Starting phenix.real_space_refine on Wed Jul 30 15:00:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsi_30834/07_2025/7dsi_30834.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsi_30834/07_2025/7dsi_30834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsi_30834/07_2025/7dsi_30834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsi_30834/07_2025/7dsi_30834.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsi_30834/07_2025/7dsi_30834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsi_30834/07_2025/7dsi_30834.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 7826 2.51 5 N 2015 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12185 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 9124 Classifications: {'peptide': 1145} Link IDs: {'PTRANS': 36, 'TRANS': 1108} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.18, per 1000 atoms: 0.67 Number of scatterers: 12185 At special positions: 0 Unit cell: (141.37, 109.72, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 3 15.00 Mg 1 11.99 O 2280 8.00 N 2015 7.00 C 7826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 777 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 35.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.574A pdb=" N VAL A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.712A pdb=" N GLY A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.164A pdb=" N THR A 455 " --> pdb=" O CYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 576 removed outlier: 3.971A pdb=" N SER A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 568 " --> pdb=" O CYS A 564 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.543A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.839A pdb=" N ILE A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.697A pdb=" N TYR A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.532A pdb=" N TYR A 639 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.676A pdb=" N ALA A 698 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.933A pdb=" N ARG A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 777 removed outlier: 4.098A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 809 removed outlier: 3.512A pdb=" N ALA A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 890 through 907 removed outlier: 4.675A pdb=" N THR A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.565A pdb=" N LYS A 925 " --> pdb=" O GLU A 922 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP A 926 " --> pdb=" O TYR A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 922 through 926' Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.779A pdb=" N GLU A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.917A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.535A pdb=" N ASN A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.526A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 removed outlier: 3.568A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 Processing helix chain 'A' and resid 1106 through 1121 removed outlier: 3.584A pdb=" N ALA A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1140 Processing helix chain 'A' and resid 1168 through 1175 removed outlier: 3.518A pdb=" N VAL A1175 " --> pdb=" O ARG A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1188 removed outlier: 3.562A pdb=" N LYS A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A1186 " --> pdb=" O LYS A1182 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1200 removed outlier: 3.510A pdb=" N ASN A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1200 " --> pdb=" O MET A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1231 through 1241 removed outlier: 3.729A pdb=" N ILE A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.621A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1261' Processing helix chain 'A' and resid 1266 through 1292 removed outlier: 3.797A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1273 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.608A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1321 removed outlier: 4.037A pdb=" N VAL A1313 " --> pdb=" O TYR A1309 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A1314 " --> pdb=" O PHE A1310 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1316 " --> pdb=" O GLY A1312 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1318 " --> pdb=" O TYR A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1335 through 1347 removed outlier: 3.654A pdb=" N GLY A1339 " --> pdb=" O ASP A1335 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A1341 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A1345 " --> pdb=" O PHE A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1357 Processing helix chain 'A' and resid 1367 through 1373 Processing helix chain 'A' and resid 1377 through 1404 removed outlier: 4.713A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Proline residue: A1392 - end of helix removed outlier: 3.684A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1417 removed outlier: 3.516A pdb=" N ILE A1410 " --> pdb=" O THR A1406 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 95 removed outlier: 4.297A pdb=" N ILE B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.573A pdb=" N VAL B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.514A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.702A pdb=" N GLN B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 388 removed outlier: 3.636A pdb=" N ILE B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 398 removed outlier: 4.424A pdb=" N TRP B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.592A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1010 through 1013 removed outlier: 6.860A pdb=" N ILE A1070 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A1100 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR A1125 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE A1145 " --> pdb=" O THR A1125 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA A1127 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 687 through 689 removed outlier: 3.508A pdb=" N VAL A 687 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A 682 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 782 removed outlier: 3.772A pdb=" N LEU A 781 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 795 " --> pdb=" O LEU A 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 814 through 817 removed outlier: 7.093A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 825 " --> pdb=" O LYS A 832 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.549A pdb=" N VAL B 178 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 360 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.146A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 246 through 247 335 hydrogen bonds defined for protein. 954 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: 4.39 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3837 1.34 - 1.46: 2992 1.46 - 1.58: 5538 1.58 - 1.70: 8 1.70 - 1.83: 91 Bond restraints: 12466 Sorted by residual: bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.597 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.607 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C4 ACP A1601 " pdb=" C5 ACP A1601 " ideal model delta sigma weight residual 1.386 1.467 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3G ACP A1601 " pdb=" PG ACP A1601 " ideal model delta sigma weight residual 1.532 1.608 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 ACP A1601 " pdb=" C6 ACP A1601 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 12461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 16252 2.33 - 4.67: 546 4.67 - 7.00: 80 7.00 - 9.33: 27 9.33 - 11.67: 7 Bond angle restraints: 16912 Sorted by residual: angle pdb=" C LYS A1294 " pdb=" N ASN A1295 " pdb=" CA ASN A1295 " ideal model delta sigma weight residual 122.46 131.31 -8.85 1.41e+00 5.03e-01 3.94e+01 angle pdb=" C GLU A1084 " pdb=" N ASP A1085 " pdb=" CA ASP A1085 " ideal model delta sigma weight residual 125.66 135.67 -10.01 1.85e+00 2.92e-01 2.93e+01 angle pdb=" C ARG A1363 " pdb=" N GLU A1364 " pdb=" CA GLU A1364 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N LEU B 393 " pdb=" CA LEU B 393 " pdb=" C LEU B 393 " ideal model delta sigma weight residual 114.56 108.96 5.60 1.27e+00 6.20e-01 1.95e+01 angle pdb=" C PHE A 232 " pdb=" N GLN A 233 " pdb=" CA GLN A 233 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 ... (remaining 16907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 7151 22.35 - 44.70: 291 44.70 - 67.05: 26 67.05 - 89.39: 13 89.39 - 111.74: 20 Dihedral angle restraints: 7501 sinusoidal: 3108 harmonic: 4393 Sorted by residual: dihedral pdb=" CA PHE A1045 " pdb=" C PHE A1045 " pdb=" N ASN A1046 " pdb=" CA ASN A1046 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N TYR A1219 " pdb=" CA TYR A1219 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA MET B 169 " pdb=" C MET B 169 " pdb=" N LYS B 170 " pdb=" CA LYS B 170 " ideal model delta harmonic sigma weight residual -180.00 -147.54 -32.46 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 7498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1307 0.055 - 0.111: 450 0.111 - 0.166: 103 0.166 - 0.222: 20 0.222 - 0.277: 8 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C5 NAG D 2 " pdb=" O4 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE B 327 " pdb=" CA ILE B 327 " pdb=" CG1 ILE B 327 " pdb=" CG2 ILE B 327 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1885 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.13e+01 pdb=" C PHE B 398 " 0.111 2.00e-02 2.50e+03 pdb=" O PHE B 398 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY B 399 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.032 2.00e-02 2.50e+03 6.20e-02 3.85e+01 pdb=" C VAL A1408 " -0.107 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " -0.025 2.00e-02 2.50e+03 2.42e-02 1.46e+01 pdb=" CG TRP B 142 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.002 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1502 2.75 - 3.29: 11320 3.29 - 3.83: 19951 3.83 - 4.36: 23933 4.36 - 4.90: 40414 Nonbonded interactions: 97120 Sorted by model distance: nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU B 102 " pdb=" OH TYR B 360 " model vdw 2.257 3.040 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 609 " pdb=" O MET A1222 " model vdw 2.307 3.040 nonbonded pdb=" O LEU A 658 " pdb=" OH TYR A1256 " model vdw 2.319 3.040 ... (remaining 97115 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.006 0.101 12476 Z= 0.272 Angle : 1.062 15.563 16939 Z= 0.554 Chirality : 0.060 0.277 1888 Planarity : 0.006 0.073 2139 Dihedral : 14.174 111.741 4676 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.66 % Rotamer: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.15), residues: 1499 helix: -4.64 (0.09), residues: 556 sheet: -2.68 (0.34), residues: 159 loop : -3.31 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 142 HIS 0.011 0.002 HIS A 778 PHE 0.039 0.003 PHE A1287 TYR 0.035 0.003 TYR B 228 ARG 0.011 0.001 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.01444 ( 3) link_NAG-ASN : angle 4.40715 ( 9) link_BETA1-4 : bond 0.01162 ( 3) link_BETA1-4 : angle 5.67540 ( 9) hydrogen bonds : bond 0.30470 ( 335) hydrogen bonds : angle 11.17711 ( 954) link_BETA1-6 : bond 0.01058 ( 1) link_BETA1-6 : angle 1.61672 ( 3) SS BOND : bond 0.00403 ( 3) SS BOND : angle 1.93889 ( 6) covalent geometry : bond 0.00588 (12466) covalent geometry : angle 1.04858 (16912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 HIS cc_start: 0.7671 (p-80) cc_final: 0.7450 (p-80) REVERT: A 827 MET cc_start: 0.8150 (mpp) cc_final: 0.7925 (mpp) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.2905 time to fit residues: 73.9057 Evaluate side-chains 102 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 0.0020 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 194 ASN A 278 HIS A 412 ASN A 550 ASN A 556 ASN A 571 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 769 HIS A1176 HIS A1307 HIS B 50 ASN B 125 HIS B 171 ASN B 172 ASN B 186 HIS B 313 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110424 restraints weight = 16603.517| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.45 r_work: 0.3227 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12476 Z= 0.144 Angle : 0.733 9.778 16939 Z= 0.380 Chirality : 0.047 0.271 1888 Planarity : 0.005 0.040 2139 Dihedral : 13.073 89.844 1824 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 1.53 % Allowed : 9.86 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.17), residues: 1499 helix: -3.22 (0.15), residues: 548 sheet: -1.93 (0.37), residues: 164 loop : -2.92 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 142 HIS 0.005 0.001 HIS A 778 PHE 0.015 0.002 PHE A 739 TYR 0.019 0.002 TYR A 740 ARG 0.006 0.001 ARG A 731 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 3) link_NAG-ASN : angle 3.47966 ( 9) link_BETA1-4 : bond 0.00696 ( 3) link_BETA1-4 : angle 3.68541 ( 9) hydrogen bonds : bond 0.05445 ( 335) hydrogen bonds : angle 5.99769 ( 954) link_BETA1-6 : bond 0.00597 ( 1) link_BETA1-6 : angle 1.68256 ( 3) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.66621 ( 6) covalent geometry : bond 0.00318 (12466) covalent geometry : angle 0.72418 (16912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 678 GLU cc_start: 0.8117 (tp30) cc_final: 0.7868 (tp30) REVERT: A 778 HIS cc_start: 0.8333 (p-80) cc_final: 0.7807 (p-80) REVERT: A 827 MET cc_start: 0.8601 (mpp) cc_final: 0.7980 (mpp) REVERT: A 925 LYS cc_start: 0.9330 (mmtm) cc_final: 0.9085 (mmmt) REVERT: A 944 LEU cc_start: 0.9573 (tt) cc_final: 0.9299 (pp) REVERT: A 945 GLU cc_start: 0.8712 (mp0) cc_final: 0.8194 (mp0) REVERT: A 1082 TYR cc_start: 0.8688 (t80) cc_final: 0.8434 (t80) REVERT: A 1218 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 1305 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8352 (pp) REVERT: A 1413 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8021 (mt-10) REVERT: B 403 ILE cc_start: 0.6900 (mm) cc_final: 0.6142 (mm) outliers start: 20 outliers final: 7 residues processed: 136 average time/residue: 0.2540 time to fit residues: 50.9932 Evaluate side-chains 109 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 149 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 278 HIS ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103782 restraints weight = 16872.725| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.56 r_work: 0.3121 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12476 Z= 0.219 Angle : 0.735 10.381 16939 Z= 0.373 Chirality : 0.049 0.306 1888 Planarity : 0.004 0.040 2139 Dihedral : 10.905 86.220 1824 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.87 % Favored : 92.06 % Rotamer: Outliers : 1.91 % Allowed : 11.70 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.19), residues: 1499 helix: -2.36 (0.18), residues: 553 sheet: -1.72 (0.39), residues: 160 loop : -2.58 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 308 HIS 0.008 0.002 HIS B 347 PHE 0.022 0.002 PHE B 128 TYR 0.023 0.002 TYR A1292 ARG 0.017 0.001 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 3) link_NAG-ASN : angle 3.77512 ( 9) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 4.06875 ( 9) hydrogen bonds : bond 0.04418 ( 335) hydrogen bonds : angle 5.46992 ( 954) link_BETA1-6 : bond 0.00467 ( 1) link_BETA1-6 : angle 1.73049 ( 3) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.75981 ( 6) covalent geometry : bond 0.00517 (12466) covalent geometry : angle 0.72348 (16912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 519 MET cc_start: 0.0257 (ptt) cc_final: -0.0675 (mmt) REVERT: A 677 MET cc_start: 0.9099 (mmt) cc_final: 0.8260 (mmt) REVERT: A 778 HIS cc_start: 0.8350 (p-80) cc_final: 0.7750 (p-80) REVERT: A 827 MET cc_start: 0.8662 (mpp) cc_final: 0.8061 (mpp) REVERT: A 849 MET cc_start: 0.8640 (ppp) cc_final: 0.8323 (ppp) REVERT: A 870 CYS cc_start: 0.9048 (t) cc_final: 0.8827 (t) REVERT: A 925 LYS cc_start: 0.9343 (mmtm) cc_final: 0.9048 (mmmt) REVERT: A 944 LEU cc_start: 0.9573 (tt) cc_final: 0.9274 (pp) REVERT: A 945 GLU cc_start: 0.8843 (mp0) cc_final: 0.8271 (mp0) REVERT: A 1082 TYR cc_start: 0.8740 (t80) cc_final: 0.8490 (t80) REVERT: A 1153 ARG cc_start: 0.7380 (mtt90) cc_final: 0.7087 (mtm180) REVERT: A 1305 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8475 (pp) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 0.2882 time to fit residues: 55.4922 Evaluate side-chains 112 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 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 = 0.4161 r_free = 0.4161 target = 0.172073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103683 restraints weight = 16732.448| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.55 r_work: 0.3119 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12476 Z= 0.190 Angle : 0.692 10.006 16939 Z= 0.351 Chirality : 0.047 0.309 1888 Planarity : 0.004 0.034 2139 Dihedral : 9.796 87.838 1824 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.40 % Favored : 92.53 % Rotamer: Outliers : 2.52 % Allowed : 12.61 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.20), residues: 1499 helix: -1.95 (0.20), residues: 563 sheet: -1.61 (0.40), residues: 160 loop : -2.46 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 308 HIS 0.007 0.001 HIS A 778 PHE 0.018 0.002 PHE A1365 TYR 0.019 0.002 TYR A 740 ARG 0.009 0.000 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 3) link_NAG-ASN : angle 3.52419 ( 9) link_BETA1-4 : bond 0.00656 ( 3) link_BETA1-4 : angle 4.03830 ( 9) hydrogen bonds : bond 0.03836 ( 335) hydrogen bonds : angle 5.18474 ( 954) link_BETA1-6 : bond 0.01143 ( 1) link_BETA1-6 : angle 1.45824 ( 3) SS BOND : bond 0.00140 ( 3) SS BOND : angle 3.01976 ( 6) covalent geometry : bond 0.00448 (12466) covalent geometry : angle 0.67833 (16912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.0953 (ptt) cc_final: -0.0733 (mmt) REVERT: A 778 HIS cc_start: 0.8382 (p-80) cc_final: 0.7813 (p-80) REVERT: A 827 MET cc_start: 0.8704 (mpp) cc_final: 0.8063 (mpp) REVERT: A 925 LYS cc_start: 0.9365 (mmtm) cc_final: 0.9062 (mmmt) REVERT: A 945 GLU cc_start: 0.8859 (mp0) cc_final: 0.8654 (mp0) REVERT: A 1153 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7110 (mtm180) REVERT: A 1305 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8406 (pp) REVERT: B 335 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8608 (tm) REVERT: B 403 ILE cc_start: 0.7004 (mm) cc_final: 0.6681 (mm) outliers start: 33 outliers final: 19 residues processed: 129 average time/residue: 0.2483 time to fit residues: 47.7850 Evaluate side-chains 115 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.167580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098670 restraints weight = 16655.747| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.44 r_work: 0.3027 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 12476 Z= 0.331 Angle : 0.773 9.940 16939 Z= 0.393 Chirality : 0.052 0.440 1888 Planarity : 0.004 0.039 2139 Dihedral : 9.492 88.869 1824 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.34 % Favored : 91.59 % Rotamer: Outliers : 3.29 % Allowed : 13.61 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.20), residues: 1499 helix: -1.93 (0.20), residues: 569 sheet: -1.67 (0.39), residues: 163 loop : -2.53 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 308 HIS 0.010 0.002 HIS B 347 PHE 0.023 0.002 PHE A1045 TYR 0.029 0.002 TYR A1292 ARG 0.006 0.001 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 3) link_NAG-ASN : angle 4.11483 ( 9) link_BETA1-4 : bond 0.00468 ( 3) link_BETA1-4 : angle 4.13044 ( 9) hydrogen bonds : bond 0.04145 ( 335) hydrogen bonds : angle 5.27798 ( 954) link_BETA1-6 : bond 0.00494 ( 1) link_BETA1-6 : angle 1.57968 ( 3) SS BOND : bond 0.00206 ( 3) SS BOND : angle 2.09232 ( 6) covalent geometry : bond 0.00790 (12466) covalent geometry : angle 0.76038 (16912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.1173 (ptt) cc_final: -0.0646 (mmt) REVERT: A 677 MET cc_start: 0.9015 (mmm) cc_final: 0.8405 (mmt) REVERT: A 778 HIS cc_start: 0.8464 (p-80) cc_final: 0.7877 (p-80) REVERT: A 827 MET cc_start: 0.8730 (mpp) cc_final: 0.8123 (mpp) REVERT: A 849 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8352 (ppp) REVERT: A 915 GLN cc_start: 0.8225 (pp30) cc_final: 0.7978 (pp30) REVERT: A 925 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9074 (mmmt) REVERT: A 1082 TYR cc_start: 0.8693 (t80) cc_final: 0.8438 (t80) REVERT: A 1153 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7190 (mtm-85) REVERT: A 1305 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8537 (pp) REVERT: B 335 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8754 (tm) outliers start: 43 outliers final: 28 residues processed: 132 average time/residue: 0.2533 time to fit residues: 49.4336 Evaluate side-chains 122 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.172402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104478 restraints weight = 16765.448| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.44 r_work: 0.3120 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12476 Z= 0.129 Angle : 0.643 8.974 16939 Z= 0.324 Chirality : 0.046 0.320 1888 Planarity : 0.003 0.036 2139 Dihedral : 8.805 89.635 1824 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 2.37 % Allowed : 15.06 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.20), residues: 1499 helix: -1.51 (0.21), residues: 553 sheet: -1.44 (0.41), residues: 160 loop : -2.34 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 603 HIS 0.005 0.001 HIS A 778 PHE 0.019 0.001 PHE A1365 TYR 0.017 0.001 TYR A 740 ARG 0.006 0.000 ARG A 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 3) link_NAG-ASN : angle 3.47751 ( 9) link_BETA1-4 : bond 0.00768 ( 3) link_BETA1-4 : angle 3.40308 ( 9) hydrogen bonds : bond 0.03405 ( 335) hydrogen bonds : angle 4.93896 ( 954) link_BETA1-6 : bond 0.00553 ( 1) link_BETA1-6 : angle 1.49617 ( 3) SS BOND : bond 0.00042 ( 3) SS BOND : angle 1.19635 ( 6) covalent geometry : bond 0.00295 (12466) covalent geometry : angle 0.63288 (16912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.1200 (ptt) cc_final: -0.0544 (mmt) REVERT: A 603 TRP cc_start: 0.7880 (m100) cc_final: 0.7577 (m100) REVERT: A 778 HIS cc_start: 0.8390 (p-80) cc_final: 0.7819 (p-80) REVERT: A 827 MET cc_start: 0.8712 (mpp) cc_final: 0.8109 (mpp) REVERT: A 849 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8327 (ppp) REVERT: A 894 GLU cc_start: 0.8257 (pp20) cc_final: 0.7941 (pp20) REVERT: A 923 TYR cc_start: 0.8716 (t80) cc_final: 0.8447 (t80) REVERT: A 925 LYS cc_start: 0.9342 (mmtm) cc_final: 0.9036 (mmmt) REVERT: A 930 TYR cc_start: 0.8303 (m-10) cc_final: 0.7834 (m-10) REVERT: A 1082 TYR cc_start: 0.8684 (t80) cc_final: 0.8429 (t80) REVERT: A 1153 ARG cc_start: 0.7366 (mtt90) cc_final: 0.6952 (mtm180) REVERT: A 1305 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8290 (pp) REVERT: B 194 SER cc_start: 0.8163 (m) cc_final: 0.7932 (m) REVERT: B 335 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8554 (tm) REVERT: B 376 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8691 (mt) outliers start: 31 outliers final: 18 residues processed: 125 average time/residue: 0.3092 time to fit residues: 57.4367 Evaluate side-chains 115 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 376 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.0070 chunk 78 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102593 restraints weight = 16579.917| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.51 r_work: 0.3097 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12476 Z= 0.165 Angle : 0.658 8.568 16939 Z= 0.334 Chirality : 0.046 0.327 1888 Planarity : 0.004 0.035 2139 Dihedral : 8.521 88.120 1824 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 2.45 % Allowed : 15.60 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.20), residues: 1499 helix: -1.37 (0.21), residues: 553 sheet: -1.36 (0.41), residues: 160 loop : -2.31 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 603 HIS 0.010 0.001 HIS A 278 PHE 0.018 0.001 PHE A1365 TYR 0.017 0.001 TYR A 740 ARG 0.016 0.001 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 3) link_NAG-ASN : angle 3.51422 ( 9) link_BETA1-4 : bond 0.00599 ( 3) link_BETA1-4 : angle 3.29901 ( 9) hydrogen bonds : bond 0.03392 ( 335) hydrogen bonds : angle 4.86594 ( 954) link_BETA1-6 : bond 0.00611 ( 1) link_BETA1-6 : angle 1.15409 ( 3) SS BOND : bond 0.00084 ( 3) SS BOND : angle 1.10476 ( 6) covalent geometry : bond 0.00386 (12466) covalent geometry : angle 0.64860 (16912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 3.159 Fit side-chains revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 519 MET cc_start: 0.1302 (ptt) cc_final: -0.0390 (mmt) REVERT: A 778 HIS cc_start: 0.8402 (p-80) cc_final: 0.7808 (p-80) REVERT: A 827 MET cc_start: 0.8735 (mpp) cc_final: 0.8167 (mpp) REVERT: A 849 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8318 (ppp) REVERT: A 894 GLU cc_start: 0.8317 (pp20) cc_final: 0.7994 (pp20) REVERT: A 923 TYR cc_start: 0.8786 (t80) cc_final: 0.8468 (t80) REVERT: A 925 LYS cc_start: 0.9347 (mmtm) cc_final: 0.9036 (mmmt) REVERT: A 930 TYR cc_start: 0.8361 (m-10) cc_final: 0.8135 (m-10) REVERT: A 1042 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7168 (mmtt) REVERT: A 1082 TYR cc_start: 0.8701 (t80) cc_final: 0.8442 (t80) REVERT: A 1153 ARG cc_start: 0.7359 (mtt90) cc_final: 0.7050 (mtm180) REVERT: A 1305 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8412 (pp) REVERT: B 170 LYS cc_start: 0.8814 (tttm) cc_final: 0.8228 (tptt) REVERT: B 194 SER cc_start: 0.8222 (m) cc_final: 0.7983 (m) REVERT: B 335 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8591 (tm) REVERT: B 376 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8725 (mt) outliers start: 32 outliers final: 23 residues processed: 128 average time/residue: 0.3978 time to fit residues: 76.5403 Evaluate side-chains 126 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 376 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.1980 chunk 114 optimal weight: 0.0470 chunk 128 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.173678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104859 restraints weight = 16725.676| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.52 r_work: 0.3127 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12476 Z= 0.119 Angle : 0.623 8.970 16939 Z= 0.316 Chirality : 0.044 0.291 1888 Planarity : 0.003 0.037 2139 Dihedral : 8.017 86.417 1824 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 2.22 % Allowed : 15.83 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.21), residues: 1499 helix: -1.18 (0.22), residues: 557 sheet: -1.25 (0.41), residues: 160 loop : -2.26 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 603 HIS 0.005 0.001 HIS A 778 PHE 0.018 0.001 PHE A1365 TYR 0.017 0.001 TYR A 740 ARG 0.012 0.000 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 3) link_NAG-ASN : angle 3.17547 ( 9) link_BETA1-4 : bond 0.00601 ( 3) link_BETA1-4 : angle 3.00696 ( 9) hydrogen bonds : bond 0.03143 ( 335) hydrogen bonds : angle 4.74615 ( 954) link_BETA1-6 : bond 0.00669 ( 1) link_BETA1-6 : angle 1.11347 ( 3) SS BOND : bond 0.00037 ( 3) SS BOND : angle 0.95917 ( 6) covalent geometry : bond 0.00272 (12466) covalent geometry : angle 0.61508 (16912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.1663 (pmm) cc_final: -0.0232 (mtm) REVERT: A 480 THR cc_start: 0.5890 (OUTLIER) cc_final: 0.5672 (p) REVERT: A 519 MET cc_start: 0.1277 (ptt) cc_final: -0.0395 (mmt) REVERT: A 603 TRP cc_start: 0.7752 (m100) cc_final: 0.7442 (m100) REVERT: A 778 HIS cc_start: 0.8340 (p-80) cc_final: 0.7785 (p-80) REVERT: A 827 MET cc_start: 0.8732 (mpp) cc_final: 0.8093 (mpp) REVERT: A 865 ARG cc_start: 0.6891 (ptm160) cc_final: 0.6669 (ptm160) REVERT: A 894 GLU cc_start: 0.8335 (pp20) cc_final: 0.8010 (pp20) REVERT: A 925 LYS cc_start: 0.9330 (mmtm) cc_final: 0.8970 (mmmt) REVERT: A 929 LYS cc_start: 0.9439 (mtpt) cc_final: 0.9230 (mttt) REVERT: A 1082 TYR cc_start: 0.8688 (t80) cc_final: 0.8433 (t80) REVERT: A 1153 ARG cc_start: 0.7321 (mtt90) cc_final: 0.6969 (mtm180) REVERT: A 1305 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8361 (pp) REVERT: B 69 VAL cc_start: 0.9052 (p) cc_final: 0.8818 (p) REVERT: B 170 LYS cc_start: 0.8820 (tttm) cc_final: 0.8270 (tptp) REVERT: B 194 SER cc_start: 0.8146 (m) cc_final: 0.7904 (m) REVERT: B 335 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8509 (tm) REVERT: B 376 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8710 (mt) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.2372 time to fit residues: 45.5998 Evaluate side-chains 125 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 376 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 0 optimal weight: 40.0000 chunk 61 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104729 restraints weight = 16632.877| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.49 r_work: 0.3129 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12476 Z= 0.131 Angle : 0.629 8.682 16939 Z= 0.318 Chirality : 0.044 0.288 1888 Planarity : 0.003 0.035 2139 Dihedral : 7.718 85.186 1824 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 2.22 % Allowed : 16.28 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.21), residues: 1499 helix: -1.08 (0.22), residues: 565 sheet: -1.15 (0.41), residues: 160 loop : -2.22 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 603 HIS 0.005 0.001 HIS A 278 PHE 0.019 0.001 PHE A1365 TYR 0.017 0.001 TYR A 740 ARG 0.010 0.000 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 3) link_NAG-ASN : angle 3.15364 ( 9) link_BETA1-4 : bond 0.00606 ( 3) link_BETA1-4 : angle 2.91586 ( 9) hydrogen bonds : bond 0.03102 ( 335) hydrogen bonds : angle 4.67424 ( 954) link_BETA1-6 : bond 0.00427 ( 1) link_BETA1-6 : angle 1.01375 ( 3) SS BOND : bond 0.00040 ( 3) SS BOND : angle 0.91119 ( 6) covalent geometry : bond 0.00304 (12466) covalent geometry : angle 0.62082 (16912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7949 (tm-30) REVERT: A 265 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.6522 (ttp-170) REVERT: A 480 THR cc_start: 0.5883 (OUTLIER) cc_final: 0.5655 (p) REVERT: A 519 MET cc_start: 0.1213 (ptt) cc_final: -0.0431 (mmt) REVERT: A 603 TRP cc_start: 0.7719 (m100) cc_final: 0.7412 (m100) REVERT: A 684 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8591 (mm) REVERT: A 778 HIS cc_start: 0.8332 (p-80) cc_final: 0.7757 (p-80) REVERT: A 827 MET cc_start: 0.8729 (mpp) cc_final: 0.8092 (mpp) REVERT: A 894 GLU cc_start: 0.8386 (pp20) cc_final: 0.8087 (pp20) REVERT: A 930 TYR cc_start: 0.8316 (m-10) cc_final: 0.7932 (m-10) REVERT: A 944 LEU cc_start: 0.9609 (tt) cc_final: 0.9256 (mt) REVERT: A 1153 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6900 (mtm-85) REVERT: A 1218 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 1305 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 69 VAL cc_start: 0.9027 (p) cc_final: 0.8799 (p) REVERT: B 96 GLN cc_start: 0.7867 (mm110) cc_final: 0.7447 (pt0) REVERT: B 170 LYS cc_start: 0.8810 (tttm) cc_final: 0.8256 (tptp) REVERT: B 194 SER cc_start: 0.8198 (m) cc_final: 0.7967 (m) REVERT: B 335 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8548 (tm) REVERT: B 402 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7323 (mmmm) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.3246 time to fit residues: 63.9316 Evaluate side-chains 127 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 116 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.173576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104743 restraints weight = 16553.498| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.49 r_work: 0.3133 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12476 Z= 0.132 Angle : 0.638 9.438 16939 Z= 0.321 Chirality : 0.044 0.286 1888 Planarity : 0.003 0.037 2139 Dihedral : 7.631 84.571 1824 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 2.29 % Allowed : 16.36 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.21), residues: 1499 helix: -1.00 (0.22), residues: 565 sheet: -1.05 (0.42), residues: 157 loop : -2.22 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 603 HIS 0.007 0.001 HIS A 778 PHE 0.019 0.001 PHE A1365 TYR 0.017 0.001 TYR A 740 ARG 0.009 0.000 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 3) link_NAG-ASN : angle 3.11350 ( 9) link_BETA1-4 : bond 0.00559 ( 3) link_BETA1-4 : angle 2.84858 ( 9) hydrogen bonds : bond 0.03115 ( 335) hydrogen bonds : angle 4.66006 ( 954) link_BETA1-6 : bond 0.00469 ( 1) link_BETA1-6 : angle 0.96702 ( 3) SS BOND : bond 0.00275 ( 3) SS BOND : angle 3.75070 ( 6) covalent geometry : bond 0.00310 (12466) covalent geometry : angle 0.62675 (16912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.1688 (pmm) cc_final: -0.0313 (mtm) REVERT: A 261 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 480 THR cc_start: 0.5948 (OUTLIER) cc_final: 0.5713 (p) REVERT: A 519 MET cc_start: 0.1256 (ptt) cc_final: -0.0420 (mmt) REVERT: A 603 TRP cc_start: 0.7724 (m100) cc_final: 0.7426 (m100) REVERT: A 684 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8598 (mm) REVERT: A 778 HIS cc_start: 0.8357 (p-80) cc_final: 0.7746 (p-80) REVERT: A 825 ILE cc_start: 0.8451 (tp) cc_final: 0.7981 (tp) REVERT: A 827 MET cc_start: 0.8736 (mpp) cc_final: 0.8103 (mpp) REVERT: A 849 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8338 (ppp) REVERT: A 894 GLU cc_start: 0.8314 (pp20) cc_final: 0.8046 (pp20) REVERT: A 930 TYR cc_start: 0.8312 (m-10) cc_final: 0.7942 (m-80) REVERT: A 944 LEU cc_start: 0.9601 (tt) cc_final: 0.9257 (mt) REVERT: A 1153 ARG cc_start: 0.7260 (mtt90) cc_final: 0.6940 (mtm-85) REVERT: A 1218 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 1305 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8367 (pp) REVERT: B 69 VAL cc_start: 0.9051 (p) cc_final: 0.8839 (p) REVERT: B 96 GLN cc_start: 0.7823 (mm110) cc_final: 0.7432 (pt0) REVERT: B 170 LYS cc_start: 0.8756 (tttm) cc_final: 0.8214 (tptp) REVERT: B 194 SER cc_start: 0.8165 (m) cc_final: 0.7888 (m) REVERT: B 335 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8515 (tm) REVERT: B 402 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7312 (mmmm) outliers start: 30 outliers final: 22 residues processed: 122 average time/residue: 0.3650 time to fit residues: 70.6388 Evaluate side-chains 125 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1219 TYR Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 145 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 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 = 0.4152 r_free = 0.4152 target = 0.174405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110801 restraints weight = 16544.806| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.96 r_work: 0.3056 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12476 Z= 0.111 Angle : 0.622 9.784 16939 Z= 0.312 Chirality : 0.043 0.263 1888 Planarity : 0.003 0.036 2139 Dihedral : 7.333 79.729 1824 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 2.14 % Allowed : 16.28 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.21), residues: 1499 helix: -0.83 (0.22), residues: 566 sheet: -1.30 (0.39), residues: 180 loop : -2.15 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 603 HIS 0.007 0.001 HIS A 778 PHE 0.016 0.001 PHE A1365 TYR 0.018 0.001 TYR A 930 ARG 0.008 0.000 ARG A 714 Details of bonding type rmsd link_NAG-ASN : bond 0.01199 ( 3) link_NAG-ASN : angle 2.82612 ( 9) link_BETA1-4 : bond 0.00573 ( 3) link_BETA1-4 : angle 2.66390 ( 9) hydrogen bonds : bond 0.02949 ( 335) hydrogen bonds : angle 4.53998 ( 954) link_BETA1-6 : bond 0.00927 ( 1) link_BETA1-6 : angle 3.14031 ( 3) SS BOND : bond 0.00158 ( 3) SS BOND : angle 3.03864 ( 6) covalent geometry : bond 0.00253 (12466) covalent geometry : angle 0.61144 (16912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9131.91 seconds wall clock time: 163 minutes 14.13 seconds (9794.13 seconds total)