Starting phenix.real_space_refine on Mon May 19 15:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ezx_50090/05_2025/9ezx_50090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ezx_50090/05_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_50090/05_2025/9ezx_50090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ezx_50090/05_2025/9ezx_50090.map" model { file = "/net/cci-nas-00/data/ceres_data/9ezx_50090/05_2025/9ezx_50090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ezx_50090/05_2025/9ezx_50090.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.65, per 1000 atoms: 0.52 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: 4.55 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.44 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: 8.42 Time building geometry restraints manager: 5.36 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: 32.720 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.770 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.016 0.001 TRP B 643 HIS 0.011 0.001 HIS A 238 PHE 0.016 0.001 PHE B 195 TYR 0.050 0.001 TYR B 315 ARG 0.005 0.000 ARG B 475 Details of bonding type rmsd hydrogen bonds : bond 0.17198 ( 1023) hydrogen bonds : angle 6.40376 ( 2910) covalent geometry : bond 0.00483 (18954) covalent geometry : angle 0.74130 (25614) *********************** 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 : 2.376 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: 1.4848 time to fit residues: 347.6275 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 : 1.912 ------------------------------------------------------------------------------- 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 194 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 805 GLN B 935 HIS B 938 HIS B1086 ASN B1188 HIS B1189 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081748 restraints weight = 33628.313| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.75 r_work: 0.2990 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18954 Z= 0.181 Angle : 0.547 11.648 25614 Z= 0.285 Chirality : 0.041 0.243 2825 Planarity : 0.004 0.057 3324 Dihedral : 4.858 52.809 2530 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.81 % Allowed : 11.87 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.18), residues: 2276 helix: 2.47 (0.15), residues: 1193 sheet: 0.12 (0.31), residues: 273 loop : 0.68 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 643 HIS 0.009 0.001 HIS B 238 PHE 0.019 0.001 PHE A 448 TYR 0.021 0.001 TYR A 713 ARG 0.010 0.001 ARG B1177 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1023) hydrogen bonds : angle 4.79345 ( 2910) covalent geometry : bond 0.00419 (18954) covalent geometry : angle 0.54679 (25614) *********************** 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 194 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8074 (tp30) REVERT: A 663 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.4651 (ttm) REVERT: A 851 GLN cc_start: 0.8056 (tt0) cc_final: 0.7448 (mm110) REVERT: B 140 GLU cc_start: 0.8273 (tp30) cc_final: 0.7928 (tp30) REVERT: B 331 GLU cc_start: 0.8819 (tt0) cc_final: 0.8606 (tt0) REVERT: B 663 MET cc_start: 0.5464 (ttm) cc_final: 0.4820 (ttm) REVERT: B 851 GLN cc_start: 0.7612 (mt0) cc_final: 0.7316 (mm110) REVERT: B 1115 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7249 (m-80) outliers start: 37 outliers final: 14 residues processed: 185 average time/residue: 1.2336 time to fit residues: 259.2700 Evaluate side-chains 143 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 158 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 174 optimal weight: 0.0170 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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 A 627 ASN B 14 GLN B 144 GLN B 151 ASN 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 = 0.3988 r_free = 0.3988 target = 0.130629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081690 restraints weight = 33584.539| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.72 r_work: 0.2974 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18954 Z= 0.202 Angle : 0.528 11.085 25614 Z= 0.274 Chirality : 0.040 0.174 2825 Planarity : 0.004 0.037 3324 Dihedral : 4.605 57.460 2521 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.16 % Allowed : 12.80 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.18), residues: 2276 helix: 2.50 (0.15), residues: 1191 sheet: 0.03 (0.31), residues: 282 loop : 0.60 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 643 HIS 0.008 0.001 HIS B 238 PHE 0.020 0.001 PHE A 448 TYR 0.019 0.001 TYR B 713 ARG 0.008 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1023) hydrogen bonds : angle 4.60875 ( 2910) covalent geometry : bond 0.00473 (18954) covalent geometry : angle 0.52777 (25614) *********************** 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 184 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8408 (mp10) cc_final: 0.7806 (mm110) REVERT: A 503 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: A 663 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.4696 (ttm) REVERT: A 851 GLN cc_start: 0.8016 (tt0) cc_final: 0.7385 (mm110) REVERT: B 140 GLU cc_start: 0.8272 (tp30) cc_final: 0.7907 (tp30) REVERT: B 331 GLU cc_start: 0.8817 (tt0) cc_final: 0.8584 (tt0) REVERT: B 663 MET cc_start: 0.5400 (ttm) cc_final: 0.4832 (ttm) REVERT: B 851 GLN cc_start: 0.7599 (mt0) cc_final: 0.7288 (mm110) REVERT: B 1115 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: B 1182 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8915 (mp0) outliers start: 44 outliers final: 15 residues processed: 172 average time/residue: 1.1721 time to fit residues: 231.5836 Evaluate side-chains 144 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 503 GLU 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 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 816 GLU 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 10 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS A 794 GLN A 822 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.130493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081603 restraints weight = 33796.002| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.72 r_work: 0.2969 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18954 Z= 0.197 Angle : 0.522 11.723 25614 Z= 0.270 Chirality : 0.040 0.173 2825 Planarity : 0.004 0.045 3324 Dihedral : 4.527 57.953 2521 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.89 % Allowed : 12.16 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2276 helix: 2.48 (0.15), residues: 1195 sheet: -0.12 (0.29), residues: 295 loop : 0.58 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 643 HIS 0.006 0.001 HIS B 935 PHE 0.014 0.001 PHE B 557 TYR 0.018 0.001 TYR B 713 ARG 0.007 0.000 ARG B 969 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1023) hydrogen bonds : angle 4.54826 ( 2910) covalent geometry : bond 0.00460 (18954) covalent geometry : angle 0.52206 (25614) *********************** 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 197 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: A 503 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: A 517 LYS cc_start: 0.9094 (tppp) cc_final: 0.8723 (tptp) REVERT: A 663 MET cc_start: 0.5484 (OUTLIER) cc_final: 0.4731 (ttm) REVERT: A 851 GLN cc_start: 0.8017 (tt0) cc_final: 0.7380 (mm110) REVERT: A 966 GLN cc_start: 0.8626 (pm20) cc_final: 0.8288 (pp30) REVERT: B 140 GLU cc_start: 0.8221 (tp30) cc_final: 0.7846 (tp30) REVERT: B 144 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8338 (pp30) REVERT: B 191 GLN cc_start: 0.8768 (mm110) cc_final: 0.8388 (mm110) REVERT: B 331 GLU cc_start: 0.8832 (tt0) cc_final: 0.8598 (tt0) REVERT: B 663 MET cc_start: 0.5338 (ttm) cc_final: 0.4732 (ttm) REVERT: B 851 GLN cc_start: 0.7577 (mt0) cc_final: 0.7266 (mm110) REVERT: B 1115 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: B 1182 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8943 (mp0) outliers start: 59 outliers final: 20 residues processed: 185 average time/residue: 1.2343 time to fit residues: 259.7011 Evaluate side-chains 154 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 144 GLN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN 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 1080 ILE 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 97 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 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 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 = 0.3995 r_free = 0.3995 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082516 restraints weight = 33776.072| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.72 r_work: 0.2994 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18954 Z= 0.141 Angle : 0.499 11.685 25614 Z= 0.257 Chirality : 0.039 0.171 2825 Planarity : 0.003 0.052 3324 Dihedral : 4.418 59.974 2521 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 13.88 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2276 helix: 2.53 (0.15), residues: 1200 sheet: -0.13 (0.29), residues: 297 loop : 0.55 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 PHE 0.011 0.001 PHE B 557 TYR 0.015 0.001 TYR B 713 ARG 0.011 0.000 ARG A 573 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1023) hydrogen bonds : angle 4.42393 ( 2910) covalent geometry : bond 0.00325 (18954) covalent geometry : angle 0.49866 (25614) *********************** 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 178 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: A 496 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8261 (m170) REVERT: A 503 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: A 663 MET cc_start: 0.5452 (OUTLIER) cc_final: 0.4745 (ttm) REVERT: A 851 GLN cc_start: 0.7983 (tt0) cc_final: 0.7335 (mm110) REVERT: A 966 GLN cc_start: 0.8581 (pm20) cc_final: 0.8291 (pp30) REVERT: B 140 GLU cc_start: 0.8265 (tp30) cc_final: 0.7918 (tp30) REVERT: B 191 GLN cc_start: 0.8755 (mm110) cc_final: 0.8373 (mm110) REVERT: B 465 GLU cc_start: 0.8869 (tt0) cc_final: 0.8636 (tt0) REVERT: B 851 GLN cc_start: 0.7595 (mt0) cc_final: 0.7292 (mm110) REVERT: B 966 GLN cc_start: 0.8318 (pm20) cc_final: 0.7956 (pp30) REVERT: B 1007 MET cc_start: 0.8815 (tpp) cc_final: 0.8512 (tpp) REVERT: B 1115 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: B 1182 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8937 (mp0) outliers start: 41 outliers final: 17 residues processed: 169 average time/residue: 1.0965 time to fit residues: 213.2965 Evaluate side-chains 147 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 496 HIS 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 663 MET 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 434 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 193 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 0.0030 chunk 116 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 144 GLN B 938 HIS B 940 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.132711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084378 restraints weight = 34032.487| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.73 r_work: 0.3028 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18954 Z= 0.109 Angle : 0.472 11.582 25614 Z= 0.242 Chirality : 0.038 0.169 2825 Planarity : 0.003 0.037 3324 Dihedral : 4.207 56.484 2521 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.11 % Allowed : 13.78 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.18), residues: 2276 helix: 2.67 (0.15), residues: 1196 sheet: -0.07 (0.30), residues: 296 loop : 0.56 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 643 HIS 0.006 0.001 HIS B 935 PHE 0.009 0.001 PHE B 557 TYR 0.017 0.001 TYR A 615 ARG 0.009 0.000 ARG B 969 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1023) hydrogen bonds : angle 4.28682 ( 2910) covalent geometry : bond 0.00244 (18954) covalent geometry : angle 0.47187 (25614) *********************** 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 193 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: A 663 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.4665 (ttm) REVERT: A 851 GLN cc_start: 0.7974 (tt0) cc_final: 0.7323 (mm110) REVERT: A 966 GLN cc_start: 0.8565 (pm20) cc_final: 0.8264 (pp30) REVERT: B 140 GLU cc_start: 0.8211 (tp30) cc_final: 0.7979 (tp30) REVERT: B 214 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8079 (tm) REVERT: B 503 GLU cc_start: 0.8439 (tp30) cc_final: 0.8125 (tp30) REVERT: B 851 GLN cc_start: 0.7511 (mt0) cc_final: 0.7167 (mm110) REVERT: B 966 GLN cc_start: 0.8304 (pm20) cc_final: 0.8006 (pp30) REVERT: B 1007 MET cc_start: 0.8857 (tpp) cc_final: 0.8455 (tpp) REVERT: B 1115 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 1182 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8937 (mp0) outliers start: 43 outliers final: 22 residues processed: 183 average time/residue: 1.1602 time to fit residues: 243.2456 Evaluate side-chains 154 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 521 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 144 GLN 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 81 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 A 496 HIS ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS B 37 ASN B 144 GLN ** B 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.128666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.078821 restraints weight = 33655.447| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.76 r_work: 0.2931 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 18954 Z= 0.292 Angle : 0.584 10.811 25614 Z= 0.299 Chirality : 0.043 0.169 2825 Planarity : 0.004 0.036 3324 Dihedral : 4.483 57.565 2519 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.35 % Allowed : 14.47 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.18), residues: 2276 helix: 2.30 (0.15), residues: 1207 sheet: -0.11 (0.30), residues: 284 loop : 0.46 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 643 HIS 0.007 0.001 HIS B 935 PHE 0.029 0.002 PHE B 195 TYR 0.017 0.002 TYR B 713 ARG 0.010 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1023) hydrogen bonds : angle 4.57802 ( 2910) covalent geometry : bond 0.00684 (18954) covalent geometry : angle 0.58450 (25614) *********************** 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 183 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7879 (mm-40) REVERT: A 503 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: A 521 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 851 GLN cc_start: 0.8045 (tt0) cc_final: 0.7415 (mm110) REVERT: A 865 GLN cc_start: 0.8268 (pt0) cc_final: 0.7604 (pm20) REVERT: A 966 GLN cc_start: 0.8668 (pm20) cc_final: 0.8387 (pp30) REVERT: B 140 GLU cc_start: 0.8208 (tp30) cc_final: 0.7764 (tp30) REVERT: B 144 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8435 (pp30) REVERT: B 185 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8746 (mttt) REVERT: B 191 GLN cc_start: 0.8768 (mm110) cc_final: 0.8508 (mm110) REVERT: B 214 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8134 (tm) REVERT: B 851 GLN cc_start: 0.7622 (mt0) cc_final: 0.7360 (mm110) REVERT: B 865 GLN cc_start: 0.8232 (pt0) cc_final: 0.7526 (pm20) REVERT: B 966 GLN cc_start: 0.8530 (pm20) cc_final: 0.8239 (pp30) REVERT: B 1007 MET cc_start: 0.8884 (tpp) cc_final: 0.8644 (tpp) REVERT: B 1115 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: B 1182 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8928 (mp0) outliers start: 48 outliers final: 20 residues processed: 173 average time/residue: 1.1603 time to fit residues: 230.2865 Evaluate side-chains 146 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 521 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 185 LYS 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 708 MET Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1044 MET 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 87 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 144 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082183 restraints weight = 34005.255| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.77 r_work: 0.2982 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18954 Z= 0.143 Angle : 0.509 11.133 25614 Z= 0.260 Chirality : 0.039 0.165 2825 Planarity : 0.003 0.061 3324 Dihedral : 4.316 58.244 2519 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.96 % Allowed : 15.40 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.18), residues: 2276 helix: 2.46 (0.15), residues: 1208 sheet: -0.13 (0.30), residues: 295 loop : 0.50 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 PHE 0.023 0.001 PHE B 195 TYR 0.017 0.001 TYR A 615 ARG 0.017 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 1023) hydrogen bonds : angle 4.41447 ( 2910) covalent geometry : bond 0.00330 (18954) covalent geometry : angle 0.50939 (25614) *********************** 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 170 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7912 (mm-40) REVERT: A 214 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8355 (tm) REVERT: A 503 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: A 851 GLN cc_start: 0.7973 (tt0) cc_final: 0.7335 (mm110) REVERT: A 865 GLN cc_start: 0.8247 (pt0) cc_final: 0.7577 (pm20) REVERT: A 966 GLN cc_start: 0.8622 (pm20) cc_final: 0.8321 (tm-30) REVERT: B 140 GLU cc_start: 0.8205 (tp30) cc_final: 0.7831 (tp30) REVERT: B 185 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8668 (mtmm) REVERT: B 191 GLN cc_start: 0.8772 (mm110) cc_final: 0.8538 (mm110) REVERT: B 503 GLU cc_start: 0.8484 (tp30) cc_final: 0.8133 (tp30) REVERT: B 851 GLN cc_start: 0.7548 (mt0) cc_final: 0.7220 (mm110) REVERT: B 865 GLN cc_start: 0.8163 (pt0) cc_final: 0.7463 (pm20) REVERT: B 966 GLN cc_start: 0.8476 (pm20) cc_final: 0.8205 (pp30) REVERT: B 1007 MET cc_start: 0.8844 (tpp) cc_final: 0.8504 (tpp) REVERT: B 1115 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: B 1182 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8926 (mp0) outliers start: 40 outliers final: 20 residues processed: 160 average time/residue: 1.1309 time to fit residues: 208.1058 Evaluate side-chains 149 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 214 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 1182 GLU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 185 LYS 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 708 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 142 optimal weight: 0.0270 chunk 219 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 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 = 0.3976 r_free = 0.3976 target = 0.130670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080942 restraints weight = 33754.746| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.81 r_work: 0.2974 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18954 Z= 0.154 Angle : 0.512 10.664 25614 Z= 0.261 Chirality : 0.039 0.166 2825 Planarity : 0.003 0.059 3324 Dihedral : 4.278 57.563 2519 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.96 % Allowed : 15.60 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.18), residues: 2276 helix: 2.46 (0.15), residues: 1213 sheet: -0.11 (0.30), residues: 297 loop : 0.50 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 PHE 0.020 0.001 PHE B 195 TYR 0.016 0.001 TYR A 615 ARG 0.015 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1023) hydrogen bonds : angle 4.37556 ( 2910) covalent geometry : bond 0.00359 (18954) covalent geometry : angle 0.51226 (25614) *********************** 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 169 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: A 214 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8370 (tm) REVERT: A 503 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: A 663 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.4792 (ttm) REVERT: A 851 GLN cc_start: 0.8020 (tt0) cc_final: 0.7380 (mm110) REVERT: A 865 GLN cc_start: 0.8224 (pt0) cc_final: 0.7601 (pm20) REVERT: A 966 GLN cc_start: 0.8625 (pm20) cc_final: 0.8406 (tm-30) REVERT: B 140 GLU cc_start: 0.8180 (tp30) cc_final: 0.7935 (tp30) REVERT: B 185 LYS cc_start: 0.9077 (mttp) cc_final: 0.8739 (mttt) REVERT: B 191 GLN cc_start: 0.8737 (mm110) cc_final: 0.8466 (mm110) REVERT: B 503 GLU cc_start: 0.8517 (tp30) cc_final: 0.8194 (tp30) REVERT: B 851 GLN cc_start: 0.7580 (mt0) cc_final: 0.7236 (mm110) REVERT: B 865 GLN cc_start: 0.8201 (pt0) cc_final: 0.7529 (pm20) REVERT: B 966 GLN cc_start: 0.8507 (pm20) cc_final: 0.8262 (pp30) REVERT: B 1007 MET cc_start: 0.8901 (tpp) cc_final: 0.8620 (tpp) REVERT: B 1115 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: B 1182 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8915 (mp0) outliers start: 40 outliers final: 20 residues processed: 158 average time/residue: 1.1465 time to fit residues: 209.8571 Evaluate side-chains 149 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 2.068 ------------------------------------------------------------------------------- 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 214 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 663 MET Chi-restraints excluded: chain A residue 1182 GLU 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 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 708 MET 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 196 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 184 optimal weight: 20.0000 chunk 99 optimal weight: 0.0070 chunk 60 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.131124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081529 restraints weight = 33694.796| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.79 r_work: 0.2984 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2642 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= 0.137 Angle : 0.515 10.787 25614 Z= 0.262 Chirality : 0.039 0.165 2825 Planarity : 0.003 0.056 3324 Dihedral : 4.264 56.675 2519 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.72 % Allowed : 15.99 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2276 helix: 2.50 (0.15), residues: 1211 sheet: -0.09 (0.30), residues: 298 loop : 0.53 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 PHE 0.019 0.001 PHE B 195 TYR 0.016 0.001 TYR A 615 ARG 0.014 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1023) hydrogen bonds : angle 4.35342 ( 2910) covalent geometry : bond 0.00318 (18954) covalent geometry : angle 0.51515 (25614) ********************** 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 159 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: A 214 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8362 (tm) REVERT: A 503 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: A 663 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.4766 (ttm) REVERT: A 851 GLN cc_start: 0.8010 (tt0) cc_final: 0.7374 (mm110) REVERT: A 865 GLN cc_start: 0.8214 (pt0) cc_final: 0.7590 (pm20) REVERT: A 966 GLN cc_start: 0.8618 (pm20) cc_final: 0.8408 (tm-30) REVERT: B 140 GLU cc_start: 0.8185 (tp30) cc_final: 0.7921 (tp30) REVERT: B 185 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8739 (mttt) REVERT: B 503 GLU cc_start: 0.8518 (tp30) cc_final: 0.8193 (tp30) REVERT: B 851 GLN cc_start: 0.7568 (mt0) cc_final: 0.7224 (mm110) REVERT: B 865 GLN cc_start: 0.8188 (pt0) cc_final: 0.7515 (pm20) REVERT: B 966 GLN cc_start: 0.8527 (pm20) cc_final: 0.8273 (pp30) REVERT: B 1007 MET cc_start: 0.8859 (tpp) cc_final: 0.8548 (tpp) REVERT: B 1115 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: B 1182 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8918 (mp0) outliers start: 35 outliers final: 18 residues processed: 150 average time/residue: 1.0809 time to fit residues: 187.1150 Evaluate side-chains 145 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 214 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 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 185 LYS 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 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 708 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082416 restraints weight = 33742.645| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.73 r_work: 0.2987 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18954 Z= 0.152 Angle : 0.518 10.455 25614 Z= 0.264 Chirality : 0.039 0.165 2825 Planarity : 0.003 0.053 3324 Dihedral : 4.251 56.404 2519 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.72 % Allowed : 15.99 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2276 helix: 2.52 (0.15), residues: 1204 sheet: -0.08 (0.30), residues: 298 loop : 0.53 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS B 935 PHE 0.018 0.001 PHE B 195 TYR 0.017 0.001 TYR A 982 ARG 0.013 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1023) hydrogen bonds : angle 4.36000 ( 2910) covalent geometry : bond 0.00354 (18954) covalent geometry : angle 0.51756 (25614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14467.72 seconds wall clock time: 250 minutes 44.15 seconds (15044.15 seconds total)