Starting phenix.real_space_refine on Mon Jun 16 03:40:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bf1_44486/06_2025/9bf1_44486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bf1_44486/06_2025/9bf1_44486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bf1_44486/06_2025/9bf1_44486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bf1_44486/06_2025/9bf1_44486.map" model { file = "/net/cci-nas-00/data/ceres_data/9bf1_44486/06_2025/9bf1_44486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bf1_44486/06_2025/9bf1_44486.cif" } resolution = 3.1 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 11484 2.51 5 N 3192 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18158 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 9079 Classifications: {'peptide': 1122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1088} Chain breaks: 3 Chain: "B" Number of atoms: 9079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 9079 Classifications: {'peptide': 1122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1088} Chain breaks: 3 Time building chain proxies: 11.86, per 1000 atoms: 0.65 Number of scatterers: 18158 At special positions: 0 Unit cell: (121.9, 132.5, 136.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 3436 8.00 N 3192 7.00 C 11484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.3 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 20 sheets defined 54.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.718A pdb=" N THR A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 37 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.511A pdb=" N SER A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.575A pdb=" N LEU A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.565A pdb=" N GLN A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 207 removed outlier: 3.805A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.028A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.577A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.544A pdb=" N GLU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 435 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.699A pdb=" N THR A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.965A pdb=" N GLN A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.590A pdb=" N HIS A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.530A pdb=" N GLY A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 621 through 629 removed outlier: 4.412A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 657 removed outlier: 4.631A pdb=" N PHE A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 691 removed outlier: 3.755A pdb=" N ILE A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 688 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 removed outlier: 3.750A pdb=" N ASN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 837 removed outlier: 4.075A pdb=" N GLN A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.878A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 880 Processing helix chain 'A' and resid 889 through 901 removed outlier: 3.687A pdb=" N SER A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 937 removed outlier: 3.970A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.732A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.708A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1068 Processing helix chain 'A' and resid 1110 through 1127 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.700A pdb=" N ILE B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 54 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.615A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 3.632A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.874A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.694A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 401 through 435 Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 443 through 460 removed outlier: 4.501A pdb=" N GLN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.663A pdb=" N GLY B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.637A pdb=" N GLU B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 604 through 616 removed outlier: 3.859A pdb=" N LYS B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.554A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 657 removed outlier: 4.257A pdb=" N ALA B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 691 removed outlier: 3.558A pdb=" N LYS B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.643A pdb=" N ASN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 827 through 836 Processing helix chain 'B' and resid 838 through 856 removed outlier: 4.048A pdb=" N GLN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 879 removed outlier: 4.450A pdb=" N ILE B 877 " --> pdb=" O GLY B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 902 Processing helix chain 'B' and resid 909 through 938 removed outlier: 4.362A pdb=" N ARG B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 960 Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1009 through 1014 removed outlier: 3.586A pdb=" N SER B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1019 Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'B' and resid 1045 through 1068 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.826A pdb=" N ILE B1080 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR B1081 " --> pdb=" O ASN B1078 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1077 through 1081' Processing helix chain 'B' and resid 1110 through 1127 Processing helix chain 'B' and resid 1176 through 1190 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.937A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 267 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU A 540 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 269 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 542 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 271 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.916A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 3.704A pdb=" N VAL A 870 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 974 through 975 Processing sheet with id=AA8, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AA9, first strand: chain 'A' and resid 1072 through 1074 Processing sheet with id=AB1, first strand: chain 'A' and resid 1097 through 1099 removed outlier: 6.542A pdb=" N PHE A1131 " --> pdb=" O ILE A1162 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE A1164 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A1133 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A1145 " --> pdb=" O GLU A1163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 47 removed outlier: 5.875A pdb=" N ALA B 43 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY B 541 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 45 " --> pdb=" O GLY B 541 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 267 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 540 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 269 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 542 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 271 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 88 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU B 242 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR B 90 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 133 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR B 243 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU B 135 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB4, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB5, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB6, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'B' and resid 595 through 601 removed outlier: 6.754A pdb=" N LEU B 664 " --> pdb=" O TYR B 775 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 974 through 975 Processing sheet with id=AB9, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC1, first strand: chain 'B' and resid 1072 through 1074 removed outlier: 4.256A pdb=" N ASN B1086 " --> pdb=" O LEU B1099 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B1099 " --> pdb=" O ASN B1086 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B1097 " --> pdb=" O VAL B1088 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP B1098 " --> pdb=" O ILE B1132 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B1134 " --> pdb=" O TRP B1098 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B1100 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B1145 " --> pdb=" O GLU B1163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1137 through 1138 removed outlier: 4.457A pdb=" N GLY B1138 " --> pdb=" O ILE B1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 934 hydrogen bonds defined for protein. 2676 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: 7.21 Time building geometry restraints manager: 5.40 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: 6079 1.34 - 1.46: 3127 1.46 - 1.57: 9242 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 18520 Sorted by residual: bond pdb=" C THR A1045 " pdb=" N PRO A1046 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.38e-02 5.25e+03 2.53e+00 bond pdb=" CG LEU B 142 " pdb=" CD1 LEU B 142 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CA ASP B1070 " pdb=" CB ASP B1070 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.90e-01 bond pdb=" CA ASN A1042 " pdb=" C ASN A1042 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.63e-01 bond pdb=" CB VAL A 502 " pdb=" CG1 VAL A 502 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.49e-01 ... (remaining 18515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 24810 2.09 - 4.17: 185 4.17 - 6.26: 23 6.26 - 8.34: 1 8.34 - 10.43: 1 Bond angle restraints: 25020 Sorted by residual: angle pdb=" C PHE B 999 " pdb=" CA PHE B 999 " pdb=" CB PHE B 999 " ideal model delta sigma weight residual 116.34 109.81 6.53 1.40e+00 5.10e-01 2.17e+01 angle pdb=" N PHE B 999 " pdb=" CA PHE B 999 " pdb=" C PHE B 999 " ideal model delta sigma weight residual 108.00 113.24 -5.24 1.48e+00 4.57e-01 1.25e+01 angle pdb=" CA LEU A 135 " pdb=" CB LEU A 135 " pdb=" CG LEU A 135 " ideal model delta sigma weight residual 116.30 126.73 -10.43 3.50e+00 8.16e-02 8.88e+00 angle pdb=" C PHE A1069 " pdb=" N ASP A1070 " pdb=" CA ASP A1070 " ideal model delta sigma weight residual 122.82 126.76 -3.94 1.42e+00 4.96e-01 7.71e+00 angle pdb=" C PHE B1069 " pdb=" N ASP B1070 " pdb=" CA ASP B1070 " ideal model delta sigma weight residual 122.82 126.63 -3.81 1.42e+00 4.96e-01 7.21e+00 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 10027 17.65 - 35.30: 964 35.30 - 52.96: 131 52.96 - 70.61: 63 70.61 - 88.26: 27 Dihedral angle restraints: 11212 sinusoidal: 4612 harmonic: 6600 Sorted by residual: dihedral pdb=" CA VAL B 98 " pdb=" C VAL B 98 " pdb=" N VAL B 99 " pdb=" CA VAL B 99 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA VAL A 98 " pdb=" C VAL A 98 " pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ARG B 675 " pdb=" C ARG B 675 " pdb=" N GLN B 676 " pdb=" CA GLN B 676 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 11209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1936 0.037 - 0.074: 625 0.074 - 0.111: 152 0.111 - 0.148: 28 0.148 - 0.185: 5 Chirality restraints: 2746 Sorted by residual: chirality pdb=" CG LEU A 135 " pdb=" CB LEU A 135 " pdb=" CD1 LEU A 135 " pdb=" CD2 LEU A 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA ASP A1070 " pdb=" N ASP A1070 " pdb=" C ASP A1070 " pdb=" CB ASP A1070 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ASP B1070 " pdb=" N ASP B1070 " pdb=" C ASP B1070 " pdb=" CB ASP B1070 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 2743 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1049 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C PHE A1049 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE A1049 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A1050 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B1049 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C PHE B1049 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE B1049 " 0.016 2.00e-02 2.50e+03 pdb=" N THR B1050 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1050 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C THR A1050 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A1050 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A1051 " -0.012 2.00e-02 2.50e+03 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 596 2.72 - 3.26: 18403 3.26 - 3.81: 29519 3.81 - 4.35: 35368 4.35 - 4.90: 60769 Nonbonded interactions: 144655 Sorted by model distance: nonbonded pdb=" OG1 THR A 121 " pdb=" OE1 GLN A 124 " model vdw 2.174 3.040 nonbonded pdb=" OG SER A 311 " pdb=" O LEU B 379 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" ND1 HIS A 799 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR B 427 " pdb=" OE2 GLU B 450 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU A 77 " pdb=" OG1 THR A 80 " model vdw 2.232 3.040 ... (remaining 144650 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 44.250 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2759 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 : 0.003 0.042 18520 Z= 0.142 Angle : 0.482 10.429 25020 Z= 0.262 Chirality : 0.040 0.185 2746 Planarity : 0.004 0.048 3256 Dihedral : 14.853 88.261 6928 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2228 helix: 1.72 (0.16), residues: 1084 sheet: -0.12 (0.31), residues: 302 loop : -0.95 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 336 HIS 0.006 0.001 HIS B 836 PHE 0.009 0.001 PHE A 157 TYR 0.021 0.001 TYR A1115 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.13903 ( 934) hydrogen bonds : angle 5.95578 ( 2676) covalent geometry : bond 0.00318 (18520) covalent geometry : angle 0.48202 (25020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ARG cc_start: 0.3167 (mtp180) cc_final: 0.2653 (ttm-80) REVERT: A 978 MET cc_start: 0.2048 (mmt) cc_final: 0.1783 (mmt) REVERT: B 500 LYS cc_start: 0.2382 (ttpt) cc_final: 0.1674 (ttpt) REVERT: B 613 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 1102 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6862 (mmtt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3551 time to fit residues: 84.3181 Evaluate side-chains 130 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 125 GLN A 131 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 495 HIS A 637 GLN A 679 ASN A 794 GLN A 799 HIS A 800 GLN A 805 GLN A 834 GLN A 935 HIS A1060 GLN A1188 HIS B 131 GLN B 141 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN B 668 ASN B 790 HIS ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 HIS B 994 ASN B1060 GLN B1078 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.217941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.187293 restraints weight = 28144.378| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.56 r_work: 0.4180 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.8317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 18520 Z= 0.343 Angle : 1.016 19.136 25020 Z= 0.536 Chirality : 0.055 0.281 2746 Planarity : 0.008 0.079 3256 Dihedral : 6.156 25.791 2460 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 1.60 % Allowed : 9.22 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2228 helix: -0.12 (0.14), residues: 1119 sheet: -0.83 (0.34), residues: 232 loop : -1.68 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 336 HIS 0.019 0.003 HIS B 458 PHE 0.035 0.004 PHE B 241 TYR 0.053 0.004 TYR A1115 ARG 0.015 0.001 ARG A 969 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 934) hydrogen bonds : angle 5.83899 ( 2676) covalent geometry : bond 0.00765 (18520) covalent geometry : angle 1.01589 (25020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.5245 (mt) cc_final: 0.4847 (pt) REVERT: A 327 GLU cc_start: 0.6935 (mp0) cc_final: 0.6348 (mp0) REVERT: A 450 GLU cc_start: 0.7619 (tt0) cc_final: 0.6755 (tt0) REVERT: A 463 GLU cc_start: 0.7326 (mp0) cc_final: 0.6743 (mp0) REVERT: A 522 ASN cc_start: 0.6199 (m-40) cc_final: 0.5737 (m110) REVERT: A 1047 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6508 (tp) REVERT: B 172 ILE cc_start: 0.6243 (mm) cc_final: 0.5469 (mm) REVERT: B 318 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7653 (mt) REVERT: B 408 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6050 (tt0) REVERT: B 469 TYR cc_start: 0.6838 (m-10) cc_final: 0.6527 (m-10) REVERT: B 576 LYS cc_start: 0.6469 (mtmm) cc_final: 0.6238 (mtpp) REVERT: B 613 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 646 LYS cc_start: 0.5437 (mttt) cc_final: 0.5100 (mttt) REVERT: B 786 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6684 (t0) REVERT: B 829 GLU cc_start: 0.6775 (mp0) cc_final: 0.6444 (mp0) REVERT: B 983 TYR cc_start: 0.6843 (p90) cc_final: 0.5816 (p90) REVERT: B 984 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5330 (mtm-85) REVERT: B 1011 GLU cc_start: 0.5773 (tp30) cc_final: 0.5495 (tp30) REVERT: B 1059 GLU cc_start: 0.7116 (pt0) cc_final: 0.6844 (pt0) outliers start: 32 outliers final: 11 residues processed: 250 average time/residue: 0.3297 time to fit residues: 128.3712 Evaluate side-chains 194 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 733 TYR Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1023 TYR Chi-restraints excluded: chain B residue 1047 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 171 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 200 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 160 ASN A 449 GLN A 460 ASN A 637 GLN A 822 GLN A 938 HIS B 70 GLN B 131 GLN B 144 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 307 HIS B 335 ASN B 637 GLN B 668 ASN B 805 GLN B 817 ASN B 821 GLN B1051 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.205607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.171405 restraints weight = 26714.729| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.56 r_work: 0.3987 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.9104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18520 Z= 0.147 Angle : 0.565 11.682 25020 Z= 0.297 Chirality : 0.041 0.200 2746 Planarity : 0.005 0.057 3256 Dihedral : 4.367 27.880 2460 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.20 % Allowed : 11.47 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2228 helix: 1.05 (0.15), residues: 1125 sheet: -0.41 (0.32), residues: 266 loop : -1.35 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 428 HIS 0.007 0.001 HIS B 399 PHE 0.021 0.002 PHE A 472 TYR 0.028 0.002 TYR A1115 ARG 0.010 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 934) hydrogen bonds : angle 4.71873 ( 2676) covalent geometry : bond 0.00327 (18520) covalent geometry : angle 0.56501 (25020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 2.022 Fit side-chains REVERT: A 74 GLU cc_start: 0.6397 (tp30) cc_final: 0.5594 (mm-30) REVERT: A 194 TYR cc_start: 0.7228 (t80) cc_final: 0.7005 (t80) REVERT: A 201 ASP cc_start: 0.7376 (t70) cc_final: 0.7131 (t0) REVERT: A 230 GLU cc_start: 0.6565 (tp30) cc_final: 0.5797 (tp30) REVERT: A 278 ASN cc_start: 0.7261 (t0) cc_final: 0.6502 (t0) REVERT: A 463 GLU cc_start: 0.7921 (mp0) cc_final: 0.7424 (mp0) REVERT: A 816 GLU cc_start: 0.5766 (tp30) cc_final: 0.5376 (tp30) REVERT: B 14 GLN cc_start: 0.6709 (tm-30) cc_final: 0.6164 (tm-30) REVERT: B 172 ILE cc_start: 0.6362 (mm) cc_final: 0.6117 (mm) REVERT: B 273 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6850 (mt-10) REVERT: B 469 TYR cc_start: 0.7378 (m-10) cc_final: 0.6961 (m-10) REVERT: B 557 PHE cc_start: 0.7870 (m-80) cc_final: 0.7615 (m-80) REVERT: B 613 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 797 GLN cc_start: 0.8163 (mp10) cc_final: 0.7922 (mp10) REVERT: B 807 ASN cc_start: 0.6531 (t0) cc_final: 0.6035 (t0) REVERT: B 829 GLU cc_start: 0.7091 (mp0) cc_final: 0.6689 (mp0) REVERT: B 980 LYS cc_start: 0.7254 (mttt) cc_final: 0.6888 (mttt) REVERT: B 983 TYR cc_start: 0.6887 (p90) cc_final: 0.5758 (p90) REVERT: B 986 GLN cc_start: 0.6927 (tp40) cc_final: 0.6607 (tp40) REVERT: B 1008 VAL cc_start: 0.6620 (t) cc_final: 0.6332 (t) REVERT: B 1029 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 1044 MET cc_start: 0.6940 (ptp) cc_final: 0.6384 (ptm) REVERT: B 1059 GLU cc_start: 0.7131 (pt0) cc_final: 0.6885 (pt0) outliers start: 24 outliers final: 11 residues processed: 228 average time/residue: 0.3165 time to fit residues: 109.5801 Evaluate side-chains 191 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 938 HIS Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 784 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 149 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 131 GLN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 HIS A 799 HIS ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN A 938 HIS A 939 ASN B 131 GLN B 141 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS B 460 ASN B 522 ASN B 628 HIS ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.197724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.159759 restraints weight = 26140.806| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.54 r_work: 0.3840 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 1.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 18520 Z= 0.309 Angle : 0.726 9.364 25020 Z= 0.383 Chirality : 0.049 0.502 2746 Planarity : 0.006 0.062 3256 Dihedral : 4.983 21.571 2460 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.61 % Allowed : 12.68 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2228 helix: 0.76 (0.15), residues: 1125 sheet: -0.55 (0.32), residues: 253 loop : -1.52 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 336 HIS 0.026 0.002 HIS A 938 PHE 0.029 0.002 PHE A 49 TYR 0.032 0.003 TYR A1115 ARG 0.015 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 934) hydrogen bonds : angle 5.15909 ( 2676) covalent geometry : bond 0.00709 (18520) covalent geometry : angle 0.72565 (25020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 1.851 Fit side-chains REVERT: A 50 GLN cc_start: 0.7838 (mp10) cc_final: 0.7438 (mp10) REVERT: A 230 GLU cc_start: 0.7172 (tp30) cc_final: 0.6694 (tp30) REVERT: A 254 THR cc_start: 0.7761 (m) cc_final: 0.7281 (p) REVERT: A 262 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7216 (mpp80) REVERT: A 271 ILE cc_start: 0.7667 (mt) cc_final: 0.7138 (mp) REVERT: A 321 LEU cc_start: 0.8093 (mt) cc_final: 0.7888 (mp) REVERT: A 421 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6908 (ttp-110) REVERT: A 466 SER cc_start: 0.8529 (t) cc_final: 0.8250 (m) REVERT: A 591 ASP cc_start: 0.1256 (OUTLIER) cc_final: 0.0641 (p0) REVERT: A 798 PHE cc_start: 0.8270 (m-10) cc_final: 0.8021 (m-80) REVERT: A 799 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7566 (t70) REVERT: A 809 GLU cc_start: 0.6586 (mp0) cc_final: 0.6127 (mp0) REVERT: A 831 SER cc_start: 0.5207 (OUTLIER) cc_final: 0.4377 (t) REVERT: A 922 ASN cc_start: 0.7641 (m-40) cc_final: 0.7410 (m110) REVERT: A 954 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7806 (mtp85) REVERT: A 990 ASP cc_start: 0.6179 (p0) cc_final: 0.5778 (p0) REVERT: A 1025 ARG cc_start: 0.7003 (mmm-85) cc_final: 0.6782 (mmm-85) REVERT: A 1028 PHE cc_start: 0.6965 (m-10) cc_final: 0.6036 (m-10) REVERT: A 1044 MET cc_start: 0.5395 (tpp) cc_final: 0.4774 (ttt) REVERT: A 1059 GLU cc_start: 0.5932 (pt0) cc_final: 0.5520 (pt0) REVERT: A 1083 ARG cc_start: 0.7922 (mmt90) cc_final: 0.7576 (mmm-85) REVERT: B 55 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6442 (mtmt) REVERT: B 117 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7525 (tp30) REVERT: B 255 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8040 (ttm-80) REVERT: B 271 ILE cc_start: 0.8229 (mt) cc_final: 0.7974 (mt) REVERT: B 273 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 552 ILE cc_start: 0.8140 (mm) cc_final: 0.7520 (tt) REVERT: B 578 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7033 (mtt-85) REVERT: B 613 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 803 SER cc_start: 0.8394 (t) cc_final: 0.8109 (p) REVERT: B 820 ARG cc_start: 0.6958 (ttp-170) cc_final: 0.6742 (ttp-170) REVERT: B 829 GLU cc_start: 0.7220 (mp0) cc_final: 0.6968 (mp0) REVERT: B 962 THR cc_start: 0.8460 (m) cc_final: 0.8062 (m) REVERT: B 983 TYR cc_start: 0.7052 (p90) cc_final: 0.5601 (p90) REVERT: B 984 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5377 (mtm-85) REVERT: B 1008 VAL cc_start: 0.7071 (t) cc_final: 0.6661 (t) REVERT: B 1029 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 1044 MET cc_start: 0.7745 (ptp) cc_final: 0.7386 (ptp) REVERT: B 1057 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8267 (mp) outliers start: 52 outliers final: 21 residues processed: 292 average time/residue: 0.3487 time to fit residues: 150.6714 Evaluate side-chains 263 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 ASP Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1023 TYR Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1057 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 214 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 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 506 HIS A 566 ASN A 581 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN A 800 GLN A 917 ASN B 144 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS B 337 ASN B 668 ASN B 805 GLN ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.199004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.160766 restraints weight = 25850.047| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.52 r_work: 0.3854 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 1.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18520 Z= 0.126 Angle : 0.524 12.542 25020 Z= 0.277 Chirality : 0.040 0.230 2746 Planarity : 0.004 0.050 3256 Dihedral : 4.182 22.828 2460 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 1.75 % Allowed : 14.48 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2228 helix: 1.37 (0.15), residues: 1116 sheet: -0.44 (0.32), residues: 261 loop : -1.28 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1186 HIS 0.013 0.001 HIS A 799 PHE 0.018 0.001 PHE A 970 TYR 0.027 0.001 TYR A1115 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 934) hydrogen bonds : angle 4.56122 ( 2676) covalent geometry : bond 0.00279 (18520) covalent geometry : angle 0.52430 (25020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7616 (mp10) cc_final: 0.7347 (mp10) REVERT: A 194 TYR cc_start: 0.7400 (t80) cc_final: 0.7179 (t80) REVERT: A 262 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7322 (mpp80) REVERT: A 421 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6926 (ttp-170) REVERT: A 543 SER cc_start: 0.8009 (t) cc_final: 0.7752 (t) REVERT: A 1025 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6771 (mmm-85) REVERT: A 1028 PHE cc_start: 0.6820 (m-10) cc_final: 0.5800 (m-10) REVERT: A 1059 GLU cc_start: 0.5845 (pt0) cc_final: 0.5452 (pt0) REVERT: A 1074 GLU cc_start: 0.7025 (mp0) cc_final: 0.6736 (pm20) REVERT: B 117 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7459 (tp30) REVERT: B 261 LEU cc_start: 0.8305 (tp) cc_final: 0.8051 (tt) REVERT: B 273 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7263 (mt-10) REVERT: B 551 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7808 (p) REVERT: B 552 ILE cc_start: 0.8101 (mm) cc_final: 0.7543 (tt) REVERT: B 613 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7807 (mt-10) REVERT: B 797 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: B 807 ASN cc_start: 0.7009 (t0) cc_final: 0.6538 (t0) REVERT: B 962 THR cc_start: 0.8478 (m) cc_final: 0.8264 (m) REVERT: B 986 GLN cc_start: 0.7236 (tp40) cc_final: 0.6905 (tp40) REVERT: B 1029 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7530 (mt-10) outliers start: 35 outliers final: 24 residues processed: 262 average time/residue: 0.3467 time to fit residues: 135.9959 Evaluate side-chains 243 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 130 optimal weight: 0.7980 chunk 211 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.0010 chunk 179 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 90 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 805 GLN A 938 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.198521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.159719 restraints weight = 25743.487| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.55 r_work: 0.3839 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 1.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18520 Z= 0.117 Angle : 0.497 9.882 25020 Z= 0.263 Chirality : 0.040 0.190 2746 Planarity : 0.004 0.045 3256 Dihedral : 3.930 23.258 2460 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.05 % Allowed : 14.93 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2228 helix: 1.56 (0.15), residues: 1131 sheet: -0.53 (0.32), residues: 272 loop : -1.14 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1186 HIS 0.003 0.001 HIS A 33 PHE 0.027 0.001 PHE A 362 TYR 0.027 0.001 TYR A1115 ARG 0.006 0.000 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 934) hydrogen bonds : angle 4.37568 ( 2676) covalent geometry : bond 0.00263 (18520) covalent geometry : angle 0.49701 (25020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7543 (mp10) cc_final: 0.7235 (mp10) REVERT: A 194 TYR cc_start: 0.7405 (t80) cc_final: 0.7203 (t80) REVERT: A 262 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7179 (mpp80) REVERT: A 421 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6915 (ttp-170) REVERT: A 551 VAL cc_start: 0.8059 (p) cc_final: 0.7846 (t) REVERT: A 824 MET cc_start: 0.8003 (mmt) cc_final: 0.7755 (mmt) REVERT: A 831 SER cc_start: 0.5996 (OUTLIER) cc_final: 0.5354 (t) REVERT: A 956 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: A 978 MET cc_start: 0.6626 (mmt) cc_final: 0.6344 (mmt) REVERT: A 1025 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6799 (mmm-85) REVERT: A 1028 PHE cc_start: 0.6797 (m-10) cc_final: 0.5840 (m-10) REVERT: A 1059 GLU cc_start: 0.5775 (pt0) cc_final: 0.5404 (pt0) REVERT: A 1083 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7508 (mmt-90) REVERT: B 110 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 117 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7452 (tp30) REVERT: B 218 SER cc_start: 0.7348 (m) cc_final: 0.7075 (p) REVERT: B 230 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6687 (tp30) REVERT: B 255 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7808 (mtm-85) REVERT: B 273 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7261 (mt-10) REVERT: B 457 THR cc_start: 0.8074 (m) cc_final: 0.7736 (p) REVERT: B 551 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7820 (p) REVERT: B 552 ILE cc_start: 0.8095 (mm) cc_final: 0.7584 (tt) REVERT: B 613 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 797 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: B 807 ASN cc_start: 0.7050 (t0) cc_final: 0.6561 (t0) REVERT: B 824 MET cc_start: 0.6475 (mpp) cc_final: 0.5779 (mpp) REVERT: B 962 THR cc_start: 0.8474 (m) cc_final: 0.8265 (m) REVERT: B 983 TYR cc_start: 0.7046 (p90) cc_final: 0.5488 (p90) REVERT: B 984 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5270 (mtm-85) REVERT: B 1029 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 1044 MET cc_start: 0.7659 (ptp) cc_final: 0.7247 (ptm) outliers start: 41 outliers final: 25 residues processed: 259 average time/residue: 0.3555 time to fit residues: 134.6760 Evaluate side-chains 256 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1047 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 213 optimal weight: 0.0870 chunk 188 optimal weight: 0.0970 chunk 150 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 97 optimal weight: 0.0980 chunk 171 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 37 ASN B 144 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.198786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160013 restraints weight = 25538.645| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.55 r_work: 0.3843 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 1.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18520 Z= 0.100 Angle : 0.473 9.340 25020 Z= 0.249 Chirality : 0.039 0.169 2746 Planarity : 0.004 0.067 3256 Dihedral : 3.800 23.770 2460 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.65 % Allowed : 15.33 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2228 helix: 1.74 (0.16), residues: 1126 sheet: -0.47 (0.32), residues: 267 loop : -1.10 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1186 HIS 0.005 0.000 HIS A 799 PHE 0.023 0.001 PHE A 362 TYR 0.026 0.001 TYR A1115 ARG 0.005 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 934) hydrogen bonds : angle 4.27117 ( 2676) covalent geometry : bond 0.00217 (18520) covalent geometry : angle 0.47316 (25020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7874 (ttpp) cc_final: 0.7655 (ttpp) REVERT: A 50 GLN cc_start: 0.7501 (mp10) cc_final: 0.7144 (mp10) REVERT: A 194 TYR cc_start: 0.7342 (t80) cc_final: 0.7117 (t80) REVERT: A 262 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7142 (mpp80) REVERT: A 421 ARG cc_start: 0.7212 (ttp-170) cc_final: 0.6938 (ttp-170) REVERT: A 831 SER cc_start: 0.6112 (OUTLIER) cc_final: 0.5492 (m) REVERT: A 954 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7304 (mtt-85) REVERT: A 956 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: A 1025 ARG cc_start: 0.7014 (mmm-85) cc_final: 0.6785 (mmm-85) REVERT: A 1028 PHE cc_start: 0.6785 (m-10) cc_final: 0.5944 (m-10) REVERT: B 110 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6849 (mt-10) REVERT: B 117 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7471 (tp30) REVERT: B 218 SER cc_start: 0.7348 (m) cc_final: 0.7067 (p) REVERT: B 273 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7229 (mt-10) REVERT: B 457 THR cc_start: 0.8048 (m) cc_final: 0.7699 (p) REVERT: B 470 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6614 (mp0) REVERT: B 551 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7800 (p) REVERT: B 552 ILE cc_start: 0.8078 (mm) cc_final: 0.7563 (tt) REVERT: B 613 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7796 (mt-10) REVERT: B 663 MET cc_start: 0.3819 (tmm) cc_final: 0.3445 (ttp) REVERT: B 797 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: B 807 ASN cc_start: 0.7066 (t0) cc_final: 0.6582 (t0) REVERT: B 824 MET cc_start: 0.6499 (mpp) cc_final: 0.5766 (mpp) REVERT: B 983 TYR cc_start: 0.7011 (p90) cc_final: 0.5372 (p90) REVERT: B 984 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5305 (mtm-85) REVERT: B 1029 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7584 (mt-10) REVERT: B 1044 MET cc_start: 0.7600 (ptp) cc_final: 0.7207 (ptm) outliers start: 33 outliers final: 21 residues processed: 258 average time/residue: 0.3600 time to fit residues: 135.7172 Evaluate side-chains 252 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1047 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 16 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 70 optimal weight: 0.0570 chunk 157 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A 449 GLN A 453 GLN A 507 ASN A 566 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 37 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN B 799 HIS ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.193611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154845 restraints weight = 25266.395| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.49 r_work: 0.3774 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 1.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18520 Z= 0.184 Angle : 0.570 11.139 25020 Z= 0.296 Chirality : 0.042 0.173 2746 Planarity : 0.004 0.072 3256 Dihedral : 4.163 21.454 2460 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.85 % Allowed : 15.88 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2228 helix: 1.51 (0.15), residues: 1127 sheet: -0.41 (0.32), residues: 263 loop : -1.12 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1027 HIS 0.007 0.001 HIS A 799 PHE 0.040 0.002 PHE A 195 TYR 0.024 0.002 TYR A1115 ARG 0.007 0.001 ARG A 972 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 934) hydrogen bonds : angle 4.58247 ( 2676) covalent geometry : bond 0.00431 (18520) covalent geometry : angle 0.57048 (25020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7340 (mp10) cc_final: 0.6798 (mp10) REVERT: A 150 LEU cc_start: 0.7946 (tp) cc_final: 0.7725 (tt) REVERT: A 195 PHE cc_start: 0.6282 (t80) cc_final: 0.5993 (t80) REVERT: A 271 ILE cc_start: 0.7714 (mt) cc_final: 0.7161 (mm) REVERT: A 284 GLU cc_start: 0.7274 (tp30) cc_final: 0.7022 (tp30) REVERT: A 421 ARG cc_start: 0.7326 (ttp-170) cc_final: 0.7016 (ttp-110) REVERT: A 549 ASP cc_start: 0.7882 (t0) cc_final: 0.7636 (t0) REVERT: A 783 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 831 SER cc_start: 0.7207 (OUTLIER) cc_final: 0.6834 (t) REVERT: A 925 ASP cc_start: 0.7611 (t0) cc_final: 0.7177 (t0) REVERT: A 956 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: A 1059 GLU cc_start: 0.6097 (pt0) cc_final: 0.5843 (pt0) REVERT: B 117 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7639 (tp30) REVERT: B 207 GLN cc_start: 0.7855 (tp40) cc_final: 0.7479 (tp40) REVERT: B 273 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 314 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7364 (ttm-80) REVERT: B 366 SER cc_start: 0.7683 (m) cc_final: 0.7442 (m) REVERT: B 457 THR cc_start: 0.8125 (m) cc_final: 0.7758 (p) REVERT: B 470 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6781 (mp0) REVERT: B 551 VAL cc_start: 0.8055 (p) cc_final: 0.7839 (p) REVERT: B 552 ILE cc_start: 0.8132 (mm) cc_final: 0.7563 (tt) REVERT: B 613 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 794 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.5799 (mp10) REVERT: B 807 ASN cc_start: 0.7076 (t0) cc_final: 0.6595 (t0) REVERT: B 824 MET cc_start: 0.6550 (mpp) cc_final: 0.5815 (mpp) REVERT: B 983 TYR cc_start: 0.6991 (p90) cc_final: 0.5407 (p90) REVERT: B 984 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5350 (mtm-85) REVERT: B 986 GLN cc_start: 0.7167 (tp40) cc_final: 0.6808 (tp40) REVERT: B 1044 MET cc_start: 0.7800 (ptp) cc_final: 0.7461 (ptm) outliers start: 37 outliers final: 19 residues processed: 260 average time/residue: 0.3786 time to fit residues: 142.6558 Evaluate side-chains 242 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 566 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS A1022 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.194650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155892 restraints weight = 25461.402| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.50 r_work: 0.3798 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 1.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18520 Z= 0.134 Angle : 0.518 9.058 25020 Z= 0.270 Chirality : 0.040 0.149 2746 Planarity : 0.004 0.045 3256 Dihedral : 3.939 23.986 2460 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.60 % Allowed : 16.83 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2228 helix: 1.55 (0.15), residues: 1144 sheet: -0.39 (0.32), residues: 266 loop : -1.07 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1186 HIS 0.006 0.001 HIS A 799 PHE 0.025 0.001 PHE A 195 TYR 0.024 0.001 TYR A1115 ARG 0.006 0.000 ARG B 914 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 934) hydrogen bonds : angle 4.40382 ( 2676) covalent geometry : bond 0.00309 (18520) covalent geometry : angle 0.51751 (25020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7732 (t0) cc_final: 0.7407 (t0) REVERT: A 50 GLN cc_start: 0.7270 (mp10) cc_final: 0.6737 (mp10) REVERT: A 124 GLN cc_start: 0.7888 (mp10) cc_final: 0.7659 (mp10) REVERT: A 150 LEU cc_start: 0.7866 (tp) cc_final: 0.7653 (tt) REVERT: A 421 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7031 (ttp-110) REVERT: A 783 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7449 (mp) REVERT: A 806 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6597 (mm-30) REVERT: A 831 SER cc_start: 0.7088 (OUTLIER) cc_final: 0.6679 (m) REVERT: A 925 ASP cc_start: 0.7675 (t0) cc_final: 0.7310 (t0) REVERT: A 954 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7274 (mtt-85) REVERT: A 956 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: B 117 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7673 (tp30) REVERT: B 207 GLN cc_start: 0.7822 (tp40) cc_final: 0.7490 (tp40) REVERT: B 273 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7227 (mt-10) REVERT: B 366 SER cc_start: 0.7623 (m) cc_final: 0.7393 (m) REVERT: B 457 THR cc_start: 0.8054 (m) cc_final: 0.7660 (p) REVERT: B 551 VAL cc_start: 0.8060 (p) cc_final: 0.7839 (p) REVERT: B 552 ILE cc_start: 0.8111 (mm) cc_final: 0.7569 (tt) REVERT: B 613 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 807 ASN cc_start: 0.7114 (t0) cc_final: 0.6652 (t0) REVERT: B 824 MET cc_start: 0.6508 (mpp) cc_final: 0.5787 (mpp) REVERT: B 984 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5330 (mtm-85) outliers start: 32 outliers final: 24 residues processed: 246 average time/residue: 0.3385 time to fit residues: 123.3338 Evaluate side-chains 247 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 10 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 453 GLN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.191845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153169 restraints weight = 25444.102| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.50 r_work: 0.3759 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 1.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18520 Z= 0.174 Angle : 0.557 8.900 25020 Z= 0.290 Chirality : 0.042 0.197 2746 Planarity : 0.004 0.048 3256 Dihedral : 4.078 22.173 2460 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.65 % Allowed : 17.33 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2228 helix: 1.54 (0.15), residues: 1128 sheet: -0.44 (0.31), residues: 276 loop : -1.06 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 336 HIS 0.006 0.001 HIS A 799 PHE 0.036 0.002 PHE A1033 TYR 0.023 0.002 TYR A1115 ARG 0.012 0.001 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 934) hydrogen bonds : angle 4.51473 ( 2676) covalent geometry : bond 0.00408 (18520) covalent geometry : angle 0.55657 (25020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7801 (t0) cc_final: 0.7476 (t0) REVERT: A 40 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7587 (ttpp) REVERT: A 50 GLN cc_start: 0.7182 (mp10) cc_final: 0.6771 (mp10) REVERT: A 124 GLN cc_start: 0.8082 (mp10) cc_final: 0.7770 (mp10) REVERT: A 150 LEU cc_start: 0.7895 (tp) cc_final: 0.7690 (tt) REVERT: A 162 GLU cc_start: 0.7948 (mp0) cc_final: 0.7725 (mp0) REVERT: A 195 PHE cc_start: 0.6828 (t80) cc_final: 0.6375 (t80) REVERT: A 421 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7127 (ttp-110) REVERT: A 466 SER cc_start: 0.8610 (t) cc_final: 0.8329 (m) REVERT: A 534 ASP cc_start: 0.7597 (m-30) cc_final: 0.7352 (m-30) REVERT: A 783 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7523 (mp) REVERT: A 831 SER cc_start: 0.7366 (OUTLIER) cc_final: 0.6989 (m) REVERT: A 925 ASP cc_start: 0.7596 (t0) cc_final: 0.7248 (t0) REVERT: A 956 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: A 990 ASP cc_start: 0.7269 (p0) cc_final: 0.6618 (p0) REVERT: A 1020 GLN cc_start: 0.7790 (mt0) cc_final: 0.7532 (mt0) REVERT: A 1059 GLU cc_start: 0.6224 (pt0) cc_final: 0.5964 (pt0) REVERT: B 117 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7708 (tp30) REVERT: B 207 GLN cc_start: 0.7867 (tp40) cc_final: 0.7551 (tp40) REVERT: B 273 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 314 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7428 (ttm-80) REVERT: B 366 SER cc_start: 0.7674 (m) cc_final: 0.7430 (m) REVERT: B 470 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6717 (mp0) REVERT: B 551 VAL cc_start: 0.8050 (p) cc_final: 0.7846 (p) REVERT: B 552 ILE cc_start: 0.8123 (mm) cc_final: 0.7577 (tt) REVERT: B 613 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 794 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.5785 (mp10) REVERT: B 824 MET cc_start: 0.6484 (mpp) cc_final: 0.5794 (mpp) REVERT: B 984 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5341 (mtm-85) outliers start: 33 outliers final: 22 residues processed: 261 average time/residue: 0.3343 time to fit residues: 128.6562 Evaluate side-chains 253 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 173 optimal weight: 0.0040 chunk 115 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 131 GLN A 160 ASN A 449 GLN A 453 GLN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.186575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148251 restraints weight = 25127.905| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.39 r_work: 0.3704 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 1.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 18520 Z= 0.339 Angle : 0.705 10.467 25020 Z= 0.362 Chirality : 0.049 0.304 2746 Planarity : 0.005 0.053 3256 Dihedral : 4.677 20.981 2460 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.00 % Allowed : 17.13 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2228 helix: 0.96 (0.15), residues: 1132 sheet: -0.65 (0.29), residues: 287 loop : -1.23 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 336 HIS 0.011 0.002 HIS A 553 PHE 0.032 0.003 PHE A 362 TYR 0.028 0.003 TYR B 89 ARG 0.007 0.001 ARG A 921 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 934) hydrogen bonds : angle 4.97261 ( 2676) covalent geometry : bond 0.00807 (18520) covalent geometry : angle 0.70465 (25020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10378.18 seconds wall clock time: 178 minutes 17.84 seconds (10697.84 seconds total)