Starting phenix.real_space_refine on Wed Jan 22 07:06:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bf1_44486/01_2025/9bf1_44486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bf1_44486/01_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_44486/01_2025/9bf1_44486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bf1_44486/01_2025/9bf1_44486.map" model { file = "/net/cci-nas-00/data/ceres_data/9bf1_44486/01_2025/9bf1_44486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bf1_44486/01_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 13.25, per 1000 atoms: 0.73 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: 4.60 Conformation dependent library (CDL) restraints added in 2.2 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: 2.28 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: 7.79 Time building geometry restraints manager: 5.29 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: 0.09 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: 10.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 45.570 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.230 ------------------------------------------------------------------------------- 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= 0.207 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 *********************** 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 : 1.926 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: 0.3654 time to fit residues: 86.5917 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 : 1.960 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.217821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.187240 restraints weight = 28159.560| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.56 r_work: 0.4180 rms_B_bonded: 3.23 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= 0.493 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 *********************** 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 : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.5244 (mt) cc_final: 0.4846 (pt) REVERT: A 327 GLU cc_start: 0.6939 (mp0) cc_final: 0.6350 (mp0) REVERT: A 450 GLU cc_start: 0.7618 (tt0) cc_final: 0.6752 (tt0) REVERT: A 463 GLU cc_start: 0.7334 (mp0) cc_final: 0.6752 (mp0) REVERT: A 522 ASN cc_start: 0.6201 (m-40) cc_final: 0.5738 (m110) REVERT: A 1047 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6503 (tp) REVERT: B 172 ILE cc_start: 0.6238 (mm) cc_final: 0.5468 (mm) REVERT: B 318 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7655 (mt) REVERT: B 408 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6050 (tt0) REVERT: B 469 TYR cc_start: 0.6837 (m-10) cc_final: 0.6526 (m-10) REVERT: B 576 LYS cc_start: 0.6474 (mtmm) cc_final: 0.6242 (mtpp) REVERT: B 613 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 646 LYS cc_start: 0.5434 (mttt) cc_final: 0.5097 (mttt) REVERT: B 786 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6682 (t0) REVERT: B 829 GLU cc_start: 0.6776 (mp0) cc_final: 0.6443 (mp0) REVERT: B 983 TYR cc_start: 0.6843 (p90) cc_final: 0.5818 (p90) REVERT: B 984 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5330 (mtm-85) REVERT: B 1011 GLU cc_start: 0.5782 (tp30) cc_final: 0.5500 (tp30) REVERT: B 1059 GLU cc_start: 0.7122 (pt0) cc_final: 0.6848 (pt0) outliers start: 32 outliers final: 11 residues processed: 250 average time/residue: 0.3018 time to fit residues: 116.3775 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 : 1.989 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 495 HIS A 637 GLN A 799 HIS A 822 GLN A 938 HIS A 956 GLN B 70 GLN B 131 GLN B 141 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 ASN B 821 GLN B 923 ASN B1051 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.202955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168312 restraints weight = 26364.215| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.70 r_work: 0.3929 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.9789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18520 Z= 0.290 Angle : 0.632 11.427 25020 Z= 0.333 Chirality : 0.044 0.208 2746 Planarity : 0.005 0.062 3256 Dihedral : 4.573 27.200 2460 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.45 % Allowed : 11.17 % Favored : 87.37 % 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: -0.22 (0.17), residues: 2228 helix: 0.88 (0.15), residues: 1121 sheet: -0.54 (0.31), residues: 276 loop : -1.38 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1037 HIS 0.009 0.001 HIS A 496 PHE 0.024 0.002 PHE A 970 TYR 0.026 0.002 TYR A1115 ARG 0.014 0.001 ARG A 478 *********************** 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 248 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.6637 (m-10) cc_final: 0.6321 (m-10) REVERT: A 50 GLN cc_start: 0.6850 (mp10) cc_final: 0.6031 (mp10) REVERT: A 74 GLU cc_start: 0.6584 (tp30) cc_final: 0.5801 (mm-30) REVERT: A 230 GLU cc_start: 0.6651 (tp30) cc_final: 0.6352 (tp30) REVERT: A 278 ASN cc_start: 0.7907 (t0) cc_final: 0.7396 (t0) REVERT: A 312 SER cc_start: 0.8400 (p) cc_final: 0.8185 (m) REVERT: A 379 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 463 GLU cc_start: 0.8136 (mp0) cc_final: 0.7514 (mp0) REVERT: A 490 SER cc_start: 0.7802 (m) cc_final: 0.7601 (t) REVERT: A 814 SER cc_start: 0.8370 (t) cc_final: 0.7945 (m) REVERT: A 816 GLU cc_start: 0.6202 (tp30) cc_final: 0.5911 (tp30) REVERT: A 928 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7342 (mp) REVERT: A 1028 PHE cc_start: 0.6035 (m-10) cc_final: 0.5333 (m-10) REVERT: B 14 GLN cc_start: 0.6934 (tm-30) cc_final: 0.6373 (tm-30) REVERT: B 105 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7042 (tp) REVERT: B 172 ILE cc_start: 0.6566 (mm) cc_final: 0.6364 (mm) REVERT: B 271 ILE cc_start: 0.8256 (mt) cc_final: 0.7615 (mp) REVERT: B 273 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7005 (mt-10) REVERT: B 366 SER cc_start: 0.8228 (p) cc_final: 0.7941 (m) REVERT: B 521 LEU cc_start: 0.8125 (tp) cc_final: 0.7879 (tt) REVERT: B 578 ARG cc_start: 0.7400 (mtt180) cc_final: 0.7063 (mtt-85) REVERT: B 613 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 797 GLN cc_start: 0.8238 (mp10) cc_final: 0.7924 (mp10) REVERT: B 807 ASN cc_start: 0.6809 (t0) cc_final: 0.6308 (t0) REVERT: B 962 THR cc_start: 0.8310 (m) cc_final: 0.7794 (p) REVERT: B 980 LYS cc_start: 0.7364 (mttt) cc_final: 0.7112 (mttt) REVERT: B 983 TYR cc_start: 0.6894 (p90) cc_final: 0.5703 (p90) REVERT: B 984 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5368 (mtm-85) REVERT: B 986 GLN cc_start: 0.7018 (tp40) cc_final: 0.6615 (tp40) REVERT: B 1008 VAL cc_start: 0.6647 (t) cc_final: 0.6364 (t) REVERT: B 1029 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 1044 MET cc_start: 0.7103 (ptp) cc_final: 0.6536 (ptm) REVERT: B 1059 GLU cc_start: 0.7203 (pt0) cc_final: 0.6937 (pt0) outliers start: 29 outliers final: 12 residues processed: 240 average time/residue: 0.3538 time to fit residues: 129.7950 Evaluate side-chains 211 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 928 LEU 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 105 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 984 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 149 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 206 optimal weight: 0.0570 chunk 15 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 GLN B 144 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** B 807 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 = 0.4490 r_free = 0.4490 target = 0.203023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166122 restraints weight = 26367.742| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.53 r_work: 0.3932 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 1.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18520 Z= 0.190 Angle : 0.524 11.889 25020 Z= 0.277 Chirality : 0.041 0.336 2746 Planarity : 0.004 0.059 3256 Dihedral : 4.123 24.990 2460 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.15 % Allowed : 12.47 % Favored : 85.37 % 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: 0.23 (0.18), residues: 2228 helix: 1.29 (0.15), residues: 1139 sheet: -0.29 (0.34), residues: 242 loop : -1.28 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.043 0.001 HIS A 938 PHE 0.024 0.001 PHE B 970 TYR 0.033 0.001 TYR A1115 ARG 0.006 0.000 ARG A 675 *********************** 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 253 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 1.844 Fit side-chains REVERT: A 49 PHE cc_start: 0.7177 (m-10) cc_final: 0.6736 (m-10) REVERT: A 50 GLN cc_start: 0.7250 (mp10) cc_final: 0.6619 (mp10) REVERT: A 230 GLU cc_start: 0.6702 (tp30) cc_final: 0.6162 (tp30) REVERT: A 234 ASN cc_start: 0.6002 (p0) cc_final: 0.5618 (p0) REVERT: A 271 ILE cc_start: 0.7227 (mt) cc_final: 0.6873 (mt) REVERT: A 278 ASN cc_start: 0.8072 (t0) cc_final: 0.7723 (t0) REVERT: A 490 SER cc_start: 0.7982 (m) cc_final: 0.7720 (t) REVERT: A 534 ASP cc_start: 0.7108 (t0) cc_final: 0.6889 (m-30) REVERT: A 568 LEU cc_start: 0.7427 (mp) cc_final: 0.7190 (mt) REVERT: A 814 SER cc_start: 0.8546 (t) cc_final: 0.8124 (m) REVERT: A 831 SER cc_start: 0.3818 (OUTLIER) cc_final: 0.2525 (p) REVERT: A 956 GLN cc_start: 0.7177 (tt0) cc_final: 0.6740 (tt0) REVERT: A 970 PHE cc_start: 0.7598 (m-80) cc_final: 0.7223 (m-80) REVERT: A 1028 PHE cc_start: 0.6230 (m-10) cc_final: 0.5352 (m-10) REVERT: A 1044 MET cc_start: 0.4217 (tpp) cc_final: 0.3473 (ttt) REVERT: A 1047 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7329 (tp) REVERT: B 1 MET cc_start: -0.1775 (OUTLIER) cc_final: -0.2364 (ptm) REVERT: B 14 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6816 (tm-30) REVERT: B 55 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6806 (mtmt) REVERT: B 249 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7426 (mmmt) REVERT: B 273 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7142 (mt-10) REVERT: B 469 TYR cc_start: 0.7740 (m-10) cc_final: 0.7400 (m-10) REVERT: B 578 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6879 (mtt-85) REVERT: B 613 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 797 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: B 807 ASN cc_start: 0.6915 (t0) cc_final: 0.6411 (t0) REVERT: B 980 LYS cc_start: 0.7339 (mttt) cc_final: 0.7097 (mttt) REVERT: B 983 TYR cc_start: 0.6955 (p90) cc_final: 0.5688 (p90) REVERT: B 984 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.5226 (mtm-85) REVERT: B 986 GLN cc_start: 0.7086 (tp40) cc_final: 0.6826 (tp40) REVERT: B 1008 VAL cc_start: 0.6718 (t) cc_final: 0.6149 (t) REVERT: B 1029 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 1044 MET cc_start: 0.7263 (ptp) cc_final: 0.6834 (ptm) outliers start: 43 outliers final: 23 residues processed: 240 average time/residue: 0.3277 time to fit residues: 118.4772 Evaluate side-chains 226 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 379 LEU 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 797 GLN Chi-restraints excluded: chain B residue 824 MET 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 1045 THR 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: 3.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 HIS A 553 HIS ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS A 939 ASN B 131 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 628 HIS ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.196243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.158071 restraints weight = 25760.641| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.46 r_work: 0.3818 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 1.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 18520 Z= 0.352 Angle : 0.652 11.909 25020 Z= 0.344 Chirality : 0.046 0.290 2746 Planarity : 0.005 0.065 3256 Dihedral : 4.639 41.074 2460 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.86 % Allowed : 14.13 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.01 (0.18), residues: 2228 helix: 1.14 (0.15), residues: 1124 sheet: -0.39 (0.32), residues: 259 loop : -1.40 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 336 HIS 0.013 0.001 HIS A 495 PHE 0.024 0.002 PHE B 195 TYR 0.025 0.002 TYR A1115 ARG 0.010 0.001 ARG A1001 *********************** 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 309 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7053 (tp30) cc_final: 0.6823 (tp30) REVERT: A 194 TYR cc_start: 0.7570 (t80) cc_final: 0.7340 (t80) REVERT: A 271 ILE cc_start: 0.7584 (mt) cc_final: 0.6819 (mp) REVERT: A 342 PHE cc_start: 0.7746 (m-80) cc_final: 0.7482 (m-80) REVERT: A 556 ASP cc_start: 0.7003 (p0) cc_final: 0.6734 (p0) REVERT: A 663 MET cc_start: 0.4291 (tmm) cc_final: 0.4082 (tmm) REVERT: A 799 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7463 (t70) REVERT: A 809 GLU cc_start: 0.6871 (mp0) cc_final: 0.6445 (mp0) REVERT: A 831 SER cc_start: 0.6334 (OUTLIER) cc_final: 0.5766 (t) REVERT: A 834 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6894 (mm-40) REVERT: A 1025 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.6845 (mmm-85) REVERT: A 1028 PHE cc_start: 0.6907 (m-10) cc_final: 0.6041 (m-10) REVERT: A 1059 GLU cc_start: 0.6543 (pt0) cc_final: 0.6025 (pt0) REVERT: A 1083 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7535 (mmm-85) REVERT: B 14 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 24 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7292 (mp) REVERT: B 117 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: B 230 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6386 (tp30) REVERT: B 271 ILE cc_start: 0.8237 (mt) cc_final: 0.7966 (mt) REVERT: B 273 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 289 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7432 (mt0) REVERT: B 521 LEU cc_start: 0.8298 (tp) cc_final: 0.8067 (tt) REVERT: B 613 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 962 THR cc_start: 0.8542 (m) cc_final: 0.7990 (p) REVERT: B 984 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5389 (mtm-85) REVERT: B 986 GLN cc_start: 0.7308 (tp40) cc_final: 0.6912 (tp40) REVERT: B 1029 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 1057 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8277 (mp) outliers start: 57 outliers final: 22 residues processed: 293 average time/residue: 0.3439 time to fit residues: 148.3649 Evaluate side-chains 256 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS 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 245 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 834 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 92 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1057 LEU 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: 0.4980 chunk 34 optimal weight: 0.0000 chunk 39 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 131 GLN A 449 GLN A 506 HIS A 566 ASN A 797 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.198012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.159477 restraints weight = 25797.801| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.56 r_work: 0.3839 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 1.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18520 Z= 0.171 Angle : 0.501 6.904 25020 Z= 0.265 Chirality : 0.040 0.173 2746 Planarity : 0.004 0.048 3256 Dihedral : 4.056 23.392 2460 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.90 % Allowed : 16.13 % Favored : 81.96 % 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 (0.18), residues: 2228 helix: 1.53 (0.15), residues: 1124 sheet: -0.50 (0.32), residues: 259 loop : -1.24 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1186 HIS 0.006 0.001 HIS A 495 PHE 0.017 0.001 PHE A 251 TYR 0.027 0.001 TYR A1115 ARG 0.005 0.000 ARG A 86 *********************** 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 272 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6949 (tp30) cc_final: 0.6700 (tp30) REVERT: A 194 TYR cc_start: 0.7420 (t80) cc_final: 0.7217 (t80) REVERT: A 262 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7565 (tpp80) REVERT: A 271 ILE cc_start: 0.7728 (mt) cc_final: 0.7395 (mt) REVERT: A 284 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7058 (tp30) REVERT: A 312 SER cc_start: 0.8572 (p) cc_final: 0.8257 (m) REVERT: A 806 GLU cc_start: 0.6875 (mp0) cc_final: 0.6612 (mp0) REVERT: A 824 MET cc_start: 0.8002 (mmt) cc_final: 0.7695 (mmt) REVERT: A 831 SER cc_start: 0.6329 (OUTLIER) cc_final: 0.5715 (m) REVERT: A 954 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7540 (mtp85) REVERT: A 1006 ASP cc_start: 0.6032 (m-30) cc_final: 0.5735 (m-30) REVERT: A 1025 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6831 (mmm-85) REVERT: A 1028 PHE cc_start: 0.6887 (m-10) cc_final: 0.5997 (m-10) REVERT: A 1059 GLU cc_start: 0.6283 (pt0) cc_final: 0.5986 (pt0) REVERT: B 14 GLN cc_start: 0.7345 (tm-30) cc_final: 0.6745 (tm-30) REVERT: B 24 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7163 (mp) REVERT: B 117 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7578 (tp30) REVERT: B 271 ILE cc_start: 0.8262 (mt) cc_final: 0.8030 (mt) REVERT: B 289 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7455 (mt0) REVERT: B 420 MET cc_start: 0.8052 (tpp) cc_final: 0.7786 (mmt) REVERT: B 613 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7791 (mt-10) REVERT: B 663 MET cc_start: 0.3946 (tmm) cc_final: 0.3554 (ttp) REVERT: B 797 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: B 807 ASN cc_start: 0.7058 (t0) cc_final: 0.6594 (t0) REVERT: B 962 THR cc_start: 0.8563 (m) cc_final: 0.8345 (m) REVERT: B 984 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5273 (mtm-85) REVERT: B 986 GLN cc_start: 0.7285 (tp40) cc_final: 0.6906 (tp40) REVERT: B 1029 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7578 (mt-10) outliers start: 38 outliers final: 25 residues processed: 263 average time/residue: 0.3512 time to fit residues: 136.8288 Evaluate side-chains 258 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 212 ARG 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 733 TYR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 831 SER 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 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 94 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 934 VAL 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: 10.0000 chunk 188 optimal weight: 0.0170 chunk 150 optimal weight: 0.0980 chunk 98 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 800 GLN A 920 GLN A 938 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.196915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158155 restraints weight = 25622.260| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.56 r_work: 0.3821 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 1.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18520 Z= 0.172 Angle : 0.492 9.094 25020 Z= 0.257 Chirality : 0.040 0.158 2746 Planarity : 0.004 0.049 3256 Dihedral : 3.917 22.596 2460 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.10 % Allowed : 16.38 % Favored : 81.51 % 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: 1.62 (0.15), residues: 1132 sheet: -0.47 (0.32), residues: 276 loop : -1.11 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1186 HIS 0.003 0.000 HIS A 33 PHE 0.024 0.001 PHE A 195 TYR 0.026 0.001 TYR A1115 ARG 0.004 0.000 ARG A 190 *********************** 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 274 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6897 (tp30) cc_final: 0.6663 (tp30) REVERT: A 194 TYR cc_start: 0.7422 (t80) cc_final: 0.7221 (t80) REVERT: A 259 SER cc_start: 0.6559 (OUTLIER) cc_final: 0.6347 (p) REVERT: A 262 ARG cc_start: 0.7858 (tpp80) cc_final: 0.7564 (tpp80) REVERT: A 271 ILE cc_start: 0.7750 (mt) cc_final: 0.7549 (mt) REVERT: A 806 GLU cc_start: 0.6874 (mp0) cc_final: 0.6665 (mp0) REVERT: A 824 MET cc_start: 0.8035 (mmt) cc_final: 0.7805 (mmt) REVERT: A 831 SER cc_start: 0.6574 (OUTLIER) cc_final: 0.5925 (m) REVERT: A 834 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7331 (mm-40) REVERT: A 954 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7641 (mtp85) REVERT: A 990 ASP cc_start: 0.6430 (p0) cc_final: 0.6122 (p0) REVERT: A 1006 ASP cc_start: 0.6382 (m-30) cc_final: 0.5993 (m-30) REVERT: A 1028 PHE cc_start: 0.6890 (m-10) cc_final: 0.6032 (m-10) REVERT: A 1059 GLU cc_start: 0.6249 (pt0) cc_final: 0.5881 (pt0) REVERT: B 14 GLN cc_start: 0.7348 (tm-30) cc_final: 0.6781 (tm-30) REVERT: B 24 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7167 (mp) REVERT: B 117 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7588 (tp30) REVERT: B 271 ILE cc_start: 0.8251 (mt) cc_final: 0.7799 (mt) REVERT: B 273 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7231 (mt-10) REVERT: B 613 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 797 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: B 807 ASN cc_start: 0.7071 (t0) cc_final: 0.6617 (t0) REVERT: B 962 THR cc_start: 0.8556 (m) cc_final: 0.8347 (m) REVERT: B 984 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5263 (mtm-85) REVERT: B 986 GLN cc_start: 0.7346 (tp40) cc_final: 0.6923 (tp40) REVERT: B 1029 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7591 (mt-10) outliers start: 42 outliers final: 29 residues processed: 258 average time/residue: 0.3354 time to fit residues: 129.5296 Evaluate side-chains 258 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 93 ASP 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 245 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 503 GLU 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 834 GLN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1132 ILE 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 94 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1018 LEU 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: 5.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 449 GLN A 938 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS B 668 ASN ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.191579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152378 restraints weight = 25189.903| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.54 r_work: 0.3750 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 1.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18520 Z= 0.326 Angle : 0.596 9.878 25020 Z= 0.309 Chirality : 0.043 0.196 2746 Planarity : 0.004 0.049 3256 Dihedral : 4.343 21.702 2460 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.51 % Allowed : 16.43 % Favored : 81.06 % 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: 0.28 (0.18), residues: 2228 helix: 1.35 (0.15), residues: 1118 sheet: -0.50 (0.31), residues: 275 loop : -1.15 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B1027 HIS 0.008 0.001 HIS A 553 PHE 0.018 0.002 PHE A 520 TYR 0.024 0.002 TYR A1115 ARG 0.006 0.001 ARG A 972 *********************** 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 311 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7685 (t0) cc_final: 0.7374 (t0) REVERT: A 195 PHE cc_start: 0.6709 (t80) cc_final: 0.6485 (t80) REVERT: A 262 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7578 (tpp80) REVERT: A 271 ILE cc_start: 0.7799 (mt) cc_final: 0.7525 (mt) REVERT: A 553 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7636 (m90) REVERT: A 783 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7668 (mp) REVERT: A 806 GLU cc_start: 0.6885 (mp0) cc_final: 0.6615 (mp0) REVERT: A 816 GLU cc_start: 0.6640 (tp30) cc_final: 0.6381 (tp30) REVERT: A 831 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.7072 (m) REVERT: A 925 ASP cc_start: 0.7515 (t0) cc_final: 0.7103 (t0) REVERT: A 990 ASP cc_start: 0.7176 (p0) cc_final: 0.6816 (p0) REVERT: A 1006 ASP cc_start: 0.7214 (m-30) cc_final: 0.6903 (m-30) REVERT: A 1033 PHE cc_start: 0.7425 (m-10) cc_final: 0.7176 (m-80) REVERT: A 1059 GLU cc_start: 0.6671 (pt0) cc_final: 0.6300 (pt0) REVERT: B 117 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7767 (tp30) REVERT: B 207 GLN cc_start: 0.7880 (tp40) cc_final: 0.7524 (tp40) REVERT: B 255 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7682 (mtm-85) REVERT: B 314 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7437 (ttm-80) REVERT: B 420 MET cc_start: 0.7979 (tpp) cc_final: 0.7521 (tpp) REVERT: B 470 GLU cc_start: 0.6956 (mp0) cc_final: 0.6640 (mp0) REVERT: B 521 LEU cc_start: 0.8334 (tp) cc_final: 0.8107 (tp) REVERT: B 613 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 797 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: B 807 ASN cc_start: 0.7043 (t0) cc_final: 0.6586 (t0) REVERT: B 984 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5392 (mtm-85) REVERT: B 986 GLN cc_start: 0.7422 (tp40) cc_final: 0.7173 (tp40) REVERT: B 1057 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (mp) outliers start: 50 outliers final: 33 residues processed: 292 average time/residue: 0.3532 time to fit residues: 152.8194 Evaluate side-chains 289 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 137 ASN 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 379 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 553 HIS 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 1072 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 824 MET 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 1018 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1057 LEU 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: 1.9990 chunk 32 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 449 GLN A 453 GLN A 938 HIS A1022 GLN B 131 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.192417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154101 restraints weight = 25575.924| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.52 r_work: 0.3774 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 1.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18520 Z= 0.227 Angle : 0.532 9.576 25020 Z= 0.276 Chirality : 0.041 0.180 2746 Planarity : 0.004 0.046 3256 Dihedral : 4.086 23.696 2460 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.15 % Allowed : 17.89 % Favored : 79.96 % 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: 0.43 (0.18), residues: 2228 helix: 1.46 (0.15), residues: 1131 sheet: -0.34 (0.32), residues: 264 loop : -1.13 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 336 HIS 0.009 0.001 HIS A 553 PHE 0.027 0.001 PHE A 13 TYR 0.024 0.001 TYR A1115 ARG 0.004 0.000 ARG A 972 *********************** 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 285 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 1.945 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7807 (t0) cc_final: 0.7483 (t0) REVERT: A 98 VAL cc_start: 0.7266 (m) cc_final: 0.6055 (t) REVERT: A 262 ARG cc_start: 0.7786 (tpp80) cc_final: 0.7216 (mpp80) REVERT: A 271 ILE cc_start: 0.7805 (mt) cc_final: 0.7150 (mm) REVERT: A 450 GLU cc_start: 0.8258 (tt0) cc_final: 0.7759 (tt0) REVERT: A 663 MET cc_start: 0.4650 (tmm) cc_final: 0.4340 (mmm) REVERT: A 806 GLU cc_start: 0.6830 (mp0) cc_final: 0.6540 (mp0) REVERT: A 831 SER cc_start: 0.7442 (OUTLIER) cc_final: 0.7032 (m) REVERT: A 954 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7312 (mtt180) REVERT: A 990 ASP cc_start: 0.7141 (p0) cc_final: 0.6856 (p0) REVERT: A 1006 ASP cc_start: 0.7314 (m-30) cc_final: 0.6947 (m-30) REVERT: A 1020 GLN cc_start: 0.7791 (mt0) cc_final: 0.7552 (mt0) REVERT: A 1033 PHE cc_start: 0.7453 (m-10) cc_final: 0.7249 (m-80) REVERT: B 207 GLN cc_start: 0.7797 (tp40) cc_final: 0.7527 (tp40) REVERT: B 255 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7674 (mtm-85) REVERT: B 314 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7403 (ttm-80) REVERT: B 420 MET cc_start: 0.8019 (tpp) cc_final: 0.7564 (tpp) REVERT: B 575 GLN cc_start: 0.7245 (mt0) cc_final: 0.6999 (mt0) REVERT: B 613 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 807 ASN cc_start: 0.7064 (t0) cc_final: 0.6647 (t0) REVERT: B 984 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5372 (mtm-85) REVERT: B 986 GLN cc_start: 0.7305 (tp40) cc_final: 0.6848 (tp40) outliers start: 43 outliers final: 31 residues processed: 270 average time/residue: 0.3614 time to fit residues: 144.8418 Evaluate side-chains 266 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 93 ASP 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 379 LEU Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 674 THR 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 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 824 MET 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 1018 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE 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: 1.9990 chunk 203 optimal weight: 0.0060 chunk 179 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 87 optimal weight: 0.0670 chunk 102 optimal weight: 8.9990 chunk 181 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 160 ASN A 449 GLN A 453 GLN A 938 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** 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 = 0.4393 r_free = 0.4393 target = 0.193999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155933 restraints weight = 25541.493| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.51 r_work: 0.3799 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 1.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18520 Z= 0.167 Angle : 0.501 7.014 25020 Z= 0.262 Chirality : 0.040 0.159 2746 Planarity : 0.004 0.047 3256 Dihedral : 3.934 23.484 2460 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.90 % Allowed : 17.59 % Favored : 80.51 % 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: 0.60 (0.18), residues: 2228 helix: 1.62 (0.16), residues: 1136 sheet: -0.18 (0.33), residues: 261 loop : -1.12 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1186 HIS 0.005 0.001 HIS A 553 PHE 0.016 0.001 PHE A 13 TYR 0.025 0.001 TYR A1115 ARG 0.006 0.000 ARG A 262 ********************** 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 281 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 2.185 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7814 (t0) cc_final: 0.7484 (t0) REVERT: A 124 GLN cc_start: 0.8133 (mp10) cc_final: 0.7821 (pm20) REVERT: A 195 PHE cc_start: 0.6293 (t80) cc_final: 0.5931 (t80) REVERT: A 271 ILE cc_start: 0.7745 (mt) cc_final: 0.6975 (mm) REVERT: A 450 GLU cc_start: 0.8282 (tt0) cc_final: 0.7784 (tt0) REVERT: A 663 MET cc_start: 0.4624 (tmm) cc_final: 0.4346 (mmm) REVERT: A 806 GLU cc_start: 0.6781 (mp0) cc_final: 0.6539 (mp0) REVERT: A 831 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.6695 (m) REVERT: A 848 TYR cc_start: 0.7373 (m-80) cc_final: 0.7170 (m-80) REVERT: A 954 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7207 (mtt180) REVERT: A 990 ASP cc_start: 0.7065 (p0) cc_final: 0.6785 (p0) REVERT: A 1006 ASP cc_start: 0.7472 (m-30) cc_final: 0.7127 (m-30) REVERT: A 1020 GLN cc_start: 0.7782 (mt0) cc_final: 0.7528 (mt0) REVERT: A 1025 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6603 (tmm-80) REVERT: A 1059 GLU cc_start: 0.6347 (pt0) cc_final: 0.5442 (pt0) REVERT: B 255 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7678 (mtm-85) REVERT: B 273 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7217 (mt-10) REVERT: B 314 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7362 (ttm-80) REVERT: B 613 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 797 GLN cc_start: 0.8254 (mp10) cc_final: 0.8020 (mp10) REVERT: B 803 SER cc_start: 0.8308 (t) cc_final: 0.8008 (p) REVERT: B 807 ASN cc_start: 0.7034 (t0) cc_final: 0.6629 (t0) REVERT: B 984 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5344 (mtm-85) REVERT: B 986 GLN cc_start: 0.7281 (tp40) cc_final: 0.6825 (tp40) outliers start: 38 outliers final: 27 residues processed: 264 average time/residue: 0.3495 time to fit residues: 136.9759 Evaluate side-chains 272 residues out of total 1996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP 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 379 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 824 MET 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 1018 LEU 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: 3.9990 chunk 43 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 173 optimal weight: 0.0010 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 160 optimal weight: 0.3980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 449 GLN A 938 HIS B 138 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.193626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155526 restraints weight = 25367.430| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.51 r_work: 0.3795 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 1.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18520 Z= 0.178 Angle : 0.502 7.075 25020 Z= 0.262 Chirality : 0.040 0.153 2746 Planarity : 0.004 0.046 3256 Dihedral : 3.895 22.664 2460 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.55 % Allowed : 18.19 % Favored : 80.26 % 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: 0.71 (0.18), residues: 2228 helix: 1.72 (0.16), residues: 1130 sheet: -0.14 (0.33), residues: 260 loop : -1.07 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1186 HIS 0.003 0.000 HIS A 553 PHE 0.024 0.001 PHE A 970 TYR 0.025 0.001 TYR A1115 ARG 0.008 0.000 ARG A1030 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9755.36 seconds wall clock time: 176 minutes 9.06 seconds (10569.06 seconds total)