Starting phenix.real_space_refine on Wed Mar 4 20:35:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5t_26358/03_2026/7u5t_26358.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5t_26358/03_2026/7u5t_26358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u5t_26358/03_2026/7u5t_26358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5t_26358/03_2026/7u5t_26358.map" model { file = "/net/cci-nas-00/data/ceres_data/7u5t_26358/03_2026/7u5t_26358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5t_26358/03_2026/7u5t_26358.cif" } resolution = 3.43 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= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8874 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5803 2.51 5 N 1534 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9093 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4529 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 33, 'TRANS': 558} Chain breaks: 4 Chain: "B" Number of atoms: 4564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4564 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 34, 'TRANS': 563} Chain breaks: 3 Time building chain proxies: 1.87, per 1000 atoms: 0.21 Number of scatterers: 9093 At special positions: 0 Unit cell: (91.2135, 134.946, 149.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1708 8.00 N 1534 7.00 C 5803 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: 0.70 Conformation dependent library (CDL) restraints added in 528.6 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 14 sheets defined 50.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.648A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.634A pdb=" N ARG A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 66 removed outlier: 5.544A pdb=" N GLU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.537A pdb=" N LYS A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 4.047A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.589A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.906A pdb=" N GLU A 178 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 179 " --> pdb=" O PHE A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 179' Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.506A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.617A pdb=" N ARG A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.819A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 249 removed outlier: 3.593A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.655A pdb=" N ALA A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 4.492A pdb=" N ILE A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.730A pdb=" N VAL A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.614A pdb=" N LYS A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.126A pdb=" N HIS A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 337 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.712A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.895A pdb=" N VAL A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 691 through 696 removed outlier: 3.647A pdb=" N ASP A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 696' Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.597A pdb=" N VAL A 742 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 removed outlier: 3.554A pdb=" N ALA A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.809A pdb=" N ALA A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 823 " --> pdb=" O MET A 819 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 836 through 841 removed outlier: 3.897A pdb=" N THR A 840 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 841 " --> pdb=" O SER A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.526A pdb=" N LEU A 851 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 852 " --> pdb=" O TRP A 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.728A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.555A pdb=" N ARG B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 66 removed outlier: 5.556A pdb=" N GLU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.591A pdb=" N ASN B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.567A pdb=" N LYS B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.532A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.917A pdb=" N GLU B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 179 " --> pdb=" O PHE B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 179' Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.910A pdb=" N GLY B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.611A pdb=" N ARG B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.583A pdb=" N VAL B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.539A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.584A pdb=" N SER B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.701A pdb=" N LEU B 260 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 280 through 298 removed outlier: 4.516A pdb=" N ILE B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.688A pdb=" N VAL B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.278A pdb=" N HIS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 337 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.680A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.744A pdb=" N VAL B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 386' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 669 through 672 removed outlier: 3.618A pdb=" N ALA B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 673 through 679 removed outlier: 3.610A pdb=" N ASP B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 679' Processing helix chain 'B' and resid 718 through 724 removed outlier: 3.698A pdb=" N VAL B 724 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 757 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.547A pdb=" N GLY B 790 " --> pdb=" O ILE B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.549A pdb=" N SER B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 805 " --> pdb=" O MET B 801 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 806 " --> pdb=" O SER B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 818 through 823 removed outlier: 3.751A pdb=" N THR B 821 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 822 " --> pdb=" O ARG B 819 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 823 " --> pdb=" O SER B 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 818 through 823' Processing helix chain 'B' and resid 828 through 835 removed outlier: 3.514A pdb=" N LEU B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 834 " --> pdb=" O TRP B 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.163A pdb=" N GLU A 4 " --> pdb=" O HIS A 15 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 15 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 6 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 13 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N VAL A 170 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 13 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS A 172 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS A 15 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 131 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N PHE A 171 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN A 133 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP A 173 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 106 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 134 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 108 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 36 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A 107 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 38 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 109 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL A 40 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 37 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR A 74 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 39 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 76 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 41 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 removed outlier: 7.144A pdb=" N LYS A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 809 through 810 removed outlier: 7.195A pdb=" N VAL A 809 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.600A pdb=" N VAL A 713 " --> pdb=" O CYS A 676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 752 through 755 removed outlier: 3.508A pdb=" N ILE A 789 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.485A pdb=" N GLU B 4 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS B 15 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 6 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 170 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 13 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N CYS B 172 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N HIS B 15 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 131 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N PHE B 171 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN B 133 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP B 173 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 106 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 134 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA B 108 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B 36 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 107 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 38 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 109 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL B 40 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR B 37 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR B 74 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B 39 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 76 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 41 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AB1, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AB2, first strand: chain 'B' and resid 363 through 365 removed outlier: 7.150A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 814 through 816 removed outlier: 3.542A pdb=" N VAL B 390 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.501A pdb=" N CYS B 658 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 695 " --> pdb=" O CYS B 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 710 removed outlier: 6.643A pdb=" N VAL B 709 " --> pdb=" O THR B 737 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 771 " --> pdb=" O ILE B 736 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 765 " --> pdb=" O GLU B 772 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1522 1.31 - 1.44: 2191 1.44 - 1.56: 5476 1.56 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9263 Sorted by residual: bond pdb=" N GLU A 730 " pdb=" CA GLU A 730 " ideal model delta sigma weight residual 1.463 1.491 -0.027 6.90e-03 2.10e+04 1.59e+01 bond pdb=" N TYR B 646 " pdb=" CA TYR B 646 " ideal model delta sigma weight residual 1.463 1.489 -0.026 6.90e-03 2.10e+04 1.42e+01 bond pdb=" C LYS B 680 " pdb=" N PRO B 681 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.28e-02 6.10e+03 1.30e+01 bond pdb=" N ILE A 794 " pdb=" CA ILE A 794 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N ILE B 776 " pdb=" CA ILE B 776 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.06e+01 ... (remaining 9258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11428 1.83 - 3.66: 994 3.66 - 5.49: 119 5.49 - 7.33: 8 7.33 - 9.16: 13 Bond angle restraints: 12562 Sorted by residual: angle pdb=" N ASN A 61 " pdb=" CA ASN A 61 " pdb=" C ASN A 61 " ideal model delta sigma weight residual 113.18 105.08 8.10 1.33e+00 5.65e-01 3.71e+01 angle pdb=" C ILE A 757 " pdb=" N ALA A 758 " pdb=" CA ALA A 758 " ideal model delta sigma weight residual 122.11 113.10 9.01 1.64e+00 3.72e-01 3.02e+01 angle pdb=" N PRO B 705 " pdb=" CA PRO B 705 " pdb=" C PRO B 705 " ideal model delta sigma weight residual 110.50 118.93 -8.43 1.57e+00 4.06e-01 2.88e+01 angle pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" O ILE A 757 " ideal model delta sigma weight residual 122.63 117.99 4.64 8.70e-01 1.32e+00 2.84e+01 angle pdb=" C GLU A 830 " pdb=" N PRO A 831 " pdb=" CA PRO A 831 " ideal model delta sigma weight residual 119.93 125.20 -5.27 1.07e+00 8.73e-01 2.42e+01 ... (remaining 12557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 5091 15.81 - 31.62: 433 31.62 - 47.43: 88 47.43 - 63.24: 23 63.24 - 79.05: 9 Dihedral angle restraints: 5644 sinusoidal: 2227 harmonic: 3417 Sorted by residual: dihedral pdb=" CA LEU A 274 " pdb=" C LEU A 274 " pdb=" N THR A 275 " pdb=" CA THR A 275 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LEU B 274 " pdb=" C LEU B 274 " pdb=" N THR B 275 " pdb=" CA THR B 275 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO A 717 " pdb=" C PRO A 717 " pdb=" N ARG A 718 " pdb=" CA ARG A 718 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1183 0.077 - 0.153: 274 0.153 - 0.230: 34 0.230 - 0.306: 7 0.306 - 0.383: 1 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA VAL A 832 " pdb=" N VAL A 832 " pdb=" C VAL A 832 " pdb=" CB VAL A 832 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1496 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 704 " -0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C LYS B 704 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS B 704 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO B 705 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 727 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.83e+00 pdb=" C VAL A 727 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 727 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 728 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 154 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO B 155 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.038 5.00e-02 4.00e+02 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2387 2.80 - 3.33: 8350 3.33 - 3.85: 15283 3.85 - 4.38: 18731 4.38 - 4.90: 30689 Nonbonded interactions: 75440 Sorted by model distance: nonbonded pdb=" O MET A 45 " pdb=" OG1 THR A 48 " model vdw 2.280 3.040 nonbonded pdb=" O SER A 838 " pdb=" OG SER A 838 " model vdw 2.291 3.040 nonbonded pdb=" O MET B 45 " pdb=" OG1 THR B 48 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASP B 710 " pdb=" OG1 THR B 737 " model vdw 2.316 3.040 nonbonded pdb=" O SER B 2 " pdb=" OG SER B 2 " model vdw 2.324 3.040 ... (remaining 75435 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' and (resid 2 through 249 or resid 256 through 662 or resid 667 throug \ h 846)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.100 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 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 : 0.008 0.059 9263 Z= 0.482 Angle : 1.089 9.158 12562 Z= 0.695 Chirality : 0.065 0.383 1499 Planarity : 0.007 0.069 1590 Dihedral : 13.049 79.052 3432 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.95 (0.17), residues: 1172 helix: -4.59 (0.10), residues: 552 sheet: -2.99 (0.36), residues: 130 loop : -3.20 (0.22), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 749 TYR 0.020 0.002 TYR B 646 PHE 0.023 0.003 PHE B 327 TRP 0.008 0.002 TRP A 848 HIS 0.005 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00836 ( 9263) covalent geometry : angle 1.08877 (12562) hydrogen bonds : bond 0.32606 ( 297) hydrogen bonds : angle 10.59058 ( 825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ILE cc_start: 0.7795 (mm) cc_final: 0.7024 (mm) REVERT: A 161 ILE cc_start: 0.8730 (mm) cc_final: 0.8502 (mm) REVERT: A 794 ILE cc_start: 0.7026 (mm) cc_final: 0.6644 (tt) outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.1047 time to fit residues: 41.4084 Evaluate side-chains 137 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 706 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 98 GLN B 376 GLN ** B 669 GLN ** 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 = 0.4374 r_free = 0.4374 target = 0.166587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143539 restraints weight = 16577.694| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.69 r_work: 0.3999 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9263 Z= 0.155 Angle : 0.681 7.653 12562 Z= 0.351 Chirality : 0.046 0.167 1499 Planarity : 0.006 0.056 1590 Dihedral : 5.393 38.438 1252 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.05 % Allowed : 12.60 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.21), residues: 1172 helix: -3.10 (0.16), residues: 547 sheet: -1.95 (0.43), residues: 108 loop : -2.16 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 743 TYR 0.023 0.002 TYR A 370 PHE 0.020 0.002 PHE B 327 TRP 0.017 0.002 TRP B 829 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9263) covalent geometry : angle 0.68121 (12562) hydrogen bonds : bond 0.04372 ( 297) hydrogen bonds : angle 5.60499 ( 825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7654 (m-30) cc_final: 0.7355 (m-30) REVERT: A 126 MET cc_start: 0.8165 (mmt) cc_final: 0.7906 (mmt) REVERT: A 232 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7437 (mt) REVERT: A 707 THR cc_start: 0.3157 (OUTLIER) cc_final: 0.2947 (m) REVERT: A 767 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7473 (mmt90) REVERT: A 771 MET cc_start: 0.7823 (mmm) cc_final: 0.7481 (mmm) REVERT: A 774 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: B 200 ASN cc_start: 0.7245 (t0) cc_final: 0.7002 (t0) REVERT: B 210 PHE cc_start: 0.7287 (t80) cc_final: 0.6949 (t80) REVERT: B 226 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7391 (tp40) REVERT: B 366 ILE cc_start: 0.8822 (mt) cc_final: 0.8470 (mm) REVERT: B 384 PHE cc_start: 0.8067 (t80) cc_final: 0.7733 (t80) REVERT: B 736 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6575 (mt) REVERT: B 750 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7417 (tp) REVERT: B 757 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8070 (tp) outliers start: 31 outliers final: 13 residues processed: 186 average time/residue: 0.0809 time to fit residues: 21.4081 Evaluate side-chains 145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 757 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 60 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 159 ASN A 393 HIS ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 688 GLN B 708 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.157434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.135423 restraints weight = 16994.838| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.44 r_work: 0.3926 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9263 Z= 0.175 Angle : 0.668 11.293 12562 Z= 0.340 Chirality : 0.046 0.200 1499 Planarity : 0.005 0.057 1590 Dihedral : 5.067 35.290 1252 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.54 % Allowed : 15.55 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.23), residues: 1172 helix: -2.13 (0.19), residues: 546 sheet: -1.72 (0.42), residues: 125 loop : -1.80 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 816 TYR 0.017 0.002 TYR A 370 PHE 0.031 0.002 PHE B 803 TRP 0.009 0.002 TRP B 830 HIS 0.004 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9263) covalent geometry : angle 0.66823 (12562) hydrogen bonds : bond 0.04512 ( 297) hydrogen bonds : angle 5.18355 ( 825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7953 (m-30) cc_final: 0.7566 (m-30) REVERT: A 189 MET cc_start: 0.7297 (mmm) cc_final: 0.7090 (mmm) REVERT: A 232 LEU cc_start: 0.8134 (mm) cc_final: 0.7714 (mt) REVERT: A 700 MET cc_start: 0.5896 (tpp) cc_final: 0.5600 (tpp) REVERT: A 734 ASP cc_start: 0.7670 (p0) cc_final: 0.6849 (m-30) REVERT: A 774 GLU cc_start: 0.7158 (mp0) cc_final: 0.6952 (mp0) REVERT: B 18 TYR cc_start: 0.6033 (t80) cc_final: 0.5727 (t80) REVERT: B 61 ASN cc_start: 0.7800 (t0) cc_final: 0.7584 (t0) REVERT: B 339 GLU cc_start: 0.7838 (pm20) cc_final: 0.7527 (pm20) REVERT: B 342 ILE cc_start: 0.8773 (tp) cc_final: 0.7335 (tp) REVERT: B 384 PHE cc_start: 0.7959 (t80) cc_final: 0.7633 (t80) REVERT: B 389 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7353 (mm-30) REVERT: B 396 THR cc_start: 0.7030 (p) cc_final: 0.6639 (t) outliers start: 36 outliers final: 24 residues processed: 184 average time/residue: 0.0710 time to fit residues: 19.8225 Evaluate side-chains 146 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 HIS B 669 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.155783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133619 restraints weight = 17229.006| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.44 r_work: 0.3894 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9263 Z= 0.145 Angle : 0.611 8.908 12562 Z= 0.308 Chirality : 0.045 0.173 1499 Planarity : 0.005 0.053 1590 Dihedral : 4.758 34.357 1252 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.44 % Allowed : 16.93 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.23), residues: 1172 helix: -1.70 (0.20), residues: 546 sheet: -1.66 (0.42), residues: 130 loop : -1.62 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 749 TYR 0.016 0.001 TYR A 370 PHE 0.036 0.002 PHE B 803 TRP 0.014 0.002 TRP A 847 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9263) covalent geometry : angle 0.61090 (12562) hydrogen bonds : bond 0.03707 ( 297) hydrogen bonds : angle 4.93238 ( 825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7841 (m-30) cc_final: 0.7433 (m-30) REVERT: A 189 MET cc_start: 0.7393 (mmm) cc_final: 0.7168 (mmm) REVERT: A 232 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 259 LEU cc_start: 0.9046 (mp) cc_final: 0.8699 (tt) REVERT: A 344 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7412 (tt) REVERT: A 767 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7265 (mpt180) REVERT: A 774 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: B 18 TYR cc_start: 0.6195 (t80) cc_final: 0.5679 (t80) REVERT: B 189 MET cc_start: 0.8238 (tpp) cc_final: 0.7848 (tpp) REVERT: B 342 ILE cc_start: 0.8735 (tp) cc_final: 0.7627 (tp) REVERT: B 384 PHE cc_start: 0.7800 (t80) cc_final: 0.7528 (t80) REVERT: B 389 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7493 (mm-30) REVERT: B 396 THR cc_start: 0.7091 (p) cc_final: 0.6709 (t) REVERT: B 669 GLN cc_start: 0.6412 (pt0) cc_final: 0.6142 (pt0) REVERT: B 714 MET cc_start: 0.5586 (mtt) cc_final: 0.5362 (mmm) REVERT: B 844 TYR cc_start: 0.7176 (t80) cc_final: 0.6893 (t80) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.0593 time to fit residues: 15.8441 Evaluate side-chains 152 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.150518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126561 restraints weight = 16655.510| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.71 r_work: 0.3767 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9263 Z= 0.132 Angle : 0.599 9.412 12562 Z= 0.301 Chirality : 0.045 0.194 1499 Planarity : 0.004 0.053 1590 Dihedral : 4.609 34.586 1252 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.54 % Allowed : 17.13 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.24), residues: 1172 helix: -1.45 (0.21), residues: 558 sheet: -1.45 (0.43), residues: 133 loop : -1.56 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 718 TYR 0.019 0.002 TYR B 51 PHE 0.025 0.002 PHE A 692 TRP 0.012 0.001 TRP B 829 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9263) covalent geometry : angle 0.59922 (12562) hydrogen bonds : bond 0.03748 ( 297) hydrogen bonds : angle 4.94014 ( 825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7919 (m-30) cc_final: 0.7459 (m-30) REVERT: A 189 MET cc_start: 0.7315 (mmm) cc_final: 0.7057 (mmm) REVERT: A 232 LEU cc_start: 0.8574 (mm) cc_final: 0.8082 (mt) REVERT: A 259 LEU cc_start: 0.9129 (mp) cc_final: 0.8692 (tt) REVERT: A 344 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 734 ASP cc_start: 0.7747 (p0) cc_final: 0.6703 (m-30) REVERT: A 767 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7375 (mpt-90) REVERT: A 835 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7031 (mm) REVERT: B 18 TYR cc_start: 0.6441 (t80) cc_final: 0.5982 (t80) REVERT: B 51 TYR cc_start: 0.7235 (t80) cc_final: 0.6638 (t80) REVERT: B 61 ASN cc_start: 0.7719 (t0) cc_final: 0.7436 (t0) REVERT: B 189 MET cc_start: 0.8150 (tpp) cc_final: 0.7684 (tpp) REVERT: B 384 PHE cc_start: 0.8061 (t80) cc_final: 0.7701 (t80) REVERT: B 389 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7531 (mm-30) REVERT: B 396 THR cc_start: 0.7270 (p) cc_final: 0.6959 (t) REVERT: B 669 GLN cc_start: 0.6127 (pt0) cc_final: 0.5867 (pt0) REVERT: B 778 ILE cc_start: 0.0434 (OUTLIER) cc_final: 0.0047 (mp) REVERT: B 844 TYR cc_start: 0.7484 (t80) cc_final: 0.7110 (t80) outliers start: 36 outliers final: 28 residues processed: 169 average time/residue: 0.0595 time to fit residues: 15.7607 Evaluate side-chains 162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.120119 restraints weight = 16865.468| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.67 r_work: 0.3661 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 9263 Z= 0.209 Angle : 0.709 11.572 12562 Z= 0.355 Chirality : 0.048 0.202 1499 Planarity : 0.005 0.054 1590 Dihedral : 5.050 31.723 1252 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.43 % Allowed : 17.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.24), residues: 1172 helix: -1.42 (0.21), residues: 548 sheet: -1.49 (0.43), residues: 135 loop : -1.60 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 718 TYR 0.015 0.002 TYR B 51 PHE 0.015 0.002 PHE A 185 TRP 0.012 0.002 TRP B 830 HIS 0.006 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 9263) covalent geometry : angle 0.70930 (12562) hydrogen bonds : bond 0.04362 ( 297) hydrogen bonds : angle 5.17488 ( 825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8081 (tpt90) cc_final: 0.7436 (ttm170) REVERT: A 232 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 259 LEU cc_start: 0.9159 (mp) cc_final: 0.8685 (tt) REVERT: A 344 LEU cc_start: 0.8022 (mp) cc_final: 0.7473 (tt) REVERT: A 745 VAL cc_start: 0.8569 (m) cc_final: 0.8274 (p) REVERT: A 767 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7331 (mpt-90) REVERT: B 18 TYR cc_start: 0.6810 (t80) cc_final: 0.6385 (t80) REVERT: B 189 MET cc_start: 0.8339 (tpp) cc_final: 0.7811 (tpp) REVERT: B 328 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5368 (mm) REVERT: B 384 PHE cc_start: 0.8177 (t80) cc_final: 0.7790 (t80) REVERT: B 396 THR cc_start: 0.7526 (p) cc_final: 0.7280 (t) REVERT: B 403 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7488 (mp) REVERT: B 669 GLN cc_start: 0.6072 (pt0) cc_final: 0.5867 (pt0) REVERT: B 803 PHE cc_start: 0.8103 (m-80) cc_final: 0.7538 (m-80) outliers start: 45 outliers final: 31 residues processed: 179 average time/residue: 0.0620 time to fit residues: 17.4479 Evaluate side-chains 164 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.145122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121586 restraints weight = 16882.474| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.66 r_work: 0.3701 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9263 Z= 0.129 Angle : 0.598 9.612 12562 Z= 0.297 Chirality : 0.045 0.201 1499 Planarity : 0.004 0.053 1590 Dihedral : 4.620 34.753 1252 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.64 % Allowed : 18.60 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.24), residues: 1172 helix: -1.10 (0.22), residues: 552 sheet: -1.17 (0.43), residues: 143 loop : -1.43 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 241 TYR 0.024 0.002 TYR B 844 PHE 0.028 0.002 PHE A 692 TRP 0.010 0.001 TRP A 847 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9263) covalent geometry : angle 0.59833 (12562) hydrogen bonds : bond 0.03611 ( 297) hydrogen bonds : angle 4.96159 ( 825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8012 (tpt90) cc_final: 0.7369 (ttm170) REVERT: A 93 ASP cc_start: 0.7797 (m-30) cc_final: 0.7552 (m-30) REVERT: A 206 ARG cc_start: 0.6331 (ttp80) cc_final: 0.5882 (ttp80) REVERT: A 232 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8328 (mt) REVERT: A 259 LEU cc_start: 0.9109 (mp) cc_final: 0.8727 (tt) REVERT: A 293 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8077 (mt-10) REVERT: A 301 LEU cc_start: 0.7562 (tt) cc_final: 0.7273 (tp) REVERT: A 732 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6665 (ptt) REVERT: A 745 VAL cc_start: 0.8451 (m) cc_final: 0.8216 (p) REVERT: A 767 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7419 (mpt-90) REVERT: B 18 TYR cc_start: 0.6528 (t80) cc_final: 0.6138 (t80) REVERT: B 95 LEU cc_start: 0.9007 (mt) cc_final: 0.8590 (mt) REVERT: B 185 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 189 MET cc_start: 0.8183 (tpp) cc_final: 0.7724 (tpp) REVERT: B 328 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5346 (mm) REVERT: B 384 PHE cc_start: 0.8134 (t80) cc_final: 0.7730 (t80) REVERT: B 669 GLN cc_start: 0.5965 (pt0) cc_final: 0.5703 (pt0) REVERT: B 803 PHE cc_start: 0.8098 (m-80) cc_final: 0.7781 (m-80) outliers start: 37 outliers final: 23 residues processed: 161 average time/residue: 0.0726 time to fit residues: 17.2206 Evaluate side-chains 153 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 82 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119836 restraints weight = 16934.827| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.64 r_work: 0.3676 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9263 Z= 0.155 Angle : 0.639 14.923 12562 Z= 0.317 Chirality : 0.046 0.204 1499 Planarity : 0.005 0.052 1590 Dihedral : 4.541 20.657 1249 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.94 % Allowed : 18.60 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.25), residues: 1172 helix: -1.10 (0.22), residues: 554 sheet: -1.11 (0.44), residues: 140 loop : -1.47 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.021 0.002 TYR B 51 PHE 0.014 0.002 PHE A 176 TRP 0.008 0.001 TRP B 830 HIS 0.004 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9263) covalent geometry : angle 0.63916 (12562) hydrogen bonds : bond 0.03774 ( 297) hydrogen bonds : angle 5.08010 ( 825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6274 (tp30) cc_final: 0.5970 (tm-30) REVERT: A 47 ARG cc_start: 0.7996 (tpt90) cc_final: 0.7354 (ttm170) REVERT: A 206 ARG cc_start: 0.6188 (ttp80) cc_final: 0.5809 (ttp80) REVERT: A 232 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8380 (mt) REVERT: A 259 LEU cc_start: 0.9109 (mp) cc_final: 0.8711 (tt) REVERT: A 697 LEU cc_start: 0.7621 (mt) cc_final: 0.7366 (mt) REVERT: A 745 VAL cc_start: 0.8479 (m) cc_final: 0.8240 (p) REVERT: A 767 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7375 (mpt-90) REVERT: B 18 TYR cc_start: 0.6665 (t80) cc_final: 0.6368 (t80) REVERT: B 95 LEU cc_start: 0.9009 (mt) cc_final: 0.8589 (mt) REVERT: B 185 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7728 (t80) REVERT: B 189 MET cc_start: 0.8249 (tpp) cc_final: 0.7740 (tpp) REVERT: B 328 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5339 (mm) REVERT: B 384 PHE cc_start: 0.8142 (t80) cc_final: 0.7777 (t80) REVERT: B 669 GLN cc_start: 0.5929 (pt0) cc_final: 0.5688 (pt0) REVERT: B 803 PHE cc_start: 0.8131 (m-80) cc_final: 0.7787 (m-80) outliers start: 40 outliers final: 32 residues processed: 164 average time/residue: 0.0689 time to fit residues: 17.0531 Evaluate side-chains 162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.0050 chunk 83 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 chunk 88 optimal weight: 0.0020 chunk 58 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.146318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122861 restraints weight = 16519.691| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.64 r_work: 0.3722 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.7665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9263 Z= 0.112 Angle : 0.602 14.479 12562 Z= 0.298 Chirality : 0.044 0.166 1499 Planarity : 0.004 0.051 1590 Dihedral : 4.273 19.524 1249 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.66 % Allowed : 19.88 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.25), residues: 1172 helix: -0.89 (0.23), residues: 552 sheet: -0.71 (0.46), residues: 133 loop : -1.34 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 761 TYR 0.015 0.001 TYR B 51 PHE 0.028 0.002 PHE A 692 TRP 0.008 0.001 TRP A 847 HIS 0.002 0.000 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9263) covalent geometry : angle 0.60181 (12562) hydrogen bonds : bond 0.03430 ( 297) hydrogen bonds : angle 4.91204 ( 825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6097 (tp30) cc_final: 0.5887 (tm-30) REVERT: A 47 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7309 (ttm170) REVERT: A 206 ARG cc_start: 0.6168 (ttp80) cc_final: 0.5805 (ttp80) REVERT: A 232 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8323 (mt) REVERT: A 259 LEU cc_start: 0.9073 (mp) cc_final: 0.8690 (tt) REVERT: A 697 LEU cc_start: 0.7650 (mt) cc_final: 0.7441 (mt) REVERT: A 745 VAL cc_start: 0.8453 (m) cc_final: 0.8207 (p) REVERT: A 767 ARG cc_start: 0.8032 (mmt90) cc_final: 0.7786 (mmt90) REVERT: B 18 TYR cc_start: 0.6508 (t80) cc_final: 0.5920 (t80) REVERT: B 95 LEU cc_start: 0.8943 (mt) cc_final: 0.8513 (mt) REVERT: B 189 MET cc_start: 0.8086 (tpp) cc_final: 0.7643 (tpp) REVERT: B 328 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5328 (mm) REVERT: B 342 ILE cc_start: 0.8859 (tp) cc_final: 0.8422 (tp) REVERT: B 384 PHE cc_start: 0.8093 (t80) cc_final: 0.7738 (t80) REVERT: B 803 PHE cc_start: 0.8221 (m-80) cc_final: 0.7779 (m-80) outliers start: 27 outliers final: 24 residues processed: 153 average time/residue: 0.0668 time to fit residues: 15.6145 Evaluate side-chains 151 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 99 optimal weight: 0.0970 chunk 29 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.146240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122555 restraints weight = 16586.707| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.64 r_work: 0.3714 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.7850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 9263 Z= 0.123 Angle : 0.619 14.225 12562 Z= 0.305 Chirality : 0.045 0.165 1499 Planarity : 0.004 0.049 1590 Dihedral : 4.241 19.431 1249 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.46 % Allowed : 20.28 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.25), residues: 1172 helix: -0.81 (0.23), residues: 547 sheet: -0.64 (0.47), residues: 133 loop : -1.31 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 749 TYR 0.015 0.001 TYR B 51 PHE 0.012 0.001 PHE B 327 TRP 0.024 0.002 TRP A 847 HIS 0.003 0.000 HIS A 852 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9263) covalent geometry : angle 0.61906 (12562) hydrogen bonds : bond 0.03505 ( 297) hydrogen bonds : angle 4.90909 ( 825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6102 (tp30) cc_final: 0.5883 (tm-30) REVERT: A 47 ARG cc_start: 0.7941 (tpt90) cc_final: 0.7340 (ttm170) REVERT: A 206 ARG cc_start: 0.6188 (ttp80) cc_final: 0.5821 (ttp80) REVERT: A 232 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8316 (mt) REVERT: A 259 LEU cc_start: 0.9077 (mp) cc_final: 0.8670 (tt) REVERT: A 697 LEU cc_start: 0.7499 (mt) cc_final: 0.7220 (mt) REVERT: A 745 VAL cc_start: 0.8455 (m) cc_final: 0.8203 (p) REVERT: A 767 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7693 (mmt90) REVERT: B 18 TYR cc_start: 0.6427 (t80) cc_final: 0.6126 (t80) REVERT: B 95 LEU cc_start: 0.8952 (mt) cc_final: 0.8517 (mt) REVERT: B 189 MET cc_start: 0.8080 (tpp) cc_final: 0.7569 (tpp) REVERT: B 328 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5332 (mm) REVERT: B 384 PHE cc_start: 0.8087 (t80) cc_final: 0.7725 (t80) REVERT: B 803 PHE cc_start: 0.8244 (m-80) cc_final: 0.7801 (m-80) outliers start: 25 outliers final: 22 residues processed: 149 average time/residue: 0.0674 time to fit residues: 15.2088 Evaluate side-chains 153 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119687 restraints weight = 16500.385| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.61 r_work: 0.3676 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9263 Z= 0.155 Angle : 0.657 14.373 12562 Z= 0.328 Chirality : 0.046 0.209 1499 Planarity : 0.005 0.049 1590 Dihedral : 4.442 19.644 1249 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.15 % Allowed : 19.78 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.25), residues: 1172 helix: -0.98 (0.22), residues: 560 sheet: -0.69 (0.48), residues: 128 loop : -1.33 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 749 TYR 0.016 0.002 TYR B 51 PHE 0.028 0.002 PHE A 692 TRP 0.025 0.002 TRP A 847 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9263) covalent geometry : angle 0.65730 (12562) hydrogen bonds : bond 0.03914 ( 297) hydrogen bonds : angle 5.13908 ( 825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.15 seconds wall clock time: 34 minutes 36.56 seconds (2076.56 seconds total)