Starting phenix.real_space_refine on Sat Jul 4 07:40:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khv_62357/07_2026/9khv_62357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khv_62357/07_2026/9khv_62357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9khv_62357/07_2026/9khv_62357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khv_62357/07_2026/9khv_62357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9khv_62357/07_2026/9khv_62357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khv_62357/07_2026/9khv_62357.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.155 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 48 5.16 5 C 12198 2.51 5 N 3397 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19377 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9443 Classifications: {'peptide': 1168} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1134} Chain breaks: 4 Chain: "C" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 9443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9443 Classifications: {'peptide': 1168} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1134} Chain breaks: 4 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 3.69, per 1000 atoms: 0.19 Number of scatterers: 19377 At special positions: 0 Unit cell: (145.435, 117.426, 133.585, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 24 15.00 O 3710 8.00 N 3397 7.00 C 12198 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: 1.37 Conformation dependent library (CDL) restraints added in 791.1 milliseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 24 sheets defined 55.6% alpha, 10.7% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.543A pdb=" N GLU A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.615A pdb=" N ASN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 77 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.576A pdb=" N GLN A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.764A pdb=" N GLU A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 removed outlier: 3.846A pdb=" N LYS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.518A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.097A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.209A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.760A pdb=" N GLN A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.889A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 401 through 435 Processing helix chain 'A' and resid 447 through 459 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 476 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.575A pdb=" N GLY A 593 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.509A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 656 removed outlier: 4.104A pdb=" N SER A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.545A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 807 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 836 Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.925A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.181A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 909 through 938 Processing helix chain 'A' and resid 944 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: 3.835A 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 1020 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.752A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1069 Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.530A pdb=" N TYR A1081 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1127 removed outlier: 3.674A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.839A pdb=" N GLU B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.657A pdb=" N SER B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 77 Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.563A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.614A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 209 removed outlier: 3.924A pdb=" N LYS B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 227 through 235 removed outlier: 4.068A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.737A 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 259 through 264 removed outlier: 4.191A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.681A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.535A pdb=" N ARG B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 337 removed outlier: 3.658A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 401 through 435 Processing helix chain 'B' and resid 447 through 459 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 476 removed outlier: 3.536A pdb=" N SER B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 556 through 565 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 589 through 593 removed outlier: 3.572A pdb=" N GLY B 593 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 removed outlier: 3.508A pdb=" N LEU B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 636 through 656 removed outlier: 3.814A pdb=" N SER B 645 " --> pdb=" O ARG B 641 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 674 No H-bonds generated for 'chain 'B' and resid 672 through 674' Processing helix chain 'B' and resid 675 through 694 Processing helix chain 'B' and resid 704 through 710 Processing helix chain 'B' and resid 713 through 723 removed outlier: 3.588A pdb=" N SER B 717 " --> pdb=" O TYR B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 807 Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 827 through 836 Processing helix chain 'B' and resid 838 through 855 removed outlier: 3.937A pdb=" N GLN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 879 Processing helix chain 'B' and resid 884 through 888 removed outlier: 4.176A pdb=" N LEU B 887 " --> pdb=" O ASP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 901 Processing helix chain 'B' and resid 909 through 938 Processing helix chain 'B' and resid 944 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 992 through 996 removed outlier: 3.833A pdb=" N PHE B 996 " --> pdb=" O PRO B 993 " (cutoff:3.500A) 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 1014 through 1020 Processing helix chain 'B' and resid 1023 through 1032 removed outlier: 3.838A pdb=" N TRP B1027 " --> pdb=" O TYR B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1052 Processing helix chain 'B' and resid 1052 through 1069 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.514A pdb=" N TYR B1081 " --> pdb=" O ASN B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1127 removed outlier: 3.658A pdb=" N GLU B1125 " --> pdb=" O LEU B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.176A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 45 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 133 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N THR A 243 " --> pdb=" O VAL A 133 " (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 Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.630A pdb=" N VAL A 595 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU A 868 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 597 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A 870 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS A 599 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA8, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.517A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1074 removed outlier: 3.609A pdb=" N GLU A1074 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A1087 " --> pdb=" O GLU A1074 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP A1098 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A1134 " --> pdb=" O TRP A1098 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP A1100 " --> pdb=" O VAL A1134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1137 through 1138 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 47 removed outlier: 6.178A pdb=" N ALA B 43 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY B 541 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 45 " --> pdb=" O GLY B 541 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR B 89 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP B 272 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 91 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 88 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 242 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR B 90 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 133 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N THR B 243 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB8, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB9, first strand: chain 'B' and resid 595 through 601 removed outlier: 6.618A pdb=" N VAL B 595 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 868 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR B 597 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL B 870 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 599 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS B 698 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N PHE B 730 " --> pdb=" O LYS B 698 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE B 700 " --> pdb=" O PHE B 730 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR B 732 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 744 through 745 Processing sheet with id=AC2, first strand: chain 'B' and resid 756 through 757 Processing sheet with id=AC3, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AC4, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC5, first strand: chain 'B' and resid 1072 through 1074 removed outlier: 3.836A pdb=" N ASN B1086 " --> pdb=" O LEU B1099 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B1097 " --> pdb=" O VAL B1088 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TRP B1098 " --> pdb=" O ILE B1132 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL B1134 " --> pdb=" O TRP B1098 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B1100 " --> pdb=" O VAL B1134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1137 through 1138 988 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5392 1.33 - 1.45: 3490 1.45 - 1.57: 10810 1.57 - 1.69: 48 1.69 - 1.81: 76 Bond restraints: 19816 Sorted by residual: bond pdb=" C3' DA D 12 " pdb=" C2' DA D 12 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C3' DA C 12 " pdb=" C2' DA C 12 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DT D 6 " pdb=" C2' DT D 6 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.14e+00 bond pdb=" C3' DA C 8 " pdb=" C2' DA C 8 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.94e+00 bond pdb=" C3' DC D 8 " pdb=" O3' DC D 8 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.82e+00 ... (remaining 19811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 26420 1.68 - 3.35: 396 3.35 - 5.03: 43 5.03 - 6.71: 8 6.71 - 8.39: 8 Bond angle restraints: 26875 Sorted by residual: angle pdb=" CA PRO A1077 " pdb=" N PRO A1077 " pdb=" CD PRO A1077 " ideal model delta sigma weight residual 112.00 105.19 6.81 1.40e+00 5.10e-01 2.37e+01 angle pdb=" CA PRO B1077 " pdb=" N PRO B1077 " pdb=" CD PRO B1077 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.35e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT D 6 " pdb=" C4 DT D 6 " pdb=" O4 DT D 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 26870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 11364 34.59 - 69.18: 519 69.18 - 103.77: 40 103.77 - 138.36: 1 138.36 - 172.95: 2 Dihedral angle restraints: 11926 sinusoidal: 5058 harmonic: 6868 Sorted by residual: dihedral pdb=" CA VAL B 711 " pdb=" C VAL B 711 " pdb=" N GLY B 712 " pdb=" CA GLY B 712 " ideal model delta harmonic sigma weight residual -180.00 -148.30 -31.70 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA VAL A 711 " pdb=" C VAL A 711 " pdb=" N GLY A 712 " pdb=" CA GLY A 712 " ideal model delta harmonic sigma weight residual 180.00 -149.37 -30.63 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" C4' DA D 12 " pdb=" C3' DA D 12 " pdb=" O3' DA D 12 " pdb=" P DT D 13 " ideal model delta sinusoidal sigma weight residual 220.00 47.05 172.95 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 11923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1886 0.031 - 0.063: 714 0.063 - 0.094: 224 0.094 - 0.125: 125 0.125 - 0.156: 11 Chirality restraints: 2960 Sorted by residual: chirality pdb=" C3' DA C 8 " pdb=" C4' DA C 8 " pdb=" O3' DA C 8 " pdb=" C2' DA C 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA VAL A1076 " pdb=" N VAL A1076 " pdb=" C VAL A1076 " pdb=" CB VAL A1076 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE A 756 " pdb=" N ILE A 756 " pdb=" C ILE A 756 " pdb=" CB ILE A 756 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2957 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1076 " 0.053 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO A1077 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B1076 " -0.048 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO B1077 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B1077 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B1077 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1098 " -0.007 2.00e-02 2.50e+03 1.13e-02 3.22e+00 pdb=" CG TRP A1098 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A1098 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1098 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1098 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1098 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1098 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1098 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1098 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1098 " 0.000 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 421 2.69 - 3.24: 18359 3.24 - 3.79: 30675 3.79 - 4.35: 42417 4.35 - 4.90: 68861 Nonbonded interactions: 160733 Sorted by model distance: nonbonded pdb=" O CYS A1013 " pdb=" OH TYR A1103 " model vdw 2.133 3.040 nonbonded pdb=" O CYS B1013 " pdb=" OH TYR B1103 " model vdw 2.155 3.040 nonbonded pdb=" OH TYR A 983 " pdb=" O MET A1044 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP B 531 " pdb=" NH2 ARG B 563 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASP A 531 " pdb=" NH2 ARG A 563 " model vdw 2.229 3.120 ... (remaining 160728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 3 through 13) selection = (chain 'D' and resid 2 through 12) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 0.107 19816 Z= 0.190 Angle : 0.540 8.387 26875 Z= 0.320 Chirality : 0.041 0.156 2960 Planarity : 0.004 0.077 3402 Dihedral : 18.578 172.948 7470 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.65 % Allowed : 20.06 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2316 helix: 1.44 (0.15), residues: 1170 sheet: 0.23 (0.33), residues: 268 loop : -0.44 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1030 TYR 0.011 0.001 TYR B1081 PHE 0.016 0.001 PHE B 472 TRP 0.028 0.002 TRP A1098 HIS 0.005 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.19 (19816) covalent geometry : angle 0.54041 / 0.32 (26875) hydrogen bonds : bond 0.14696 / 9.03 ( 988) hydrogen bonds : angle 6.17425 / 4.49 ( 2805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.737 Fit side-chains REVERT: A 197 ARG cc_start: 0.7819 (ttt90) cc_final: 0.7438 (ttp-170) REVERT: A 577 GLN cc_start: 0.7400 (tp40) cc_final: 0.7166 (tt0) REVERT: B 577 GLN cc_start: 0.7332 (tp40) cc_final: 0.7078 (tt0) outliers start: 55 outliers final: 47 residues processed: 244 average time/residue: 0.5680 time to fit residues: 156.4469 Evaluate side-chains 238 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1154 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 50 GLN B 189 ASN B 291 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 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 = 0.4088 r_free = 0.4088 target = 0.170270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117811 restraints weight = 23691.476| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.09 r_work: 0.3367 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19816 Z= 0.267 Angle : 0.625 8.480 26875 Z= 0.329 Chirality : 0.046 0.168 2960 Planarity : 0.004 0.036 3402 Dihedral : 12.622 167.891 2920 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.71 % Allowed : 18.56 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2316 helix: 1.71 (0.15), residues: 1174 sheet: 0.15 (0.31), residues: 288 loop : -0.48 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 197 TYR 0.016 0.002 TYR B 494 PHE 0.020 0.002 PHE B 332 TRP 0.029 0.002 TRP A 643 HIS 0.007 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (19816) covalent geometry : angle 0.62462 / 0.33 (26875) hydrogen bonds : bond 0.06562 / 4.31 ( 988) hydrogen bonds : angle 4.69010 / 3.43 ( 2805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7593 (ttp-170) REVERT: A 274 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8554 (tp) REVERT: A 330 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: B 249 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8674 (mttm) REVERT: B 274 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 330 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: B 966 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7709 (tp-100) outliers start: 77 outliers final: 46 residues processed: 258 average time/residue: 0.5196 time to fit residues: 152.4163 Evaluate side-chains 244 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 966 GLN Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 220 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 32 ASN B 50 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.164423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107246 restraints weight = 22276.253| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.08 r_work: 0.3138 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19816 Z= 0.216 Angle : 0.574 8.322 26875 Z= 0.304 Chirality : 0.043 0.158 2960 Planarity : 0.004 0.036 3402 Dihedral : 12.343 168.269 2888 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.24 % Allowed : 18.61 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2316 helix: 1.94 (0.15), residues: 1156 sheet: 0.15 (0.31), residues: 288 loop : -0.50 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.014 0.002 TYR A 494 PHE 0.019 0.002 PHE B 332 TRP 0.026 0.002 TRP A 643 HIS 0.007 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (19816) covalent geometry : angle 0.57417 / 0.30 (26875) hydrogen bonds : bond 0.05958 / 3.90 ( 988) hydrogen bonds : angle 4.55436 / 3.33 ( 2805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 203 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8119 (ttt90) cc_final: 0.7700 (ttt180) REVERT: A 390 LYS cc_start: 0.5287 (OUTLIER) cc_final: 0.4917 (ptpp) REVERT: A 906 ILE cc_start: 0.4332 (OUTLIER) cc_final: 0.4008 (tt) REVERT: B 1 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.4470 (tmt) REVERT: B 249 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8651 (mttm) REVERT: B 274 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 330 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: B 390 LYS cc_start: 0.5196 (OUTLIER) cc_final: 0.4907 (ptpp) REVERT: B 968 GLU cc_start: 0.8056 (tt0) cc_final: 0.7851 (tm-30) REVERT: B 1030 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7222 (ptm160) REVERT: B 1100 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6263 (m-30) outliers start: 88 outliers final: 50 residues processed: 274 average time/residue: 0.5265 time to fit residues: 163.7773 Evaluate side-chains 256 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 186 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 177 optimal weight: 0.4980 chunk 192 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 39 optimal weight: 0.0270 chunk 153 optimal weight: 4.9990 overall best weight: 0.9038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.167134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110200 restraints weight = 22247.546| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.37 r_work: 0.3169 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19816 Z= 0.118 Angle : 0.491 8.459 26875 Z= 0.265 Chirality : 0.039 0.181 2960 Planarity : 0.003 0.037 3402 Dihedral : 12.219 176.375 2881 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.18 % Allowed : 18.76 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.18), residues: 2316 helix: 2.21 (0.15), residues: 1168 sheet: 0.51 (0.32), residues: 274 loop : -0.47 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.012 0.001 TYR B1103 PHE 0.014 0.001 PHE A 607 TRP 0.022 0.001 TRP A 643 HIS 0.004 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (19816) covalent geometry : angle 0.49136 / 0.26 (26875) hydrogen bonds : bond 0.04587 / 3.03 ( 988) hydrogen bonds : angle 4.31951 / 3.16 ( 2805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8103 (ttt90) cc_final: 0.7709 (ttt180) REVERT: A 274 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 288 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7462 (pp30) REVERT: A 663 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8485 (ttt) REVERT: A 906 ILE cc_start: 0.4456 (OUTLIER) cc_final: 0.4142 (tt) REVERT: B 249 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8611 (mttm) REVERT: B 906 ILE cc_start: 0.4471 (OUTLIER) cc_final: 0.4135 (tt) REVERT: B 927 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8719 (mtp) REVERT: B 951 GLN cc_start: 0.8634 (tp40) cc_final: 0.8278 (mm110) REVERT: B 1100 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6097 (m-30) outliers start: 66 outliers final: 39 residues processed: 255 average time/residue: 0.5043 time to fit residues: 146.8719 Evaluate side-chains 245 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 202 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 182 optimal weight: 0.0870 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 ASN A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 865 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.166397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109686 restraints weight = 22206.163| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.08 r_work: 0.3176 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19816 Z= 0.144 Angle : 0.506 8.271 26875 Z= 0.270 Chirality : 0.040 0.187 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.126 174.435 2873 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.62 % Allowed : 18.47 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.18), residues: 2316 helix: 2.27 (0.15), residues: 1168 sheet: 0.58 (0.32), residues: 274 loop : -0.45 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.010 0.001 TYR B1103 PHE 0.016 0.001 PHE A 472 TRP 0.020 0.001 TRP A 643 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (19816) covalent geometry : angle 0.50562 / 0.27 (26875) hydrogen bonds : bond 0.04809 / 3.16 ( 988) hydrogen bonds : angle 4.26915 / 3.12 ( 2805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 203 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 906 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.4073 (tt) REVERT: B 162 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6761 (tm-30) REVERT: B 249 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8637 (mttm) REVERT: B 274 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8412 (tp) REVERT: B 927 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8696 (mtp) REVERT: B 951 GLN cc_start: 0.8635 (tp40) cc_final: 0.8313 (mm110) REVERT: B 1100 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6099 (m-30) outliers start: 75 outliers final: 44 residues processed: 263 average time/residue: 0.5048 time to fit residues: 151.2248 Evaluate side-chains 252 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 223 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A 966 GLN B 50 GLN B 234 ASN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** B 935 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 = 0.3963 r_free = 0.3963 target = 0.162956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105980 restraints weight = 22104.014| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.06 r_work: 0.3118 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 19816 Z= 0.300 Angle : 0.638 8.609 26875 Z= 0.333 Chirality : 0.047 0.172 2960 Planarity : 0.004 0.035 3402 Dihedral : 12.144 163.664 2873 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.15 % Allowed : 18.42 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2316 helix: 1.93 (0.15), residues: 1162 sheet: 0.18 (0.31), residues: 288 loop : -0.61 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.018 0.002 TYR B 494 PHE 0.028 0.003 PHE A 472 TRP 0.023 0.002 TRP A 643 HIS 0.009 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.30 (19816) covalent geometry : angle 0.63849 / 0.33 (26875) hydrogen bonds : bond 0.06453 / 4.22 ( 988) hydrogen bonds : angle 4.47975 / 3.27 ( 2805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 195 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8163 (ttt90) cc_final: 0.7642 (ttt180) REVERT: A 274 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8603 (tp) REVERT: A 390 LYS cc_start: 0.5622 (OUTLIER) cc_final: 0.4917 (ptpp) REVERT: A 906 ILE cc_start: 0.4493 (OUTLIER) cc_final: 0.4173 (tt) REVERT: B 162 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 249 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8650 (mttm) REVERT: B 274 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8568 (tp) REVERT: B 330 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: B 390 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.4963 (ptpp) REVERT: B 1100 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.5977 (m-30) outliers start: 86 outliers final: 59 residues processed: 262 average time/residue: 0.5397 time to fit residues: 160.6983 Evaluate side-chains 258 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 92 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 50 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** B 935 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 = 0.3980 r_free = 0.3980 target = 0.164514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107674 restraints weight = 22171.489| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.06 r_work: 0.3145 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19816 Z= 0.191 Angle : 0.556 8.241 26875 Z= 0.294 Chirality : 0.042 0.156 2960 Planarity : 0.003 0.037 3402 Dihedral : 12.134 169.699 2873 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.10 % Allowed : 18.51 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2316 helix: 2.10 (0.15), residues: 1156 sheet: 0.24 (0.32), residues: 288 loop : -0.59 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1030 TYR 0.012 0.001 TYR B 494 PHE 0.019 0.002 PHE B 472 TRP 0.025 0.002 TRP A 643 HIS 0.006 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (19816) covalent geometry : angle 0.55628 / 0.29 (26875) hydrogen bonds : bond 0.05472 / 3.59 ( 988) hydrogen bonds : angle 4.37368 / 3.19 ( 2805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8502 (tp) REVERT: A 330 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: A 390 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.4827 (mtmm) REVERT: A 663 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8659 (ttt) REVERT: A 906 ILE cc_start: 0.4752 (OUTLIER) cc_final: 0.4381 (tt) REVERT: A 1059 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6696 (tm-30) REVERT: B 162 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6906 (tm-30) REVERT: B 249 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8635 (mttm) REVERT: B 274 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 390 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.4992 (ptpp) REVERT: B 432 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7666 (ttp-110) REVERT: B 663 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8415 (ttt) REVERT: B 951 GLN cc_start: 0.8625 (tp40) cc_final: 0.8308 (mm110) REVERT: B 968 GLU cc_start: 0.8065 (tt0) cc_final: 0.7859 (tm-30) REVERT: B 1100 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6120 (m-30) outliers start: 85 outliers final: 55 residues processed: 265 average time/residue: 0.5483 time to fit residues: 164.6175 Evaluate side-chains 261 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 46 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 233 optimal weight: 10.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 230 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 50 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** B 935 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 = 0.3994 r_free = 0.3994 target = 0.165746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108988 restraints weight = 22229.507| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.08 r_work: 0.3164 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19816 Z= 0.148 Angle : 0.520 8.272 26875 Z= 0.277 Chirality : 0.041 0.158 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.129 173.717 2873 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.28 % Allowed : 19.53 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.17), residues: 2316 helix: 2.27 (0.15), residues: 1156 sheet: 0.55 (0.32), residues: 274 loop : -0.59 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1030 TYR 0.010 0.001 TYR B1103 PHE 0.019 0.001 PHE A 472 TRP 0.027 0.002 TRP B 643 HIS 0.006 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (19816) covalent geometry : angle 0.51988 / 0.28 (26875) hydrogen bonds : bond 0.04895 / 3.20 ( 988) hydrogen bonds : angle 4.27065 / 3.12 ( 2805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7713 (ttt180) REVERT: A 274 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 1 MET cc_start: 0.4807 (tpt) cc_final: 0.2972 (tmm) REVERT: B 31 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7303 (mtmm) REVERT: B 162 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: B 249 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (mttm) REVERT: B 274 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 663 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8373 (ttt) REVERT: B 927 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8616 (mtp) REVERT: B 951 GLN cc_start: 0.8631 (tp40) cc_final: 0.8281 (mm110) REVERT: B 968 GLU cc_start: 0.8066 (tt0) cc_final: 0.7863 (tm-30) REVERT: B 1023 TYR cc_start: 0.7086 (m-80) cc_final: 0.6845 (m-80) REVERT: B 1100 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6002 (m-30) outliers start: 68 outliers final: 47 residues processed: 255 average time/residue: 0.5723 time to fit residues: 166.1337 Evaluate side-chains 246 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 9.9990 chunk 39 optimal weight: 0.0070 chunk 129 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 195 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN B 37 ASN B 50 GLN B 234 ASN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.167019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110557 restraints weight = 22216.685| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.06 r_work: 0.3186 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19816 Z= 0.122 Angle : 0.500 8.409 26875 Z= 0.267 Chirality : 0.039 0.150 2960 Planarity : 0.003 0.037 3402 Dihedral : 12.126 176.727 2873 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.75 % Allowed : 20.15 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.17), residues: 2316 helix: 2.41 (0.15), residues: 1158 sheet: 0.58 (0.32), residues: 274 loop : -0.55 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1030 TYR 0.010 0.001 TYR B1103 PHE 0.015 0.001 PHE B 472 TRP 0.023 0.001 TRP A 643 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19816) covalent geometry : angle 0.49978 / 0.27 (26875) hydrogen bonds : bond 0.04417 / 2.91 ( 988) hydrogen bonds : angle 4.16643 / 3.04 ( 2805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 577 GLN cc_start: 0.7491 (tp40) cc_final: 0.7151 (tm130) REVERT: B 1 MET cc_start: 0.4760 (tpt) cc_final: 0.3037 (tmm) REVERT: B 31 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7242 (mtmm) REVERT: B 162 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: B 249 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8601 (mttm) REVERT: B 274 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 577 GLN cc_start: 0.7494 (tp40) cc_final: 0.7145 (tm130) REVERT: B 663 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8334 (ttt) REVERT: B 927 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8705 (mtp) REVERT: B 951 GLN cc_start: 0.8617 (tp40) cc_final: 0.8275 (mm110) REVERT: B 1023 TYR cc_start: 0.7042 (m-80) cc_final: 0.6784 (m-80) REVERT: B 1100 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6057 (m-30) outliers start: 57 outliers final: 40 residues processed: 240 average time/residue: 0.5844 time to fit residues: 159.5978 Evaluate side-chains 238 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 18 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 167 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 154 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN A1086 ASN B 50 GLN B 137 ASN B 865 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110335 restraints weight = 22186.905| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.07 r_work: 0.3185 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19816 Z= 0.129 Angle : 0.508 8.422 26875 Z= 0.270 Chirality : 0.040 0.163 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.114 176.059 2871 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 20.35 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.17), residues: 2316 helix: 2.44 (0.15), residues: 1158 sheet: 0.65 (0.33), residues: 254 loop : -0.50 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.010 0.001 TYR B1103 PHE 0.015 0.001 PHE A 472 TRP 0.022 0.001 TRP A 643 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19816) covalent geometry : angle 0.50754 / 0.27 (26875) hydrogen bonds : bond 0.04467 / 2.93 ( 988) hydrogen bonds : angle 4.14597 / 3.03 ( 2805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8382 (tp) REVERT: B 1 MET cc_start: 0.4872 (tpt) cc_final: 0.3156 (tmm) REVERT: B 31 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7252 (mtmm) REVERT: B 249 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8606 (mttm) REVERT: B 274 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8385 (tp) REVERT: B 927 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8690 (mtp) REVERT: B 951 GLN cc_start: 0.8596 (tp40) cc_final: 0.8310 (mm110) REVERT: B 1023 TYR cc_start: 0.7057 (m-80) cc_final: 0.6796 (m-80) REVERT: B 1100 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.5959 (m-30) outliers start: 53 outliers final: 40 residues processed: 231 average time/residue: 0.5720 time to fit residues: 150.0096 Evaluate side-chains 234 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1110 GLU Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 32 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A 966 GLN B 50 GLN B 865 GLN ** B 935 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 = 0.3994 r_free = 0.3994 target = 0.165827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109054 restraints weight = 22263.313| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.07 r_work: 0.3166 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19816 Z= 0.164 Angle : 0.539 8.406 26875 Z= 0.285 Chirality : 0.041 0.160 2960 Planarity : 0.003 0.035 3402 Dihedral : 12.021 172.844 2867 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.70 % Allowed : 20.35 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.17), residues: 2316 helix: 2.35 (0.15), residues: 1160 sheet: 0.32 (0.31), residues: 288 loop : -0.48 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.012 0.001 TYR A 494 PHE 0.018 0.002 PHE A 472 TRP 0.022 0.001 TRP A 643 HIS 0.006 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19816) covalent geometry : angle 0.53872 / 0.28 (26875) hydrogen bonds : bond 0.04922 / 3.23 ( 988) hydrogen bonds : angle 4.18125 / 3.05 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8074.09 seconds wall clock time: 137 minutes 50.61 seconds (8270.61 seconds total)