0.7606 (m-30) cc_final: 0.7184 (m-30) REVERT: B 143 PHE cc_start: 0.9160 (m-10) cc_final: 0.8925 (m-10) outliers start: 43 outliers final: 28 residues processed: 200 average time/residue: 0.1002 time to fit residues: 31.0471 Evaluate side-chains 187 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 91 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100448 restraints weight = 17857.313| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.18 r_work: 0.3018 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12563 Z= 0.295 Angle : 0.734 8.478 17047 Z= 0.375 Chirality : 0.050 0.206 1904 Planarity : 0.006 0.113 2172 Dihedral : 5.941 45.607 1671 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.61 % Favored : 92.33 % Rotamer: Outliers : 3.12 % Allowed : 12.86 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.21), residues: 1512 helix: -1.23 (0.57), residues: 85 sheet: -0.92 (0.20), residues: 619 loop : -1.92 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1298 TYR 0.026 0.002 TYR A 345 PHE 0.025 0.003 PHE A 892 TRP 0.025 0.003 TRP A1337 HIS 0.009 0.002 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00713 (12563) covalent geometry : angle 0.73445 (17047) hydrogen bonds : bond 0.03734 ( 326) hydrogen bonds : angle 5.85249 ( 888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 659 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7878 (ttm) REVERT: A 857 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.8073 (mmm-85) REVERT: A 1032 LYS cc_start: 0.9262 (mttt) cc_final: 0.9031 (mttp) REVERT: A 1092 ILE cc_start: 0.9280 (mm) cc_final: 0.9008 (mm) REVERT: A 1208 THR cc_start: 0.8480 (t) cc_final: 0.8179 (m) REVERT: A 1393 ASN cc_start: 0.6766 (t0) cc_final: 0.5774 (p0) REVERT: B 371 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 372 MET cc_start: 0.8036 (tmm) cc_final: 0.7774 (ttp) outliers start: 42 outliers final: 34 residues processed: 192 average time/residue: 0.0967 time to fit residues: 28.7977 Evaluate side-chains 183 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 310 HIS B 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104454 restraints weight = 17523.568| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.10 r_work: 0.3067 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12563 Z= 0.167 Angle : 0.626 8.999 17047 Z= 0.321 Chirality : 0.047 0.287 1904 Planarity : 0.005 0.114 2172 Dihedral : 5.558 29.093 1671 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.88 % Favored : 93.06 % Rotamer: Outliers : 2.45 % Allowed : 13.90 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.21), residues: 1512 helix: -0.89 (0.59), residues: 85 sheet: -0.78 (0.20), residues: 616 loop : -1.85 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1298 TYR 0.024 0.001 TYR A 989 PHE 0.013 0.002 PHE B 198 TRP 0.019 0.002 TRP A1337 HIS 0.007 0.001 HIS A1372 Details of bonding type rmsd covalent geometry : bond 0.00406 (12563) covalent geometry : angle 0.62587 (17047) hydrogen bonds : bond 0.03195 ( 326) hydrogen bonds : angle 5.62768 ( 888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8385 (pp) REVERT: A 857 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8056 (mmm-85) REVERT: A 1032 LYS cc_start: 0.9234 (mttt) cc_final: 0.8997 (mttp) REVERT: A 1092 ILE cc_start: 0.9267 (mm) cc_final: 0.9015 (mm) REVERT: A 1273 ASP cc_start: 0.8683 (p0) cc_final: 0.8442 (p0) REVERT: A 1393 ASN cc_start: 0.6778 (t0) cc_final: 0.5824 (p0) REVERT: A 1414 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 1434 LEU cc_start: 0.9357 (mt) cc_final: 0.9101 (mp) REVERT: B 75 ASP cc_start: 0.7719 (m-30) cc_final: 0.7312 (m-30) REVERT: B 371 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7258 (mm-30) outliers start: 33 outliers final: 29 residues processed: 182 average time/residue: 0.0990 time to fit residues: 27.9066 Evaluate side-chains 181 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 134 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 147 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 145 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106843 restraints weight = 17461.012| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.16 r_work: 0.3123 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12563 Z= 0.108 Angle : 0.578 8.323 17047 Z= 0.296 Chirality : 0.045 0.299 1904 Planarity : 0.005 0.114 2172 Dihedral : 5.135 21.918 1669 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 1.93 % Allowed : 14.50 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.21), residues: 1512 helix: -0.27 (0.63), residues: 79 sheet: -0.57 (0.21), residues: 615 loop : -1.78 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.023 0.001 TYR A 989 PHE 0.012 0.001 PHE B 198 TRP 0.020 0.001 TRP A1337 HIS 0.006 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00260 (12563) covalent geometry : angle 0.57775 (17047) hydrogen bonds : bond 0.02915 ( 326) hydrogen bonds : angle 5.42168 ( 888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 256 TRP cc_start: 0.8362 (t60) cc_final: 0.8059 (t60) REVERT: A 320 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 857 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.8001 (mmm-85) REVERT: A 1032 LYS cc_start: 0.9159 (mttt) cc_final: 0.8918 (mttp) REVERT: A 1092 ILE cc_start: 0.9269 (mm) cc_final: 0.9041 (mm) REVERT: A 1273 ASP cc_start: 0.8601 (p0) cc_final: 0.8342 (p0) REVERT: A 1291 PHE cc_start: 0.7339 (m-10) cc_final: 0.7118 (m-10) REVERT: A 1393 ASN cc_start: 0.6735 (t0) cc_final: 0.5814 (p0) REVERT: A 1414 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 1434 LEU cc_start: 0.9301 (mt) cc_final: 0.9056 (mp) REVERT: B 75 ASP cc_start: 0.7610 (m-30) cc_final: 0.7246 (m-30) REVERT: B 198 PHE cc_start: 0.7801 (p90) cc_final: 0.7512 (p90) REVERT: B 229 TRP cc_start: 0.8486 (m100) cc_final: 0.8278 (m100) outliers start: 26 outliers final: 21 residues processed: 188 average time/residue: 0.0931 time to fit residues: 27.4203 Evaluate side-chains 177 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 114 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104936 restraints weight = 17472.677| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.15 r_work: 0.3086 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12563 Z= 0.158 Angle : 0.607 8.270 17047 Z= 0.310 Chirality : 0.046 0.277 1904 Planarity : 0.005 0.115 2172 Dihedral : 5.204 29.279 1669 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 2.01 % Allowed : 15.02 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1512 helix: -0.17 (0.63), residues: 79 sheet: -0.57 (0.21), residues: 624 loop : -1.72 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1298 TYR 0.026 0.001 TYR A 989 PHE 0.015 0.002 PHE B 198 TRP 0.019 0.002 TRP A1337 HIS 0.006 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00386 (12563) covalent geometry : angle 0.60657 (17047) hydrogen bonds : bond 0.03019 ( 326) hydrogen bonds : angle 5.42279 ( 888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.511 Fit side-chains REVERT: A 320 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8386 (pp) REVERT: A 1032 LYS cc_start: 0.9199 (mttt) cc_final: 0.8957 (mttp) REVERT: A 1092 ILE cc_start: 0.9288 (mm) cc_final: 0.9055 (mm) REVERT: A 1273 ASP cc_start: 0.8664 (p0) cc_final: 0.8439 (p0) REVERT: A 1393 ASN cc_start: 0.6737 (t0) cc_final: 0.5915 (p0) REVERT: A 1414 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7998 (mt-10) REVERT: A 1434 LEU cc_start: 0.9307 (mt) cc_final: 0.9058 (mp) REVERT: B 75 ASP cc_start: 0.7641 (m-30) cc_final: 0.7244 (m-30) REVERT: B 198 PHE cc_start: 0.7797 (p90) cc_final: 0.7293 (p90) outliers start: 27 outliers final: 26 residues processed: 173 average time/residue: 0.0934 time to fit residues: 25.4681 Evaluate side-chains 178 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1128 MET Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 372 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 103 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 148 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 0.0170 chunk 139 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110252 restraints weight = 17379.150| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.12 r_work: 0.3156 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 12563 Z= 0.101 Angle : 0.554 8.465 17047 Z= 0.284 Chirality : 0.045 0.307 1904 Planarity : 0.005 0.115 2172 Dihedral : 4.888 27.068 1669 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 1.93 % Allowed : 15.32 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1512 helix: 0.11 (0.64), residues: 78 sheet: -0.35 (0.21), residues: 611 loop : -1.69 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 857 TYR 0.023 0.001 TYR A 989 PHE 0.012 0.001 PHE A 987 TRP 0.019 0.001 TRP A1337 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00245 (12563) covalent geometry : angle 0.55390 (17047) hydrogen bonds : bond 0.02729 ( 326) hydrogen bonds : angle 5.26224 ( 888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.426 Fit side-chains REVERT: A 256 TRP cc_start: 0.8408 (t60) cc_final: 0.8127 (t60) REVERT: A 608 PHE cc_start: 0.7463 (t80) cc_final: 0.6969 (t80) REVERT: A 1092 ILE cc_start: 0.9264 (mm) cc_final: 0.9059 (mm) REVERT: A 1273 ASP cc_start: 0.8592 (p0) cc_final: 0.8350 (p0) REVERT: A 1414 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 1434 LEU cc_start: 0.9277 (mt) cc_final: 0.9028 (mp) REVERT: A 1435 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 75 ASP cc_start: 0.7589 (m-30) cc_final: 0.7271 (m-30) REVERT: B 98 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8129 (ptm) REVERT: B 198 PHE cc_start: 0.7657 (p90) cc_final: 0.7383 (p90) REVERT: B 207 GLU cc_start: 0.7940 (tp30) cc_final: 0.7320 (tp30) outliers start: 26 outliers final: 20 residues processed: 181 average time/residue: 0.0975 time to fit residues: 26.9916 Evaluate side-chains 174 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1128 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS B 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106311 restraints weight = 17342.878| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.14 r_work: 0.3101 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12563 Z= 0.152 Angle : 0.599 8.837 17047 Z= 0.305 Chirality : 0.046 0.297 1904 Planarity : 0.005 0.115 2172 Dihedral : 5.021 28.233 1669 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 2.01 % Allowed : 15.76 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.22), residues: 1512 helix: 0.14 (0.64), residues: 78 sheet: -0.36 (0.21), residues: 623 loop : -1.65 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 857 TYR 0.044 0.002 TYR A 19 PHE 0.014 0.002 PHE A 987 TRP 0.023 0.002 TRP A1337 HIS 0.007 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00372 (12563) covalent geometry : angle 0.59912 (17047) hydrogen bonds : bond 0.02959 ( 326) hydrogen bonds : angle 5.30511 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.08 seconds wall clock time: 52 minutes 34.63 seconds (3154.63 seconds total)