Starting phenix.real_space_refine on Thu Sep 18 19:06:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khv_62357/09_2025/9khv_62357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khv_62357/09_2025/9khv_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_62357/09_2025/9khv_62357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khv_62357/09_2025/9khv_62357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9khv_62357/09_2025/9khv_62357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khv_62357/09_2025/9khv_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 4.55, per 1000 atoms: 0.23 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: 1.63 Conformation dependent library (CDL) restraints added in 816.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.25 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: 4.34 Time building geometry restraints manager: 2.06 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=" CB PRO B1077 " pdb=" CG PRO B1077 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.57e+00 bond pdb=" CB PRO A1077 " pdb=" CG PRO A1077 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.50e+00 bond pdb=" O4' DA C 12 " pdb=" C1' DA C 12 " ideal model delta sigma weight residual 1.414 1.391 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C3' DA D 12 " pdb=" C2' DA D 12 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" CG1 ILE A 172 " pdb=" CD1 ILE A 172 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.06e+00 ... (remaining 19811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 26453 1.68 - 3.35: 363 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=" N GLU A 162 " pdb=" CA GLU A 162 " pdb=" C GLU A 162 " ideal model delta sigma weight residual 114.64 110.22 4.42 1.52e+00 4.33e-01 8.45e+00 angle pdb=" CA MET A 1 " pdb=" CB MET A 1 " pdb=" CG MET A 1 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.39e+00 angle pdb=" C ASP B 316 " pdb=" N LYS B 317 " pdb=" CA LYS B 317 " ideal model delta sigma weight residual 122.08 126.26 -4.18 1.47e+00 4.63e-01 8.10e+00 ... (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 - 0.030: 1858 0.030 - 0.060: 726 0.060 - 0.090: 230 0.090 - 0.120: 133 0.120 - 0.150: 13 Chirality restraints: 2960 Sorted by residual: 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 chirality pdb=" CA VAL B1076 " pdb=" N VAL B1076 " pdb=" C VAL B1076 " pdb=" CB VAL B1076 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.320 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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= 0.144 Angle : 0.532 8.387 26875 Z= 0.294 Chirality : 0.040 0.150 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 aren 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 covalent geometry : bond 0.00330 (19816) covalent geometry : angle 0.53150 (26875) hydrogen bonds : bond 0.14696 ( 988) hydrogen bonds : angle 6.17425 ( 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 : 0.499 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: 0.7167 (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: 0.5548 time to fit residues: 152.6735 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 : 0.726 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106244 restraints weight = 22196.436| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.08 r_work: 0.3122 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19816 Z= 0.272 Angle : 0.628 8.541 26875 Z= 0.329 Chirality : 0.046 0.166 2960 Planarity : 0.004 0.036 3402 Dihedral : 12.440 162.800 2920 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.95 % Allowed : 18.51 % Favored : 77.53 % 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 aren not related in a simple way. whole: 1.08 (0.17), residues: 2316 helix: 1.75 (0.15), residues: 1160 sheet: 0.08 (0.31), residues: 306 loop : -0.44 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.014 0.002 TYR A 494 PHE 0.020 0.002 PHE B 332 TRP 0.028 0.002 TRP A 643 HIS 0.009 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00648 (19816) covalent geometry : angle 0.62770 (26875) hydrogen bonds : bond 0.06473 ( 988) hydrogen bonds : angle 4.62695 ( 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 285 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 203 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7702 (ttt180) REVERT: A 274 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 906 ILE cc_start: 0.4456 (OUTLIER) cc_final: 0.4122 (tt) REVERT: A 986 GLN cc_start: 0.8507 (tt0) cc_final: 0.8260 (tp40) REVERT: B 140 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: B 249 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8678 (mttm) REVERT: B 274 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8566 (tp) REVERT: B 276 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8553 (tttm) REVERT: B 420 MET cc_start: 0.9221 (mmm) cc_final: 0.8969 (mmm) REVERT: B 906 ILE cc_start: 0.4542 (OUTLIER) cc_final: 0.4206 (tt) REVERT: B 1100 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6245 (m-30) outliers start: 82 outliers final: 46 residues processed: 268 average time/residue: 0.5668 time to fit residues: 171.1874 Evaluate side-chains 247 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE 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 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 595 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 724 LEU 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 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 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 140 GLU 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 276 LYS 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 429 GLU Chi-restraints excluded: chain B residue 510 THR 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 724 LEU Chi-restraints excluded: chain B residue 860 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 1057 LEU Chi-restraints excluded: chain B residue 1065 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 220 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN A1086 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 = 0.4006 r_free = 0.4006 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111657 restraints weight = 22282.842| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.58 r_work: 0.3120 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0990 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= 0.127 Angle : 0.492 8.377 26875 Z= 0.262 Chirality : 0.040 0.156 2960 Planarity : 0.003 0.037 3402 Dihedral : 12.254 172.348 2885 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.99 % Allowed : 19.00 % Favored : 78.01 % 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 aren not related in a simple way. whole: 1.47 (0.17), residues: 2316 helix: 2.15 (0.15), residues: 1170 sheet: 0.50 (0.32), residues: 274 loop : -0.49 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.009 0.001 TYR B1081 PHE 0.014 0.001 PHE A 607 TRP 0.023 0.001 TRP A 643 HIS 0.004 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00286 (19816) covalent geometry : angle 0.49165 (26875) hydrogen bonds : bond 0.04573 ( 988) hydrogen bonds : angle 4.29225 ( 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 279 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7641 (ttt180) REVERT: A 288 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7453 (pp30) REVERT: A 330 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: A 626 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 986 GLN cc_start: 0.8469 (tt0) cc_final: 0.8195 (tp40) REVERT: B 162 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6743 (tm-30) REVERT: B 178 HIS cc_start: 0.7853 (m90) cc_final: 0.7575 (m90) REVERT: B 249 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8641 (mttm) REVERT: B 330 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: B 663 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8486 (ttt) REVERT: B 927 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8711 (mtp) REVERT: B 951 GLN cc_start: 0.8653 (tp40) cc_final: 0.8299 (mm110) REVERT: B 1100 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6049 (m-30) outliers start: 62 outliers final: 26 residues processed: 262 average time/residue: 0.6228 time to fit residues: 183.4682 Evaluate side-chains 235 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 284 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 330 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 626 LEU 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 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 3 VAL Chi-restraints excluded: chain B residue 25 VAL 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 330 GLU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 186 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 39 optimal weight: 0.0270 chunk 153 optimal weight: 5.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 50 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.164976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107996 restraints weight = 22188.221| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.09 r_work: 0.3151 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19816 Z= 0.182 Angle : 0.537 8.268 26875 Z= 0.283 Chirality : 0.042 0.153 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.173 166.911 2871 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.24 % Allowed : 17.94 % Favored : 77.82 % 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 aren not related in a simple way. whole: 1.41 (0.17), residues: 2316 helix: 2.13 (0.15), residues: 1170 sheet: 0.23 (0.31), residues: 288 loop : -0.46 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.012 0.001 TYR B 494 PHE 0.016 0.002 PHE B 332 TRP 0.023 0.002 TRP A 643 HIS 0.006 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00427 (19816) covalent geometry : angle 0.53728 (26875) hydrogen bonds : bond 0.05315 ( 988) hydrogen bonds : angle 4.32741 ( 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 293 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 205 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8140 (ttt90) cc_final: 0.7629 (ttt180) REVERT: A 274 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 330 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: A 390 LYS cc_start: 0.5669 (OUTLIER) cc_final: 0.4809 (mtmm) REVERT: A 432 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7644 (ttp-110) REVERT: A 626 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 880 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 986 GLN cc_start: 0.8498 (tt0) cc_final: 0.8225 (tp40) REVERT: B 1 MET cc_start: 0.5322 (OUTLIER) cc_final: 0.4098 (tmt) REVERT: B 31 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7364 (mtmm) REVERT: B 162 GLU cc_start: 0.7265 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 178 HIS cc_start: 0.7880 (m90) cc_final: 0.7624 (m90) REVERT: B 249 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8633 (mttm) REVERT: B 274 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8470 (tp) REVERT: B 330 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: B 390 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.4963 (ptpp) REVERT: B 951 GLN cc_start: 0.8656 (tp40) cc_final: 0.8345 (mm110) REVERT: B 1059 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6906 (tm-30) REVERT: B 1100 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6098 (m-30) outliers start: 88 outliers final: 45 residues processed: 271 average time/residue: 0.5847 time to fit residues: 178.3944 Evaluate side-chains 257 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 390 LYS Chi-restraints excluded: chain A residue 432 ARG 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 626 LEU 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 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 1 MET 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 53 ILE 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 284 GLU 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 643 TRP Chi-restraints excluded: chain B residue 663 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 150 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3986 r_free = 0.3986 target = 0.165051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108223 restraints weight = 22169.609| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.07 r_work: 0.3152 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19816 Z= 0.180 Angle : 0.530 8.310 26875 Z= 0.279 Chirality : 0.041 0.174 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.215 168.424 2871 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.39 % Allowed : 17.89 % 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 aren not related in a simple way. whole: 1.44 (0.17), residues: 2316 helix: 2.20 (0.15), residues: 1156 sheet: 0.25 (0.31), residues: 288 loop : -0.49 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 604 TYR 0.012 0.001 TYR A 494 PHE 0.016 0.002 PHE B 332 TRP 0.022 0.002 TRP A 643 HIS 0.006 0.001 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00422 (19816) covalent geometry : angle 0.52999 (26875) hydrogen bonds : bond 0.05194 ( 988) hydrogen bonds : angle 4.29059 ( 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 297 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 206 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7694 (ttt180) REVERT: A 274 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 330 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: A 390 LYS cc_start: 0.5724 (OUTLIER) cc_final: 0.4979 (ptpp) REVERT: A 626 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 880 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7983 (mt-10) REVERT: A 986 GLN cc_start: 0.8494 (tt0) cc_final: 0.8216 (tp40) REVERT: A 1059 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6817 (tm-30) REVERT: B 162 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 249 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8635 (mttm) REVERT: B 274 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 330 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: B 390 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.5015 (ptpp) REVERT: B 604 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6521 (mmt-90) REVERT: B 951 GLN cc_start: 0.8659 (tp40) cc_final: 0.8347 (mm110) REVERT: B 1100 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.5961 (m-30) outliers start: 91 outliers final: 56 residues processed: 276 average time/residue: 0.5973 time to fit residues: 185.9227 Evaluate side-chains 267 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 201 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 ILE 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 330 GLU Chi-restraints excluded: chain A residue 361 SER 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 626 LEU 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 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 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 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 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 306 ASP Chi-restraints excluded: chain B residue 330 GLU 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 510 THR Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 604 ARG 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 772 ASP 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=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: 2.9990 chunk 158 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 50 GLN A 65 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.162607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105587 restraints weight = 22109.926| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.07 r_work: 0.3114 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1363 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= 0.296 Angle : 0.634 8.508 26875 Z= 0.330 Chirality : 0.047 0.173 2960 Planarity : 0.004 0.036 3402 Dihedral : 12.280 161.992 2871 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.24 % Allowed : 18.51 % Favored : 77.24 % 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 aren not related in a simple way. whole: 1.12 (0.17), residues: 2316 helix: 1.84 (0.15), residues: 1170 sheet: 0.20 (0.31), residues: 286 loop : -0.57 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.017 0.002 TYR B 494 PHE 0.023 0.002 PHE B 472 TRP 0.025 0.002 TRP A 643 HIS 0.008 0.001 HIS B 496 Details of bonding type rmsd covalent geometry : bond 0.00707 (19816) covalent geometry : angle 0.63391 (26875) hydrogen bonds : bond 0.06432 ( 988) hydrogen bonds : angle 4.50382 ( 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 286 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 198 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8183 (ttt90) cc_final: 0.7667 (ttt180) REVERT: A 274 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 330 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: A 390 LYS cc_start: 0.5719 (OUTLIER) cc_final: 0.4930 (ptpp) REVERT: A 880 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 986 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8203 (tp40) REVERT: B 51 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7819 (p) REVERT: B 162 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6915 (tm-30) REVERT: B 249 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8652 (mttm) REVERT: B 274 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8576 (tp) REVERT: B 330 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: B 390 LYS cc_start: 0.5762 (OUTLIER) cc_final: 0.4936 (ptpp) REVERT: B 604 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6584 (mmt-90) REVERT: B 966 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7769 (tp-100) REVERT: B 1030 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7542 (ptm160) REVERT: B 1100 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6090 (m-30) outliers start: 88 outliers final: 58 residues processed: 263 average time/residue: 0.5674 time to fit residues: 168.4021 Evaluate side-chains 267 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 196 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 155 ILE 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 330 GLU Chi-restraints excluded: chain A residue 361 SER 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 731 SER 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 986 GLN 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 155 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 284 GLU 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 361 SER 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 604 ARG 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 731 SER 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 966 GLN Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1030 ARG Chi-restraints excluded: chain B residue 1065 VAL 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: 4.9990 chunk 132 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 50 GLN 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** B1189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109570 restraints weight = 22190.261| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.07 r_work: 0.3174 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19816 Z= 0.139 Angle : 0.504 8.319 26875 Z= 0.267 Chirality : 0.040 0.152 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.222 171.768 2871 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.28 % Allowed : 19.24 % Favored : 77.48 % 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 aren not related in a simple way. whole: 1.49 (0.17), residues: 2316 helix: 2.26 (0.15), residues: 1156 sheet: 0.50 (0.32), residues: 274 loop : -0.57 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.010 0.001 TYR B 494 PHE 0.015 0.001 PHE B 472 TRP 0.022 0.002 TRP A 643 HIS 0.020 0.001 HIS B1189 Details of bonding type rmsd covalent geometry : bond 0.00318 (19816) covalent geometry : angle 0.50402 (26875) hydrogen bonds : bond 0.04593 ( 988) hydrogen bonds : angle 4.21192 ( 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 276 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7549 (p) REVERT: A 330 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: A 880 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 935 HIS cc_start: 0.7518 (t70) cc_final: 0.7306 (t-90) REVERT: A 968 GLU cc_start: 0.8031 (tt0) cc_final: 0.7798 (tm-30) REVERT: A 986 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8187 (tp40) REVERT: B 31 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7304 (mtmm) REVERT: B 162 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: B 249 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8604 (mttm) REVERT: B 274 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8396 (tp) REVERT: B 330 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: B 604 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6622 (mmt-90) REVERT: B 927 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8645 (mtp) REVERT: B 951 GLN cc_start: 0.8620 (tp40) cc_final: 0.8277 (mm110) REVERT: B 1100 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6126 (m-30) outliers start: 68 outliers final: 46 residues processed: 257 average time/residue: 0.6022 time to fit residues: 174.5356 Evaluate side-chains 259 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 39 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 236 SER 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 361 SER 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 626 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 772 ASP 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 986 GLN 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 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 306 ASP Chi-restraints excluded: chain B residue 330 GLU 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 604 ARG 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 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: 8.9990 chunk 78 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 865 GLN A 966 GLN B 50 GLN B 137 ASN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108237 restraints weight = 22226.240| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.07 r_work: 0.3150 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19816 Z= 0.181 Angle : 0.542 8.243 26875 Z= 0.285 Chirality : 0.042 0.158 2960 Planarity : 0.003 0.035 3402 Dihedral : 12.217 167.360 2871 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.52 % Allowed : 19.29 % 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 aren not related in a simple way. whole: 1.46 (0.17), residues: 2316 helix: 2.24 (0.15), residues: 1158 sheet: 0.26 (0.32), residues: 288 loop : -0.54 (0.20), residues: 870 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 0.020 0.002 PHE B 472 TRP 0.024 0.002 TRP A 643 HIS 0.013 0.001 HIS B1189 Details of bonding type rmsd covalent geometry : bond 0.00424 (19816) covalent geometry : angle 0.54207 (26875) hydrogen bonds : bond 0.05175 ( 988) hydrogen bonds : angle 4.26882 ( 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 271 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5233 (tpt) cc_final: 0.3194 (tmm) REVERT: A 51 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 274 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 330 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 880 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 968 GLU cc_start: 0.8040 (tt0) cc_final: 0.7798 (tm-30) REVERT: A 986 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8185 (tp40) REVERT: B 31 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7333 (mtmm) REVERT: B 123 GLU cc_start: 0.7606 (mp0) cc_final: 0.7357 (mp0) REVERT: B 162 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: B 249 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8630 (mttm) REVERT: B 274 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8446 (tp) REVERT: B 330 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7240 (tp30) REVERT: B 604 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6531 (mmt-90) REVERT: B 951 GLN cc_start: 0.8628 (tp40) cc_final: 0.8322 (mm110) REVERT: B 966 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8049 (tp40) REVERT: B 1100 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6033 (m-30) outliers start: 73 outliers final: 50 residues processed: 251 average time/residue: 0.5676 time to fit residues: 161.0464 Evaluate side-chains 258 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 72 ARG 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 330 GLU Chi-restraints excluded: chain A residue 361 SER 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 626 LEU 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 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 986 GLN 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 155 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 284 GLU 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 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 604 ARG 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 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: 10.0000 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 154 optimal weight: 0.0370 chunk 176 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 50 GLN A 966 GLN B 37 ASN B 189 ASN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112510 restraints weight = 22205.061| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.08 r_work: 0.3169 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19816 Z= 0.106 Angle : 0.472 8.421 26875 Z= 0.250 Chirality : 0.038 0.161 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.193 176.600 2871 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.17 % Allowed : 20.73 % 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 aren not related in a simple way. whole: 1.77 (0.17), residues: 2316 helix: 2.52 (0.15), residues: 1158 sheet: 0.67 (0.34), residues: 254 loop : -0.48 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.008 0.001 TYR B1103 PHE 0.015 0.001 PHE B 472 TRP 0.021 0.001 TRP A 643 HIS 0.010 0.001 HIS B1189 Details of bonding type rmsd covalent geometry : bond 0.00231 (19816) covalent geometry : angle 0.47154 (26875) hydrogen bonds : bond 0.03840 ( 988) hydrogen bonds : angle 4.04249 ( 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 270 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5159 (tpt) cc_final: 0.3226 (tmm) REVERT: A 162 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6266 (tm-30) REVERT: A 197 ARG cc_start: 0.8179 (ttt90) cc_final: 0.7722 (ttt180) REVERT: A 288 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7455 (pp30) REVERT: A 577 GLN cc_start: 0.7497 (tp40) cc_final: 0.7153 (tt0) REVERT: A 663 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8629 (ttt) REVERT: A 880 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 968 GLU cc_start: 0.7979 (tt0) cc_final: 0.7746 (tm-30) REVERT: A 986 GLN cc_start: 0.8449 (tt0) cc_final: 0.8163 (tp40) REVERT: B 31 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7134 (mtmm) REVERT: B 150 LEU cc_start: 0.8623 (mt) cc_final: 0.8423 (mm) REVERT: B 249 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: B 274 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8211 (tt) REVERT: B 577 GLN cc_start: 0.7475 (tp40) cc_final: 0.7105 (tt0) REVERT: B 663 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8503 (ttt) REVERT: B 927 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8610 (mtp) REVERT: B 951 GLN cc_start: 0.8661 (tp40) cc_final: 0.8435 (mm-40) REVERT: B 1100 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6053 (m-30) outliers start: 45 outliers final: 32 residues processed: 256 average time/residue: 0.5792 time to fit residues: 167.1268 Evaluate side-chains 247 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 1017 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 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 LYS 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 306 ASP 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 772 ASP Chi-restraints excluded: chain B residue 824 MET 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 1175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 18 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A1022 GLN 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 = 0.3998 r_free = 0.3998 target = 0.166166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109260 restraints weight = 22145.655| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.08 r_work: 0.3168 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19816 Z= 0.155 Angle : 0.527 8.323 26875 Z= 0.277 Chirality : 0.041 0.163 2960 Planarity : 0.003 0.035 3402 Dihedral : 12.028 169.635 2865 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.03 % Allowed : 21.02 % 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 aren not related in a simple way. whole: 1.67 (0.17), residues: 2316 helix: 2.45 (0.15), residues: 1158 sheet: 0.30 (0.32), residues: 288 loop : -0.46 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.011 0.001 TYR A 494 PHE 0.020 0.002 PHE B 472 TRP 0.024 0.001 TRP A 643 HIS 0.006 0.001 HIS B 496 Details of bonding type rmsd covalent geometry : bond 0.00361 (19816) covalent geometry : angle 0.52662 (26875) hydrogen bonds : bond 0.04749 ( 988) hydrogen bonds : angle 4.15537 ( 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 243 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5158 (tpt) cc_final: 0.3144 (tmm) REVERT: A 197 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7735 (ttt180) REVERT: A 508 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7525 (pp30) REVERT: A 577 GLN cc_start: 0.7528 (tp40) cc_final: 0.7182 (tt0) REVERT: A 880 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 968 GLU cc_start: 0.8029 (tt0) cc_final: 0.7779 (tm-30) REVERT: A 986 GLN cc_start: 0.8460 (tt0) cc_final: 0.8179 (tp40) REVERT: B 31 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7266 (mtmm) REVERT: B 249 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8625 (mttm) REVERT: B 274 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 508 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7603 (pp30) REVERT: B 577 GLN cc_start: 0.7468 (tp40) cc_final: 0.7103 (tt0) REVERT: B 927 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8599 (mtp) REVERT: B 951 GLN cc_start: 0.8636 (tp40) cc_final: 0.8392 (mm-40) REVERT: B 1100 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.6054 (m-30) outliers start: 42 outliers final: 34 residues processed: 231 average time/residue: 0.6028 time to fit residues: 157.2867 Evaluate side-chains 237 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 663 MET 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 1017 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 39 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 249 LYS 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 306 ASP 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 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 1175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 32 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111928 restraints weight = 22239.569| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.07 r_work: 0.3206 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19816 Z= 0.114 Angle : 0.487 8.393 26875 Z= 0.257 Chirality : 0.039 0.159 2960 Planarity : 0.003 0.036 3402 Dihedral : 12.047 175.449 2865 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.12 % Allowed : 20.88 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.82 (0.17), residues: 2316 helix: 2.57 (0.15), residues: 1158 sheet: 0.57 (0.32), residues: 274 loop : -0.44 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1030 TYR 0.008 0.001 TYR B1103 PHE 0.016 0.001 PHE A 472 TRP 0.021 0.001 TRP A 643 HIS 0.005 0.001 HIS B 496 Details of bonding type rmsd covalent geometry : bond 0.00256 (19816) covalent geometry : angle 0.48676 (26875) hydrogen bonds : bond 0.03982 ( 988) hydrogen bonds : angle 4.03965 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8779.21 seconds wall clock time: 149 minutes 40.12 seconds (8980.12 seconds total)