Starting phenix.real_space_refine on Tue Nov 18 23:58:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ezx_50090/11_2025/9ezx_50090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ezx_50090/11_2025/9ezx_50090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ezx_50090/11_2025/9ezx_50090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ezx_50090/11_2025/9ezx_50090.map" model { file = "/net/cci-nas-00/data/ceres_data/9ezx_50090/11_2025/9ezx_50090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ezx_50090/11_2025/9ezx_50090.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 11777 2.51 5 N 3247 2.21 5 O 3513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18585 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9299 Classifications: {'peptide': 1152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1117} Chain breaks: 5 Chain: "B" Number of atoms: 9286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9286 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1115} Chain breaks: 6 Time building chain proxies: 4.61, per 1000 atoms: 0.25 Number of scatterers: 18585 At special positions: 0 Unit cell: (143.65, 113.75, 131.95, 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 3513 8.00 N 3247 7.00 C 11777 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: 2.79 Conformation dependent library (CDL) restraints added in 934.3 milliseconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 24 sheets defined 60.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.819A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.110A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.155A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.553A pdb=" N GLN A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 removed outlier: 4.177A pdb=" N ASP A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.665A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.527A pdb=" N ASN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 435 Processing helix chain 'A' and resid 444 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 477 removed outlier: 3.967A pdb=" N ASP A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 656 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 711 through 723 Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.752A pdb=" N GLY A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 737' Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 789 through 808 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 836 Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.710A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 873 through 880 removed outlier: 4.470A pdb=" N ILE A 877 " --> pdb=" O GLY A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.014A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 902 removed outlier: 4.010A pdb=" N ALA A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 939 Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.700A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1014 through 1020 removed outlier: 3.700A pdb=" N GLN A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1069 removed outlier: 3.728A pdb=" N PHE A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1114 through 1127 removed outlier: 3.844A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.518A pdb=" N GLU B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 54 through 78 Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.682A pdb=" N ARG B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 209 Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.978A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.192A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.580A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 337 removed outlier: 3.752A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 402 through 435 removed outlier: 3.600A pdb=" N GLY B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.137A pdb=" N ASP B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 474 " --> pdb=" O GLU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 604 through 616 Processing helix chain 'B' and resid 623 through 631 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 636 through 656 Processing helix chain 'B' and resid 672 through 674 No H-bonds generated for 'chain 'B' and resid 672 through 674' Processing helix chain 'B' and resid 675 through 694 Processing helix chain 'B' and resid 704 through 711 Processing helix chain 'B' and resid 711 through 723 Processing helix chain 'B' and resid 733 through 737 removed outlier: 3.818A pdb=" N GLY B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 733 through 737' Processing helix chain 'B' and resid 747 through 752 Processing helix chain 'B' and resid 789 through 808 Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 827 through 837 removed outlier: 3.843A pdb=" N GLN B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 855 removed outlier: 3.667A pdb=" N GLN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 858 No H-bonds generated for 'chain 'B' and resid 856 through 858' Processing helix chain 'B' and resid 873 through 880 removed outlier: 4.538A pdb=" N ILE B 877 " --> pdb=" O GLY B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.995A pdb=" N LEU B 887 " --> pdb=" O ASP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 902 removed outlier: 4.070A pdb=" N ALA B 902 " --> pdb=" O LYS B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 Processing helix chain 'B' and resid 943 through 960 Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 992 through 996 removed outlier: 3.705A pdb=" N PHE B 996 " --> pdb=" O PRO B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1009 through 1014 removed outlier: 3.526A pdb=" N CYS B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1020 removed outlier: 3.693A pdb=" N GLN B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'B' and resid 1045 through 1052 Processing helix chain 'B' and resid 1052 through 1068 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1114 through 1127 Processing helix chain 'B' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.164A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 45 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 133 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N THR A 243 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.463A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER A 387 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.070A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 662 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR A 775 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745 Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 Processing sheet with id=AB1, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1074 removed outlier: 4.032A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1137 through 1138 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 47 removed outlier: 6.213A pdb=" N ALA B 43 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY B 541 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 45 " --> pdb=" O GLY B 541 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 89 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP B 272 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 91 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 88 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 242 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR B 90 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 133 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR B 243 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB8, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.350A pdb=" N ALA B 341 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE B 385 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN B 343 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N SER B 387 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 595 through 601 removed outlier: 6.858A pdb=" N VAL B 595 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 868 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 597 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL B 870 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS B 599 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 774 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASP B 871 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU B 776 " --> pdb=" O ASP B 871 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 662 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR B 775 " --> pdb=" O TYR B 662 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 664 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS B 698 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE B 730 " --> pdb=" O LYS B 698 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 700 " --> pdb=" O PHE B 730 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR B 732 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 743 through 745 Processing sheet with id=AC2, first strand: chain 'B' and resid 755 through 757 Processing sheet with id=AC3, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AC4, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC5, first strand: chain 'B' and resid 1072 through 1074 removed outlier: 4.034A pdb=" N ILE B1097 " --> pdb=" O VAL B1088 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B1134 " --> pdb=" O ASP B1100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1137 through 1138 1023 hydrogen bonds defined for protein. 2910 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: 4.68 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3290 1.32 - 1.44: 4975 1.44 - 1.57: 10613 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 18954 Sorted by residual: bond pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.20e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N VAL B 239 " pdb=" CA VAL B 239 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ARG B 475 " pdb=" CA ARG B 475 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.23e-02 6.61e+03 9.94e+00 ... (remaining 18949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 24152 1.51 - 3.02: 1118 3.02 - 4.54: 314 4.54 - 6.05: 26 6.05 - 7.56: 4 Bond angle restraints: 25614 Sorted by residual: angle pdb=" CA VAL B 16 " pdb=" C VAL B 16 " pdb=" N PRO B 17 " ideal model delta sigma weight residual 116.57 121.96 -5.39 9.80e-01 1.04e+00 3.02e+01 angle pdb=" CA VAL B 133 " pdb=" C VAL B 133 " pdb=" O VAL B 133 " ideal model delta sigma weight residual 121.67 116.24 5.43 1.05e+00 9.07e-01 2.67e+01 angle pdb=" CA GLY A 346 " pdb=" C GLY A 346 " pdb=" O GLY A 346 " ideal model delta sigma weight residual 122.24 117.83 4.41 8.70e-01 1.32e+00 2.57e+01 angle pdb=" N GLY B 476 " pdb=" CA GLY B 476 " pdb=" C GLY B 476 " ideal model delta sigma weight residual 115.32 109.19 6.13 1.31e+00 5.83e-01 2.19e+01 angle pdb=" CA LEU B 784 " pdb=" C LEU B 784 " pdb=" O LEU B 784 " ideal model delta sigma weight residual 121.56 116.55 5.01 1.09e+00 8.42e-01 2.12e+01 ... (remaining 25609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10256 17.97 - 35.95: 873 35.95 - 53.92: 237 53.92 - 71.89: 53 71.89 - 89.86: 25 Dihedral angle restraints: 11444 sinusoidal: 4679 harmonic: 6765 Sorted by residual: dihedral pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" N LEU A 521 " pdb=" CA LEU A 521 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N LEU B 521 " pdb=" CA LEU B 521 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N LEU A 488 " pdb=" CA LEU A 488 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2415 0.059 - 0.118: 337 0.118 - 0.176: 63 0.176 - 0.235: 7 0.235 - 0.294: 3 Chirality restraints: 2825 Sorted by residual: chirality pdb=" CA LYS B 862 " pdb=" N LYS B 862 " pdb=" C LYS B 862 " pdb=" CB LYS B 862 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA VAL B 16 " pdb=" N VAL B 16 " pdb=" C VAL B 16 " pdb=" CB VAL B 16 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL B 153 " pdb=" CA VAL B 153 " pdb=" CG1 VAL B 153 " pdb=" CG2 VAL B 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2822 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 315 " -0.049 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR B 315 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 315 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 315 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 315 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 315 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 315 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 315 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 862 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C LYS B 862 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 862 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 863 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 782 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C LEU B 782 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU B 782 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 783 " -0.018 2.00e-02 2.50e+03 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 214 2.64 - 3.20: 17700 3.20 - 3.77: 29256 3.77 - 4.33: 41718 4.33 - 4.90: 68709 Nonbonded interactions: 157597 Sorted by model distance: nonbonded pdb=" O LEU A 488 " pdb=" OG SER A 489 " model vdw 2.072 3.040 nonbonded pdb=" N GLN A 508 " pdb=" OE1 GLN A 508 " model vdw 2.134 3.120 nonbonded pdb=" O ASP A1070 " pdb=" OD1 ASP A1070 " model vdw 2.141 3.040 nonbonded pdb=" OG SER A 839 " pdb=" NH1 ARG A 910 " model vdw 2.210 3.120 nonbonded pdb=" O CYS A1013 " pdb=" OH TYR A1103 " model vdw 2.214 3.040 ... (remaining 157592 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' and (resid 1 through 507 or resid 510 through 1190)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.140 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.005 0.042 18954 Z= 0.332 Angle : 0.741 7.560 25614 Z= 0.526 Chirality : 0.045 0.294 2825 Planarity : 0.003 0.044 3324 Dihedral : 15.187 89.863 7054 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.03 % Allowed : 10.89 % Favored : 88.08 % 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: 2.19 (0.18), residues: 2276 helix: 2.45 (0.15), residues: 1165 sheet: -0.06 (0.30), residues: 299 loop : 0.69 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 475 TYR 0.050 0.001 TYR B 315 PHE 0.016 0.001 PHE B 195 TRP 0.016 0.001 TRP B 643 HIS 0.011 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00483 (18954) covalent geometry : angle 0.74130 (25614) hydrogen bonds : bond 0.17198 ( 1023) hydrogen bonds : angle 6.40376 ( 2910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 503 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7926 (tp30) REVERT: A 851 GLN cc_start: 0.8224 (tt0) cc_final: 0.7729 (mm110) REVERT: A 1023 TYR cc_start: 0.8911 (m-80) cc_final: 0.8541 (m-80) REVERT: B 140 GLU cc_start: 0.8057 (tp30) cc_final: 0.7731 (tp30) REVERT: B 168 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7682 (mt-10) REVERT: B 663 MET cc_start: 0.5263 (ttm) cc_final: 0.4809 (ttm) REVERT: B 851 GLN cc_start: 0.7612 (mt0) cc_final: 0.7359 (mm110) outliers start: 21 outliers final: 5 residues processed: 210 average time/residue: 0.7303 time to fit residues: 170.0457 Evaluate side-chains 139 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 938 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 289 GLN A 805 GLN B 144 GLN B 207 GLN B 935 HIS B 938 HIS B1086 ASN B1188 HIS B1189 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.131595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083201 restraints weight = 33668.729| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.71 r_work: 0.3000 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18954 Z= 0.170 Angle : 0.541 11.583 25614 Z= 0.282 Chirality : 0.041 0.238 2825 Planarity : 0.004 0.056 3324 Dihedral : 4.814 51.845 2530 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.81 % Allowed : 11.82 % Favored : 86.37 % 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: 2.32 (0.18), residues: 2276 helix: 2.51 (0.15), residues: 1191 sheet: 0.12 (0.31), residues: 273 loop : 0.69 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1177 TYR 0.021 0.001 TYR A 713 PHE 0.017 0.001 PHE A 448 TRP 0.020 0.002 TRP B 643 HIS 0.008 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00390 (18954) covalent geometry : angle 0.54093 (25614) hydrogen bonds : bond 0.04449 ( 1023) hydrogen bonds : angle 4.80388 ( 2910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8031 (tp30) REVERT: A 663 MET cc_start: 0.5542 (OUTLIER) cc_final: 0.4581 (ttm) REVERT: A 851 GLN cc_start: 0.7996 (tt0) cc_final: 0.7409 (mm110) REVERT: A 1085 ASP cc_start: 0.8220 (t0) cc_final: 0.8016 (t0) REVERT: B 140 GLU cc_start: 0.8247 (tp30) cc_final: 0.7904 (tp30) REVERT: B 331 GLU cc_start: 0.8796 (tt0) cc_final: 0.8566 (tt0) REVERT: B 663 MET cc_start: 0.5385 (ttm) cc_final: 0.4795 (ttm) REVERT: B 851 GLN cc_start: 0.7571 (mt0) cc_final: 0.7246 (mm110) REVERT: B 1115 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: B 1182 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8896 (mp0) outliers start: 37 outliers final: 13 residues processed: 182 average time/residue: 0.6304 time to fit residues: 129.6454 Evaluate side-chains 146 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 5 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 496 HIS B 14 GLN B 144 GLN B 151 ASN B 805 GLN B 938 HIS B 940 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.130502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081009 restraints weight = 33854.675| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.76 r_work: 0.2978 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18954 Z= 0.186 Angle : 0.522 10.943 25614 Z= 0.271 Chirality : 0.040 0.173 2825 Planarity : 0.004 0.043 3324 Dihedral : 4.570 59.812 2521 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.81 % Allowed : 12.80 % Favored : 85.38 % 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: 2.29 (0.18), residues: 2276 helix: 2.52 (0.15), residues: 1192 sheet: 0.02 (0.31), residues: 282 loop : 0.65 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 190 TYR 0.019 0.001 TYR B 713 PHE 0.018 0.001 PHE A 472 TRP 0.017 0.001 TRP A 643 HIS 0.008 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00434 (18954) covalent geometry : angle 0.52169 (25614) hydrogen bonds : bond 0.04304 ( 1023) hydrogen bonds : angle 4.59911 ( 2910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9553 (tttt) cc_final: 0.9343 (tppp) REVERT: A 191 GLN cc_start: 0.8375 (mp10) cc_final: 0.7705 (mm110) REVERT: A 503 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8039 (tp30) REVERT: A 663 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.4713 (ttm) REVERT: A 851 GLN cc_start: 0.8033 (tt0) cc_final: 0.7412 (mm110) REVERT: A 1115 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: B 14 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8472 (mm110) REVERT: B 140 GLU cc_start: 0.8291 (tp30) cc_final: 0.7938 (tp30) REVERT: B 331 GLU cc_start: 0.8811 (tt0) cc_final: 0.8591 (tt0) REVERT: B 663 MET cc_start: 0.5414 (ttm) cc_final: 0.4848 (ttm) REVERT: B 851 GLN cc_start: 0.7622 (mt0) cc_final: 0.7311 (mm110) REVERT: B 1115 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: B 1182 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8910 (mp0) outliers start: 37 outliers final: 13 residues processed: 166 average time/residue: 0.6009 time to fit residues: 113.4756 Evaluate side-chains 140 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1115 TYR Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 188 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN B 14 GLN B 134 HIS B 144 GLN B 794 GLN B 822 GLN B 938 HIS B 940 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.130613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081185 restraints weight = 33962.272| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.75 r_work: 0.2974 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18954 Z= 0.175 Angle : 0.510 11.229 25614 Z= 0.264 Chirality : 0.039 0.172 2825 Planarity : 0.003 0.046 3324 Dihedral : 4.495 57.198 2521 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.50 % Allowed : 12.90 % Favored : 84.60 % 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: 2.27 (0.18), residues: 2276 helix: 2.54 (0.15), residues: 1194 sheet: -0.09 (0.30), residues: 295 loop : 0.63 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.018 0.001 TYR B 713 PHE 0.013 0.001 PHE B 557 TRP 0.016 0.001 TRP B 643 HIS 0.006 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00406 (18954) covalent geometry : angle 0.51021 (25614) hydrogen bonds : bond 0.04048 ( 1023) hydrogen bonds : angle 4.51190 ( 2910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7911 (mm110) REVERT: A 503 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: A 663 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.4743 (ttm) REVERT: A 851 GLN cc_start: 0.8038 (tt0) cc_final: 0.7403 (mm110) REVERT: A 966 GLN cc_start: 0.8514 (pm20) cc_final: 0.8193 (pp30) REVERT: B 140 GLU cc_start: 0.8282 (tp30) cc_final: 0.7918 (tp30) REVERT: B 331 GLU cc_start: 0.8832 (tt0) cc_final: 0.8621 (tt0) REVERT: B 663 MET cc_start: 0.5388 (ttm) cc_final: 0.4758 (ttm) REVERT: B 851 GLN cc_start: 0.7618 (mt0) cc_final: 0.7317 (mm110) REVERT: B 1115 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: B 1182 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8911 (mp0) outliers start: 51 outliers final: 16 residues processed: 179 average time/residue: 0.6055 time to fit residues: 123.2302 Evaluate side-chains 146 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 142 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 822 GLN B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.131779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083187 restraints weight = 33609.591| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.73 r_work: 0.2999 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18954 Z= 0.136 Angle : 0.492 11.931 25614 Z= 0.253 Chirality : 0.039 0.171 2825 Planarity : 0.003 0.054 3324 Dihedral : 4.260 59.379 2519 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.21 % Allowed : 13.73 % Favored : 84.06 % 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: 2.32 (0.18), residues: 2276 helix: 2.60 (0.15), residues: 1196 sheet: -0.11 (0.29), residues: 297 loop : 0.64 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 573 TYR 0.016 0.001 TYR B 713 PHE 0.011 0.001 PHE B 557 TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00311 (18954) covalent geometry : angle 0.49172 (25614) hydrogen bonds : bond 0.03728 ( 1023) hydrogen bonds : angle 4.40071 ( 2910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9293 (ttpp) cc_final: 0.9064 (ptpp) REVERT: A 191 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: A 503 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: A 663 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.4750 (ttm) REVERT: A 851 GLN cc_start: 0.7972 (tt0) cc_final: 0.7321 (mm110) REVERT: A 966 GLN cc_start: 0.8589 (pm20) cc_final: 0.8264 (pp30) REVERT: B 140 GLU cc_start: 0.8230 (tp30) cc_final: 0.7863 (tp30) REVERT: B 185 LYS cc_start: 0.9034 (mttp) cc_final: 0.8791 (mttp) REVERT: B 191 GLN cc_start: 0.8707 (mm110) cc_final: 0.8328 (mm-40) REVERT: B 331 GLU cc_start: 0.8793 (tt0) cc_final: 0.8588 (tt0) REVERT: B 465 GLU cc_start: 0.8826 (tt0) cc_final: 0.8583 (tt0) REVERT: B 851 GLN cc_start: 0.7578 (mt0) cc_final: 0.7236 (mm110) REVERT: B 966 GLN cc_start: 0.8311 (pm20) cc_final: 0.7923 (pp30) REVERT: B 1115 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: B 1182 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8934 (mp0) outliers start: 45 outliers final: 18 residues processed: 175 average time/residue: 0.5797 time to fit residues: 116.2212 Evaluate side-chains 151 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 186 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 120 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN B 144 GLN B 938 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082096 restraints weight = 33572.568| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.79 r_work: 0.2994 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18954 Z= 0.139 Angle : 0.492 11.628 25614 Z= 0.252 Chirality : 0.038 0.169 2825 Planarity : 0.003 0.045 3324 Dihedral : 4.221 59.795 2519 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.86 % Allowed : 14.42 % Favored : 83.72 % 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: 2.31 (0.18), residues: 2276 helix: 2.62 (0.15), residues: 1193 sheet: -0.09 (0.30), residues: 297 loop : 0.58 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 573 TYR 0.017 0.001 TYR A 615 PHE 0.011 0.001 PHE B 557 TRP 0.015 0.001 TRP B 643 HIS 0.006 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00321 (18954) covalent geometry : angle 0.49227 (25614) hydrogen bonds : bond 0.03678 ( 1023) hydrogen bonds : angle 4.36469 ( 2910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9308 (ttpp) cc_final: 0.9067 (ptpp) REVERT: A 191 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: A 503 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: A 663 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.4750 (ttm) REVERT: A 851 GLN cc_start: 0.8034 (tt0) cc_final: 0.7386 (mm110) REVERT: A 966 GLN cc_start: 0.8583 (pm20) cc_final: 0.8312 (pp30) REVERT: B 140 GLU cc_start: 0.8236 (tp30) cc_final: 0.7868 (tp30) REVERT: B 185 LYS cc_start: 0.9067 (mttp) cc_final: 0.8715 (mttt) REVERT: B 214 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8133 (tm) REVERT: B 331 GLU cc_start: 0.8813 (tt0) cc_final: 0.8604 (tt0) REVERT: B 503 GLU cc_start: 0.8475 (tp30) cc_final: 0.8177 (tp30) REVERT: B 851 GLN cc_start: 0.7569 (mt0) cc_final: 0.7222 (mm110) REVERT: B 966 GLN cc_start: 0.8335 (pm20) cc_final: 0.8022 (pp30) REVERT: B 1115 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: B 1182 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8943 (mp0) outliers start: 38 outliers final: 18 residues processed: 169 average time/residue: 0.5581 time to fit residues: 108.2011 Evaluate side-chains 149 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 175 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 199 optimal weight: 0.0170 chunk 5 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 938 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.132638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083504 restraints weight = 33937.459| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.80 r_work: 0.3023 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18954 Z= 0.111 Angle : 0.483 11.271 25614 Z= 0.246 Chirality : 0.038 0.168 2825 Planarity : 0.003 0.038 3324 Dihedral : 4.105 56.607 2519 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 14.42 % Favored : 83.57 % 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 (0.18), residues: 2276 helix: 2.67 (0.15), residues: 1198 sheet: -0.07 (0.30), residues: 296 loop : 0.61 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 969 TYR 0.015 0.001 TYR A 982 PHE 0.010 0.001 PHE B 557 TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00250 (18954) covalent geometry : angle 0.48253 (25614) hydrogen bonds : bond 0.03390 ( 1023) hydrogen bonds : angle 4.27867 ( 2910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8154 (tp30) cc_final: 0.7945 (tp30) REVERT: A 185 LYS cc_start: 0.9309 (ttpp) cc_final: 0.9100 (ptpp) REVERT: A 191 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8114 (mm110) REVERT: A 503 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: A 648 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5874 (mm) REVERT: A 663 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.4831 (ttm) REVERT: A 851 GLN cc_start: 0.7989 (tt0) cc_final: 0.7341 (mm110) REVERT: A 966 GLN cc_start: 0.8567 (pm20) cc_final: 0.8278 (pp30) REVERT: B 140 GLU cc_start: 0.8206 (tp30) cc_final: 0.7973 (tp30) REVERT: B 185 LYS cc_start: 0.9085 (mttp) cc_final: 0.8728 (mttt) REVERT: B 191 GLN cc_start: 0.8689 (mm110) cc_final: 0.8252 (mm-40) REVERT: B 214 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8138 (tm) REVERT: B 331 GLU cc_start: 0.8792 (tt0) cc_final: 0.8580 (tt0) REVERT: B 503 GLU cc_start: 0.8472 (tp30) cc_final: 0.8159 (tp30) REVERT: B 648 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5854 (mm) REVERT: B 851 GLN cc_start: 0.7537 (mt0) cc_final: 0.7201 (mm110) REVERT: B 966 GLN cc_start: 0.8319 (pm20) cc_final: 0.8028 (pp30) REVERT: B 1115 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: B 1182 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8922 (mp0) outliers start: 41 outliers final: 18 residues processed: 177 average time/residue: 0.5981 time to fit residues: 120.1294 Evaluate side-chains 156 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 146 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 214 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 144 GLN B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.131521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082644 restraints weight = 33921.918| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.74 r_work: 0.2992 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18954 Z= 0.157 Angle : 0.504 10.913 25614 Z= 0.257 Chirality : 0.039 0.166 2825 Planarity : 0.003 0.037 3324 Dihedral : 4.185 58.127 2519 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.31 % Allowed : 14.76 % Favored : 82.93 % 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: 2.34 (0.18), residues: 2276 helix: 2.64 (0.15), residues: 1194 sheet: -0.07 (0.30), residues: 295 loop : 0.60 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 969 TYR 0.014 0.001 TYR B 615 PHE 0.033 0.001 PHE B 195 TRP 0.014 0.001 TRP B 643 HIS 0.006 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00367 (18954) covalent geometry : angle 0.50356 (25614) hydrogen bonds : bond 0.03707 ( 1023) hydrogen bonds : angle 4.33706 ( 2910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8147 (tp30) cc_final: 0.7929 (tp30) REVERT: A 191 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: A 503 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: A 648 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5865 (mm) REVERT: A 663 MET cc_start: 0.5414 (OUTLIER) cc_final: 0.4748 (ttm) REVERT: A 851 GLN cc_start: 0.7966 (tt0) cc_final: 0.7332 (mm110) REVERT: A 966 GLN cc_start: 0.8597 (pm20) cc_final: 0.8271 (pp30) REVERT: B 140 GLU cc_start: 0.8181 (tp30) cc_final: 0.7939 (tp30) REVERT: B 185 LYS cc_start: 0.9098 (mttp) cc_final: 0.8739 (mttt) REVERT: B 214 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8111 (tm) REVERT: B 331 GLU cc_start: 0.8787 (tt0) cc_final: 0.8568 (tt0) REVERT: B 503 GLU cc_start: 0.8507 (tp30) cc_final: 0.8142 (tp30) REVERT: B 648 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5841 (mm) REVERT: B 851 GLN cc_start: 0.7504 (mt0) cc_final: 0.7150 (mm110) REVERT: B 865 GLN cc_start: 0.8165 (pt0) cc_final: 0.7472 (pm20) REVERT: B 966 GLN cc_start: 0.8433 (pm20) cc_final: 0.8078 (pp30) REVERT: B 1115 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: B 1182 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8911 (mp0) outliers start: 47 outliers final: 20 residues processed: 173 average time/residue: 0.5695 time to fit residues: 112.8416 Evaluate side-chains 154 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 129 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 486 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.131803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082974 restraints weight = 33640.913| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.73 r_work: 0.3001 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18954 Z= 0.146 Angle : 0.508 11.023 25614 Z= 0.259 Chirality : 0.039 0.166 2825 Planarity : 0.003 0.064 3324 Dihedral : 4.171 57.645 2519 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 15.15 % Favored : 82.93 % 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: 2.33 (0.18), residues: 2276 helix: 2.63 (0.15), residues: 1192 sheet: -0.04 (0.30), residues: 297 loop : 0.58 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 573 TYR 0.014 0.001 TYR A 615 PHE 0.027 0.001 PHE B 195 TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00339 (18954) covalent geometry : angle 0.50843 (25614) hydrogen bonds : bond 0.03623 ( 1023) hydrogen bonds : angle 4.32581 ( 2910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8145 (tp30) cc_final: 0.7927 (tp30) REVERT: A 185 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8783 (ptpt) REVERT: A 191 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: A 503 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: A 648 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5859 (mm) REVERT: A 663 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.4785 (ttm) REVERT: A 851 GLN cc_start: 0.7965 (tt0) cc_final: 0.7332 (mm110) REVERT: A 966 GLN cc_start: 0.8593 (pm20) cc_final: 0.8271 (pp30) REVERT: B 140 GLU cc_start: 0.8170 (tp30) cc_final: 0.7931 (tp30) REVERT: B 185 LYS cc_start: 0.9107 (mttp) cc_final: 0.8750 (mttt) REVERT: B 191 GLN cc_start: 0.8674 (mm110) cc_final: 0.8297 (mm-40) REVERT: B 331 GLU cc_start: 0.8775 (tt0) cc_final: 0.8569 (tt0) REVERT: B 503 GLU cc_start: 0.8499 (tp30) cc_final: 0.8132 (tp30) REVERT: B 648 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5866 (mm) REVERT: B 851 GLN cc_start: 0.7529 (mt0) cc_final: 0.7174 (mm110) REVERT: B 865 GLN cc_start: 0.8168 (pt0) cc_final: 0.7485 (pm20) REVERT: B 966 GLN cc_start: 0.8458 (pm20) cc_final: 0.8130 (pp30) REVERT: B 1115 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: B 1182 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8914 (mp0) outliers start: 39 outliers final: 22 residues processed: 164 average time/residue: 0.5584 time to fit residues: 104.7855 Evaluate side-chains 159 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 48 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.131737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083160 restraints weight = 33617.374| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.71 r_work: 0.3001 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 18954 Z= 0.170 Angle : 0.823 59.188 25614 Z= 0.430 Chirality : 0.039 0.271 2825 Planarity : 0.004 0.072 3324 Dihedral : 4.158 57.640 2519 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.77 % Allowed : 15.64 % Favored : 82.59 % Cbeta Deviations : 0.05 % 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: 2.33 (0.18), residues: 2276 helix: 2.63 (0.15), residues: 1192 sheet: -0.04 (0.30), residues: 297 loop : 0.57 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 573 TYR 0.013 0.001 TYR A 615 PHE 0.023 0.001 PHE B 195 TRP 0.014 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00379 (18954) covalent geometry : angle 0.82320 (25614) hydrogen bonds : bond 0.03618 ( 1023) hydrogen bonds : angle 4.32348 ( 2910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8140 (tp30) cc_final: 0.7922 (tp30) REVERT: A 185 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8782 (ptpt) REVERT: A 191 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8125 (mm-40) REVERT: A 503 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: A 648 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5828 (mm) REVERT: A 663 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.4742 (ttm) REVERT: A 851 GLN cc_start: 0.7974 (tt0) cc_final: 0.7345 (mm110) REVERT: A 966 GLN cc_start: 0.8594 (pm20) cc_final: 0.8275 (pp30) REVERT: B 140 GLU cc_start: 0.8167 (tp30) cc_final: 0.7929 (tp30) REVERT: B 185 LYS cc_start: 0.9104 (mttp) cc_final: 0.8745 (mttt) REVERT: B 191 GLN cc_start: 0.8679 (mm110) cc_final: 0.8247 (mm-40) REVERT: B 331 GLU cc_start: 0.8770 (tt0) cc_final: 0.8564 (tt0) REVERT: B 503 GLU cc_start: 0.8495 (tp30) cc_final: 0.8194 (tp30) REVERT: B 648 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5842 (mm) REVERT: B 851 GLN cc_start: 0.7540 (mt0) cc_final: 0.7186 (mm110) REVERT: B 865 GLN cc_start: 0.8162 (pt0) cc_final: 0.7475 (pm20) REVERT: B 966 GLN cc_start: 0.8457 (pm20) cc_final: 0.8136 (pp30) REVERT: B 1115 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: B 1182 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8922 (mp0) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 0.5805 time to fit residues: 106.2958 Evaluate side-chains 158 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 193 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.131633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083115 restraints weight = 33782.575| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.72 r_work: 0.3000 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.570 18954 Z= 0.353 Angle : 0.793 51.971 25614 Z= 0.405 Chirality : 0.039 0.270 2825 Planarity : 0.005 0.193 3324 Dihedral : 4.158 57.640 2519 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.52 % Allowed : 15.94 % Favored : 82.54 % Cbeta Deviations : 0.05 % 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: 2.33 (0.18), residues: 2276 helix: 2.63 (0.15), residues: 1192 sheet: -0.04 (0.30), residues: 297 loop : 0.57 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 573 TYR 0.013 0.001 TYR A 615 PHE 0.023 0.001 PHE B 195 TRP 0.014 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00770 (18954) covalent geometry : angle 0.79284 (25614) hydrogen bonds : bond 0.03618 ( 1023) hydrogen bonds : angle 4.32349 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8131.63 seconds wall clock time: 139 minutes 11.34 seconds (8351.34 seconds total)