Starting phenix.real_space_refine on Sun Aug 24 09:26:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bqv_44825/08_2025/9bqv_44825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bqv_44825/08_2025/9bqv_44825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bqv_44825/08_2025/9bqv_44825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bqv_44825/08_2025/9bqv_44825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bqv_44825/08_2025/9bqv_44825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bqv_44825/08_2025/9bqv_44825.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 11833 2.51 5 N 3274 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18697 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9373 Classifications: {'peptide': 1161} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1127} Chain breaks: 3 Chain: "F" Number of atoms: 9324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 9324 Classifications: {'peptide': 1155} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1121} Chain breaks: 3 Time building chain proxies: 3.93, per 1000 atoms: 0.21 Number of scatterers: 18697 At special positions: 0 Unit cell: (123.14, 145.7, 131.6, 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 3542 8.00 N 3274 7.00 C 11833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 663.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 26 sheets defined 54.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 35 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 removed outlier: 3.723A pdb=" N LYS A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 163 through 177 removed outlier: 4.108A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 208 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.052A pdb=" N ARG A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.605A pdb=" N ASP A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.676A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 401 through 433 Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.935A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) 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 472 removed outlier: 3.613A pdb=" N PHE A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.860A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 656 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 693 Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.594A pdb=" N MET A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.839A pdb=" N ILE A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.732A 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 760 through 764 Processing helix chain 'A' and resid 789 through 807 removed outlier: 3.551A pdb=" N ASN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 removed outlier: 3.630A pdb=" N MET A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 836 removed outlier: 3.821A pdb=" N GLN A 834 " --> pdb=" O ARG A 830 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 853 removed outlier: 3.946A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.553A pdb=" N GLY A 857 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 858 " --> pdb=" O ARG A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'A' and resid 873 through 879 removed outlier: 4.049A pdb=" N ILE A 877 " --> pdb=" O GLY A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.109A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 909 through 938 removed outlier: 3.580A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 1014 through 1019 removed outlier: 3.527A pdb=" N LEU A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.816A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 removed outlier: 3.829A pdb=" N ALA A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.729A pdb=" N TYR A1081 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 removed outlier: 3.954A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 20 through 38 Processing helix chain 'F' and resid 54 through 78 Processing helix chain 'F' and resid 94 through 111 Processing helix chain 'F' and resid 121 through 131 removed outlier: 3.766A pdb=" N LYS F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 143 Processing helix chain 'F' and resid 146 through 157 Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 163 through 177 removed outlier: 4.138A pdb=" N ARG F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 209 removed outlier: 3.889A pdb=" N GLY F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 227 Processing helix chain 'F' and resid 229 through 234 removed outlier: 4.037A pdb=" N ARG F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.602A pdb=" N ASP F 263 " --> pdb=" O PRO F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.736A pdb=" N VAL F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 322 through 336 Processing helix chain 'F' and resid 401 through 433 removed outlier: 4.362A pdb=" N GLY F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'F' and resid 464 through 472 removed outlier: 3.535A pdb=" N VAL F 468 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 472 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.844A pdb=" N HIS F 496 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 536 Processing helix chain 'F' and resid 556 through 565 Processing helix chain 'F' and resid 572 through 585 Processing helix chain 'F' and resid 604 through 616 removed outlier: 3.563A pdb=" N LEU F 608 " --> pdb=" O ARG F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 629 Processing helix chain 'F' and resid 636 through 656 Processing helix chain 'F' and resid 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 675 through 693 Processing helix chain 'F' and resid 704 through 711 Processing helix chain 'F' and resid 712 through 723 removed outlier: 3.768A pdb=" N ILE F 716 " --> pdb=" O GLY F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 739 removed outlier: 3.568A pdb=" N ALA F 738 " --> pdb=" O SER F 735 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY F 739 " --> pdb=" O MET F 736 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 760 through 764 removed outlier: 3.604A pdb=" N SER F 764 " --> pdb=" O VAL F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 807 removed outlier: 3.597A pdb=" N ASN F 793 " --> pdb=" O SER F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 824 Processing helix chain 'F' and resid 827 through 836 removed outlier: 3.503A pdb=" N HIS F 836 " --> pdb=" O LEU F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 838 through 853 removed outlier: 3.949A pdb=" N GLN F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 858 removed outlier: 3.533A pdb=" N GLY F 857 " --> pdb=" O GLY F 854 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG F 858 " --> pdb=" O ARG F 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 854 through 858' Processing helix chain 'F' and resid 873 through 880 removed outlier: 4.436A pdb=" N ILE F 877 " --> pdb=" O GLY F 873 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 884 through 888 removed outlier: 4.107A pdb=" N LEU F 887 " --> pdb=" O ASP F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 889 through 901 Processing helix chain 'F' and resid 909 through 938 removed outlier: 3.808A pdb=" N ARG F 913 " --> pdb=" O ASP F 909 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 960 Processing helix chain 'F' and resid 992 through 996 removed outlier: 4.133A pdb=" N PHE F 996 " --> pdb=" O PRO F 993 " (cutoff:3.500A) Processing helix chain 'F' and resid 1014 through 1019 Processing helix chain 'F' and resid 1023 through 1032 removed outlier: 3.843A pdb=" N TRP F1027 " --> pdb=" O TYR F1023 " (cutoff:3.500A) Processing helix chain 'F' and resid 1045 through 1052 Processing helix chain 'F' and resid 1052 through 1068 removed outlier: 3.814A pdb=" N ALA F1068 " --> pdb=" O ALA F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1081 removed outlier: 3.736A pdb=" N TYR F1081 " --> pdb=" O ASN F1078 " (cutoff:3.500A) Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.965A pdb=" N GLU F1125 " --> pdb=" O LEU F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.051A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 269 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE A 542 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 271 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.788A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.591A pdb=" N GLU A 503 " --> pdb=" O LYS A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.731A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 382 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.518A pdb=" N VAL A 595 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU A 868 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR A 597 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 870 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS A 599 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET A 663 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER A 731 " --> pdb=" O MET A 663 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER A 665 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 743 through 745 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.573A pdb=" N LYS A 862 " --> pdb=" O ILE A 756 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.637A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 982 through 985 Processing sheet with id=AB3, first strand: chain 'A' and resid 1071 through 1074 removed outlier: 3.640A pdb=" N ARG A1087 " --> pdb=" O GLU A1074 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1162 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1137 through 1138 removed outlier: 3.696A pdb=" N GLY A1138 " --> pdb=" O ILE A1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.072A pdb=" N ALA F 43 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY F 541 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 269 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE F 542 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE F 271 " --> pdb=" O ILE F 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 89 through 91 removed outlier: 5.794A pdb=" N TYR F 90 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AB8, first strand: chain 'F' and resid 251 through 252 Processing sheet with id=AB9, first strand: chain 'F' and resid 291 through 292 removed outlier: 3.563A pdb=" N GLU F 503 " --> pdb=" O LYS F 517 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 342 through 344 removed outlier: 7.224A pdb=" N ASN F 343 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 382 " --> pdb=" O ASP F 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 595 through 601 removed outlier: 6.398A pdb=" N VAL F 595 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU F 868 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR F 597 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 870 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS F 599 " --> pdb=" O VAL F 870 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 774 " --> pdb=" O PHE F 869 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP F 871 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU F 776 " --> pdb=" O ASP F 871 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET F 663 " --> pdb=" O VAL F 729 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER F 731 " --> pdb=" O MET F 663 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER F 665 " --> pdb=" O SER F 731 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS F 698 " --> pdb=" O VAL F 728 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE F 730 " --> pdb=" O LYS F 698 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE F 700 " --> pdb=" O PHE F 730 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR F 732 " --> pdb=" O PHE F 700 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 743 through 745 Processing sheet with id=AC4, first strand: chain 'F' and resid 755 through 757 Processing sheet with id=AC5, first strand: chain 'F' and resid 962 through 963 removed outlier: 3.653A pdb=" N ASN F1042 " --> pdb=" O VAL F 963 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 983 through 985 Processing sheet with id=AC7, first strand: chain 'F' and resid 1071 through 1074 removed outlier: 3.703A pdb=" N ARG F1087 " --> pdb=" O GLU F1074 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F1162 " --> pdb=" O PHE F1131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 1137 through 1138 removed outlier: 3.764A pdb=" N GLY F1138 " --> pdb=" O ILE F1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 916 hydrogen bonds defined for protein. 2613 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: 3.89 Time building geometry restraints manager: 1.68 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: 3678 1.32 - 1.44: 4908 1.44 - 1.56: 10398 1.56 - 1.69: 5 1.69 - 1.81: 76 Bond restraints: 19065 Sorted by residual: bond pdb=" CB VAL F 91 " pdb=" CG2 VAL F 91 " ideal model delta sigma weight residual 1.521 1.365 0.156 3.30e-02 9.18e+02 2.22e+01 bond pdb=" CA LYS A 382 " pdb=" CB LYS A 382 " ideal model delta sigma weight residual 1.536 1.439 0.097 2.08e-02 2.31e+03 2.16e+01 bond pdb=" CB VAL A 91 " pdb=" CG2 VAL A 91 " ideal model delta sigma weight residual 1.521 1.378 0.143 3.30e-02 9.18e+02 1.88e+01 bond pdb=" CB VAL A 514 " pdb=" CG1 VAL A 514 " ideal model delta sigma weight residual 1.521 1.381 0.140 3.30e-02 9.18e+02 1.80e+01 bond pdb=" CB VAL F 514 " pdb=" CG1 VAL F 514 " ideal model delta sigma weight residual 1.521 1.384 0.137 3.30e-02 9.18e+02 1.71e+01 ... (remaining 19060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 24690 2.97 - 5.94: 921 5.94 - 8.91: 116 8.91 - 11.88: 36 11.88 - 14.85: 4 Bond angle restraints: 25767 Sorted by residual: angle pdb=" C SER F 361 " pdb=" N PHE F 362 " pdb=" CA PHE F 362 " ideal model delta sigma weight residual 121.54 133.24 -11.70 1.91e+00 2.74e-01 3.75e+01 angle pdb=" C HIS F 238 " pdb=" CA HIS F 238 " pdb=" CB HIS F 238 " ideal model delta sigma weight residual 110.56 100.29 10.27 1.83e+00 2.99e-01 3.15e+01 angle pdb=" C HIS A 238 " pdb=" CA HIS A 238 " pdb=" CB HIS A 238 " ideal model delta sigma weight residual 111.03 100.91 10.12 1.87e+00 2.86e-01 2.93e+01 angle pdb=" CB ARG A 305 " pdb=" CG ARG A 305 " pdb=" CD ARG A 305 " ideal model delta sigma weight residual 111.30 99.63 11.67 2.30e+00 1.89e-01 2.58e+01 angle pdb=" CA ARG A 563 " pdb=" CB ARG A 563 " pdb=" CG ARG A 563 " ideal model delta sigma weight residual 114.10 124.15 -10.05 2.00e+00 2.50e-01 2.52e+01 ... (remaining 25762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10440 17.95 - 35.90: 854 35.90 - 53.85: 180 53.85 - 71.80: 33 71.80 - 89.75: 22 Dihedral angle restraints: 11529 sinusoidal: 4719 harmonic: 6810 Sorted by residual: dihedral pdb=" CA VAL A 711 " pdb=" C VAL A 711 " pdb=" N GLY A 712 " pdb=" CA GLY A 712 " ideal model delta harmonic sigma weight residual 180.00 -140.35 -39.65 0 5.00e+00 4.00e-02 6.29e+01 dihedral pdb=" CA VAL F 711 " pdb=" C VAL F 711 " pdb=" N GLY F 712 " pdb=" CA GLY F 712 " ideal model delta harmonic sigma weight residual -180.00 -143.13 -36.87 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLU F 440 " pdb=" C GLU F 440 " pdb=" N ASN F 441 " pdb=" CA ASN F 441 " ideal model delta harmonic sigma weight residual 180.00 144.59 35.41 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 11526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1847 0.067 - 0.134: 822 0.134 - 0.201: 137 0.201 - 0.268: 32 0.268 - 0.335: 9 Chirality restraints: 2847 Sorted by residual: chirality pdb=" CB VAL F 239 " pdb=" CA VAL F 239 " pdb=" CG1 VAL F 239 " pdb=" CG2 VAL F 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL F 91 " pdb=" CA VAL F 91 " pdb=" CG1 VAL F 91 " pdb=" CG2 VAL F 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL A 91 " pdb=" CA VAL A 91 " pdb=" CG1 VAL A 91 " pdb=" CG2 VAL A 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2844 not shown) Planarity restraints: 3349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F1033 " 0.021 2.00e-02 2.50e+03 2.55e-02 1.14e+01 pdb=" CG PHE F1033 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE F1033 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE F1033 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F1033 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F1033 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE F1033 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 312 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A 313 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 238 " 0.017 2.00e-02 2.50e+03 2.62e-02 1.03e+01 pdb=" CG HIS F 238 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS F 238 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS F 238 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS F 238 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS F 238 " 0.005 2.00e-02 2.50e+03 ... (remaining 3346 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1404 2.70 - 3.25: 18243 3.25 - 3.80: 29364 3.80 - 4.35: 37726 4.35 - 4.90: 65536 Nonbonded interactions: 152273 Sorted by model distance: nonbonded pdb=" OH TYR A 427 " pdb=" OE2 GLU A 450 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR F 427 " pdb=" OE2 GLU F 450 " model vdw 2.169 3.040 nonbonded pdb=" O PHE F 999 " pdb=" N ARG F1001 " model vdw 2.171 3.120 nonbonded pdb=" O PHE A 999 " pdb=" N ARG A1001 " model vdw 2.171 3.120 nonbonded pdb=" OE1 GLU A 440 " pdb=" NH2 ARG A 442 " model vdw 2.176 3.120 ... (remaining 152268 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 387 or resid 400 through 478 or resid 489 throug \ h 1190)) selection = chain 'F' } 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: 4.130 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.340 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.021 0.156 19065 Z= 0.844 Angle : 1.348 14.853 25767 Z= 0.727 Chirality : 0.074 0.335 2847 Planarity : 0.007 0.083 3349 Dihedral : 14.531 89.748 7109 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.15), residues: 2300 helix: -1.28 (0.13), residues: 1144 sheet: -1.50 (0.32), residues: 241 loop : -1.58 (0.18), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG A 305 TYR 0.030 0.004 TYR F 559 PHE 0.057 0.005 PHE F1033 TRP 0.036 0.005 TRP A 707 HIS 0.035 0.004 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.02093 (19065) covalent geometry : angle 1.34846 (25767) hydrogen bonds : bond 0.17614 ( 916) hydrogen bonds : angle 7.37007 ( 2613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.613 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 700 PHE cc_start: 0.7479 (m-80) cc_final: 0.7179 (m-80) REVERT: F 641 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.7908 (mtp-110) REVERT: F 1132 ILE cc_start: 0.9174 (mt) cc_final: 0.8848 (mm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1517 time to fit residues: 37.1618 Evaluate side-chains 96 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 238 HIS A 522 ASN A 923 ASN F 238 HIS F 522 ASN F 584 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.110916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.071882 restraints weight = 47637.863| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.51 r_work: 0.3007 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19065 Z= 0.153 Angle : 0.580 8.552 25767 Z= 0.308 Chirality : 0.041 0.177 2847 Planarity : 0.004 0.052 3349 Dihedral : 5.414 45.119 2536 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.70 % Favored : 97.13 % Rotamer: Outliers : 0.68 % Allowed : 5.16 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.17), residues: 2300 helix: 0.56 (0.15), residues: 1141 sheet: -1.23 (0.31), residues: 279 loop : -1.11 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 863 TYR 0.016 0.001 TYR A1081 PHE 0.026 0.002 PHE A 362 TRP 0.021 0.001 TRP F 707 HIS 0.009 0.001 HIS F 623 Details of bonding type rmsd covalent geometry : bond 0.00338 (19065) covalent geometry : angle 0.58045 (25767) hydrogen bonds : bond 0.04428 ( 916) hydrogen bonds : angle 4.81876 ( 2613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLN cc_start: 0.8747 (mt0) cc_final: 0.8532 (tt0) REVERT: A 629 TYR cc_start: 0.8667 (m-80) cc_final: 0.8405 (m-80) REVERT: A 648 LEU cc_start: 0.8946 (mt) cc_final: 0.8572 (mt) REVERT: A 1023 TYR cc_start: 0.8847 (m-80) cc_final: 0.8145 (m-80) REVERT: F 1 MET cc_start: 0.8177 (pmm) cc_final: 0.7695 (pmm) REVERT: F 168 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8705 (mm-30) REVERT: F 453 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8563 (mm-40) REVERT: F 641 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.7664 (mtp-110) outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 0.1381 time to fit residues: 29.7054 Evaluate side-chains 106 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 162 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 348 ASN A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN F 238 HIS F 584 HIS F 592 ASN F 623 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1060 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.110403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071442 restraints weight = 47884.723| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.53 r_work: 0.2997 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19065 Z= 0.141 Angle : 0.512 8.244 25767 Z= 0.270 Chirality : 0.040 0.170 2847 Planarity : 0.003 0.038 3349 Dihedral : 4.863 43.975 2536 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.13 % Favored : 96.70 % Rotamer: Outliers : 0.92 % Allowed : 7.10 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2300 helix: 1.36 (0.15), residues: 1148 sheet: -1.03 (0.31), residues: 280 loop : -0.83 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 863 TYR 0.016 0.001 TYR F1133 PHE 0.026 0.002 PHE F 472 TRP 0.016 0.001 TRP A 643 HIS 0.016 0.001 HIS F1188 Details of bonding type rmsd covalent geometry : bond 0.00319 (19065) covalent geometry : angle 0.51250 (25767) hydrogen bonds : bond 0.03963 ( 916) hydrogen bonds : angle 4.44393 ( 2613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8575 (mm-30) REVERT: A 629 TYR cc_start: 0.8526 (m-80) cc_final: 0.8225 (m-80) REVERT: A 648 LEU cc_start: 0.8987 (mt) cc_final: 0.8623 (mt) REVERT: A 927 MET cc_start: 0.8834 (ttm) cc_final: 0.8528 (mtm) REVERT: A 1023 TYR cc_start: 0.8803 (m-80) cc_final: 0.8163 (m-80) REVERT: F 1 MET cc_start: 0.8182 (pmm) cc_final: 0.7701 (pmm) REVERT: F 158 ASN cc_start: 0.9052 (t0) cc_final: 0.8755 (t0) REVERT: F 168 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8800 (mm-30) REVERT: F 331 GLU cc_start: 0.8170 (tp30) cc_final: 0.7814 (tp30) REVERT: F 608 LEU cc_start: 0.8407 (tp) cc_final: 0.7405 (pp) REVERT: F 629 TYR cc_start: 0.8572 (m-80) cc_final: 0.8217 (m-80) REVERT: F 641 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.7663 (mtp-110) outliers start: 19 outliers final: 7 residues processed: 135 average time/residue: 0.1589 time to fit residues: 33.0873 Evaluate side-chains 104 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 1060 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 0 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN F 453 GLN ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 938 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1060 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.108451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070581 restraints weight = 48751.099| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.30 r_work: 0.3025 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19065 Z= 0.238 Angle : 0.568 8.090 25767 Z= 0.296 Chirality : 0.042 0.174 2847 Planarity : 0.003 0.036 3349 Dihedral : 4.831 41.865 2536 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 1.22 % Allowed : 8.32 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2300 helix: 1.63 (0.15), residues: 1147 sheet: -0.74 (0.31), residues: 286 loop : -0.72 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 828 TYR 0.015 0.001 TYR A1081 PHE 0.027 0.002 PHE F 472 TRP 0.015 0.001 TRP A 643 HIS 0.014 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00550 (19065) covalent geometry : angle 0.56846 (25767) hydrogen bonds : bond 0.04324 ( 916) hydrogen bonds : angle 4.54465 ( 2613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8643 (mm-30) REVERT: A 629 TYR cc_start: 0.8462 (m-80) cc_final: 0.8203 (m-80) REVERT: A 648 LEU cc_start: 0.9054 (mt) cc_final: 0.8671 (mt) REVERT: A 1023 TYR cc_start: 0.8798 (m-80) cc_final: 0.8204 (m-80) REVERT: F 1 MET cc_start: 0.8133 (pmm) cc_final: 0.7604 (pmm) REVERT: F 2 ASN cc_start: 0.8517 (m-40) cc_final: 0.7716 (p0) REVERT: F 158 ASN cc_start: 0.8996 (t0) cc_final: 0.8715 (t0) REVERT: F 168 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8828 (mm-30) REVERT: F 331 GLU cc_start: 0.8349 (tp30) cc_final: 0.8037 (tp30) REVERT: F 608 LEU cc_start: 0.8419 (tp) cc_final: 0.7785 (pp) REVERT: F 629 TYR cc_start: 0.8579 (m-80) cc_final: 0.8226 (m-80) REVERT: F 648 LEU cc_start: 0.8967 (mt) cc_final: 0.8742 (mt) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.1604 time to fit residues: 32.2261 Evaluate side-chains 111 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 930 ILE Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.1980 chunk 222 optimal weight: 10.0000 chunk 1 optimal weight: 0.0270 chunk 228 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 238 HIS A 515 ASN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.111375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073786 restraints weight = 48273.742| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.78 r_work: 0.3067 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19065 Z= 0.098 Angle : 0.456 7.809 25767 Z= 0.242 Chirality : 0.038 0.157 2847 Planarity : 0.003 0.034 3349 Dihedral : 4.406 42.671 2536 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.39 % Favored : 97.43 % Rotamer: Outliers : 1.26 % Allowed : 9.14 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.18), residues: 2300 helix: 1.99 (0.15), residues: 1155 sheet: -0.75 (0.30), residues: 312 loop : -0.44 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F1087 TYR 0.016 0.001 TYR F1133 PHE 0.028 0.001 PHE F1071 TRP 0.017 0.001 TRP F 643 HIS 0.015 0.001 HIS F1188 Details of bonding type rmsd covalent geometry : bond 0.00210 (19065) covalent geometry : angle 0.45623 (25767) hydrogen bonds : bond 0.03391 ( 916) hydrogen bonds : angle 4.16750 ( 2613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8429 (pmm) cc_final: 0.8217 (pmm) REVERT: A 168 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8649 (mm-30) REVERT: A 629 TYR cc_start: 0.8475 (m-80) cc_final: 0.8142 (m-80) REVERT: A 648 LEU cc_start: 0.8974 (mt) cc_final: 0.8607 (mt) REVERT: A 663 MET cc_start: 0.6787 (ttp) cc_final: 0.6114 (ttp) REVERT: A 1007 MET cc_start: 0.8231 (tpt) cc_final: 0.8011 (tpp) REVERT: A 1023 TYR cc_start: 0.8881 (m-80) cc_final: 0.8202 (m-80) REVERT: F 1 MET cc_start: 0.8234 (pmm) cc_final: 0.7899 (pmm) REVERT: F 2 ASN cc_start: 0.8581 (m-40) cc_final: 0.7713 (p0) REVERT: F 158 ASN cc_start: 0.9006 (t0) cc_final: 0.8474 (t0) REVERT: F 168 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8796 (mm-30) REVERT: F 331 GLU cc_start: 0.8338 (tp30) cc_final: 0.7981 (tp30) REVERT: F 608 LEU cc_start: 0.8068 (tp) cc_final: 0.7598 (pp) REVERT: F 629 TYR cc_start: 0.8519 (m-80) cc_final: 0.8106 (m-80) REVERT: F 648 LEU cc_start: 0.8836 (mt) cc_final: 0.8600 (mt) REVERT: F 787 ASP cc_start: 0.8932 (p0) cc_final: 0.8713 (p0) REVERT: F 1084 PHE cc_start: 0.8718 (m-80) cc_final: 0.8437 (m-10) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 0.1542 time to fit residues: 32.1219 Evaluate side-chains 108 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 212 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 201 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 238 HIS A 453 GLN A 584 HIS A 592 ASN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.109661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071908 restraints weight = 48322.252| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.65 r_work: 0.3025 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19065 Z= 0.159 Angle : 0.497 8.559 25767 Z= 0.260 Chirality : 0.040 0.165 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.436 40.911 2536 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.91 % Favored : 96.91 % Rotamer: Outliers : 1.41 % Allowed : 9.73 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.18), residues: 2300 helix: 2.11 (0.15), residues: 1157 sheet: -0.58 (0.31), residues: 297 loop : -0.38 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 475 TYR 0.014 0.001 TYR F1133 PHE 0.024 0.001 PHE A 362 TRP 0.014 0.001 TRP A 643 HIS 0.021 0.001 HIS A1188 Details of bonding type rmsd covalent geometry : bond 0.00365 (19065) covalent geometry : angle 0.49728 (25767) hydrogen bonds : bond 0.03709 ( 916) hydrogen bonds : angle 4.25993 ( 2613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8696 (mm-30) REVERT: A 629 TYR cc_start: 0.8406 (m-80) cc_final: 0.8101 (m-80) REVERT: A 648 LEU cc_start: 0.9028 (mt) cc_final: 0.8646 (mt) REVERT: A 663 MET cc_start: 0.7137 (ttp) cc_final: 0.6508 (ttp) REVERT: A 927 MET cc_start: 0.8951 (ttm) cc_final: 0.8667 (mtm) REVERT: A 1007 MET cc_start: 0.8150 (tpt) cc_final: 0.7893 (tpp) REVERT: A 1023 TYR cc_start: 0.8768 (m-80) cc_final: 0.8160 (m-80) REVERT: F 1 MET cc_start: 0.8221 (pmm) cc_final: 0.7877 (pmm) REVERT: F 2 ASN cc_start: 0.8521 (m-40) cc_final: 0.7662 (p0) REVERT: F 158 ASN cc_start: 0.8855 (t0) cc_final: 0.8525 (t0) REVERT: F 168 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8843 (mm-30) REVERT: F 331 GLU cc_start: 0.8393 (tp30) cc_final: 0.8114 (tp30) REVERT: F 608 LEU cc_start: 0.8171 (tp) cc_final: 0.7632 (pp) REVERT: F 629 TYR cc_start: 0.8497 (m-80) cc_final: 0.8103 (m-80) REVERT: F 648 LEU cc_start: 0.8892 (mt) cc_final: 0.8642 (mt) REVERT: F 787 ASP cc_start: 0.8941 (p0) cc_final: 0.8718 (p0) REVERT: F 1084 PHE cc_start: 0.8690 (m-80) cc_final: 0.8395 (m-10) REVERT: F 1145 ARG cc_start: 0.8785 (mtp180) cc_final: 0.8584 (ttp-110) outliers start: 29 outliers final: 22 residues processed: 119 average time/residue: 0.1477 time to fit residues: 28.0457 Evaluate side-chains 110 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1044 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 88 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 169 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.110786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.073201 restraints weight = 48709.675| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.73 r_work: 0.3054 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19065 Z= 0.108 Angle : 0.460 7.548 25767 Z= 0.242 Chirality : 0.038 0.159 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.262 40.301 2536 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.26 % Favored : 97.57 % Rotamer: Outliers : 1.31 % Allowed : 10.17 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2300 helix: 2.30 (0.15), residues: 1156 sheet: -0.61 (0.31), residues: 312 loop : -0.24 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.012 0.001 TYR F 713 PHE 0.026 0.001 PHE F1071 TRP 0.016 0.001 TRP A 643 HIS 0.005 0.001 HIS A1188 Details of bonding type rmsd covalent geometry : bond 0.00241 (19065) covalent geometry : angle 0.46019 (25767) hydrogen bonds : bond 0.03348 ( 916) hydrogen bonds : angle 4.14889 ( 2613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8722 (mm-30) REVERT: A 629 TYR cc_start: 0.8405 (m-80) cc_final: 0.8105 (m-80) REVERT: A 648 LEU cc_start: 0.8989 (mt) cc_final: 0.8608 (mt) REVERT: A 663 MET cc_start: 0.6997 (ttp) cc_final: 0.6421 (ttp) REVERT: A 666 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7954 (mm) REVERT: A 1007 MET cc_start: 0.8157 (tpt) cc_final: 0.7889 (tpp) REVERT: A 1023 TYR cc_start: 0.8802 (m-80) cc_final: 0.8154 (m-80) REVERT: F 1 MET cc_start: 0.8370 (pmm) cc_final: 0.8133 (pmm) REVERT: F 2 ASN cc_start: 0.8528 (m-40) cc_final: 0.7657 (p0) REVERT: F 158 ASN cc_start: 0.8882 (t0) cc_final: 0.8543 (t0) REVERT: F 168 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8856 (mm-30) REVERT: F 331 GLU cc_start: 0.8423 (tp30) cc_final: 0.8116 (tp30) REVERT: F 608 LEU cc_start: 0.8038 (tp) cc_final: 0.7580 (pp) REVERT: F 629 TYR cc_start: 0.8503 (m-80) cc_final: 0.8070 (m-80) REVERT: F 648 LEU cc_start: 0.8856 (mt) cc_final: 0.8612 (mt) REVERT: F 787 ASP cc_start: 0.8939 (p0) cc_final: 0.8716 (p0) REVERT: F 997 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6973 (tp30) outliers start: 27 outliers final: 15 residues processed: 128 average time/residue: 0.1539 time to fit residues: 30.7766 Evaluate side-chains 107 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1043 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN F 627 ASN ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.109599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072364 restraints weight = 48708.587| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.47 r_work: 0.3024 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19065 Z= 0.157 Angle : 0.502 10.626 25767 Z= 0.259 Chirality : 0.040 0.164 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.334 37.135 2536 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % Rotamer: Outliers : 1.41 % Allowed : 10.55 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.18), residues: 2300 helix: 2.31 (0.15), residues: 1156 sheet: -0.46 (0.32), residues: 295 loop : -0.26 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 475 TYR 0.017 0.001 TYR F1133 PHE 0.026 0.001 PHE A1071 TRP 0.032 0.001 TRP A1186 HIS 0.005 0.001 HIS F1188 Details of bonding type rmsd covalent geometry : bond 0.00360 (19065) covalent geometry : angle 0.50162 (25767) hydrogen bonds : bond 0.03668 ( 916) hydrogen bonds : angle 4.19761 ( 2613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8792 (mm-30) REVERT: A 629 TYR cc_start: 0.8391 (m-80) cc_final: 0.8119 (m-80) REVERT: A 648 LEU cc_start: 0.8988 (mt) cc_final: 0.8653 (mt) REVERT: A 663 MET cc_start: 0.6986 (ttp) cc_final: 0.6416 (ttp) REVERT: A 666 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 708 MET cc_start: 0.5168 (mpp) cc_final: 0.4933 (mpp) REVERT: A 927 MET cc_start: 0.8871 (ttm) cc_final: 0.8559 (mtm) REVERT: A 1007 MET cc_start: 0.8200 (tpt) cc_final: 0.7932 (tpp) REVERT: A 1023 TYR cc_start: 0.8823 (m-80) cc_final: 0.8159 (m-80) REVERT: F 1 MET cc_start: 0.8471 (pmm) cc_final: 0.8234 (pmm) REVERT: F 2 ASN cc_start: 0.8559 (m-40) cc_final: 0.7677 (p0) REVERT: F 158 ASN cc_start: 0.8870 (t0) cc_final: 0.8574 (t0) REVERT: F 168 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8842 (mm-30) REVERT: F 331 GLU cc_start: 0.8483 (tp30) cc_final: 0.8168 (tp30) REVERT: F 608 LEU cc_start: 0.8158 (tp) cc_final: 0.7662 (pp) REVERT: F 629 TYR cc_start: 0.8472 (m-80) cc_final: 0.8079 (m-80) REVERT: F 648 LEU cc_start: 0.8842 (mt) cc_final: 0.8608 (mt) REVERT: F 787 ASP cc_start: 0.8989 (p0) cc_final: 0.8759 (p0) REVERT: F 997 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: F 1084 PHE cc_start: 0.8635 (m-80) cc_final: 0.8335 (m-10) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.1381 time to fit residues: 26.4932 Evaluate side-chains 111 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.110468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073353 restraints weight = 48708.411| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.48 r_work: 0.3041 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19065 Z= 0.122 Angle : 0.472 9.811 25767 Z= 0.245 Chirality : 0.039 0.159 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.241 38.659 2536 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.35 % Favored : 97.48 % Rotamer: Outliers : 1.31 % Allowed : 10.51 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 2300 helix: 2.42 (0.15), residues: 1157 sheet: -0.60 (0.31), residues: 313 loop : -0.15 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 475 TYR 0.011 0.001 TYR F 713 PHE 0.030 0.001 PHE A1071 TRP 0.019 0.001 TRP A1186 HIS 0.005 0.001 HIS A1188 Details of bonding type rmsd covalent geometry : bond 0.00278 (19065) covalent geometry : angle 0.47240 (25767) hydrogen bonds : bond 0.03366 ( 916) hydrogen bonds : angle 4.08696 ( 2613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 TYR cc_start: 0.8351 (m-80) cc_final: 0.8123 (m-80) REVERT: A 648 LEU cc_start: 0.8971 (mt) cc_final: 0.8621 (mt) REVERT: A 663 MET cc_start: 0.7033 (ttp) cc_final: 0.6446 (ttp) REVERT: A 666 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 708 MET cc_start: 0.5414 (mpp) cc_final: 0.5119 (mpp) REVERT: A 927 MET cc_start: 0.8897 (ttm) cc_final: 0.8587 (mtm) REVERT: A 1007 MET cc_start: 0.8265 (tpt) cc_final: 0.8018 (tpp) REVERT: A 1023 TYR cc_start: 0.8826 (m-80) cc_final: 0.8147 (m-80) REVERT: F 2 ASN cc_start: 0.8538 (m-40) cc_final: 0.7650 (p0) REVERT: F 158 ASN cc_start: 0.8829 (t0) cc_final: 0.8536 (t0) REVERT: F 331 GLU cc_start: 0.8433 (tp30) cc_final: 0.8147 (tp30) REVERT: F 432 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8157 (mtp180) REVERT: F 629 TYR cc_start: 0.8424 (m-80) cc_final: 0.8062 (m-80) REVERT: F 648 LEU cc_start: 0.8877 (mt) cc_final: 0.8574 (mt) REVERT: F 787 ASP cc_start: 0.8968 (p0) cc_final: 0.8738 (p0) REVERT: F 997 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: F 1071 PHE cc_start: 0.8307 (t80) cc_final: 0.7989 (t80) REVERT: F 1084 PHE cc_start: 0.8618 (m-80) cc_final: 0.8323 (m-10) outliers start: 27 outliers final: 19 residues processed: 121 average time/residue: 0.1302 time to fit residues: 25.0180 Evaluate side-chains 114 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 432 ARG Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 736 MET Chi-restraints excluded: chain F residue 872 SER Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 138 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 180 optimal weight: 0.2980 chunk 204 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.111286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073531 restraints weight = 48467.642| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.77 r_work: 0.3061 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19065 Z= 0.102 Angle : 0.469 8.974 25767 Z= 0.242 Chirality : 0.038 0.153 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.123 37.798 2536 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.26 % Favored : 97.57 % Rotamer: Outliers : 1.22 % Allowed : 10.65 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.18), residues: 2300 helix: 2.54 (0.15), residues: 1156 sheet: -0.51 (0.32), residues: 301 loop : -0.09 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 475 TYR 0.015 0.001 TYR F1133 PHE 0.023 0.001 PHE F 362 TRP 0.016 0.001 TRP F 643 HIS 0.005 0.001 HIS A1188 Details of bonding type rmsd covalent geometry : bond 0.00229 (19065) covalent geometry : angle 0.46860 (25767) hydrogen bonds : bond 0.03176 ( 916) hydrogen bonds : angle 4.01608 ( 2613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 TYR cc_start: 0.8326 (m-80) cc_final: 0.8103 (m-80) REVERT: A 648 LEU cc_start: 0.8936 (mt) cc_final: 0.8598 (mt) REVERT: A 663 MET cc_start: 0.7065 (ttp) cc_final: 0.6534 (ttp) REVERT: A 666 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8009 (mm) REVERT: A 708 MET cc_start: 0.5615 (mpp) cc_final: 0.5357 (mpp) REVERT: A 826 MET cc_start: 0.8375 (ttp) cc_final: 0.8068 (ttm) REVERT: A 952 ASP cc_start: 0.9436 (m-30) cc_final: 0.9135 (m-30) REVERT: A 1007 MET cc_start: 0.8262 (tpt) cc_final: 0.8021 (tpp) REVERT: A 1023 TYR cc_start: 0.8828 (m-80) cc_final: 0.8160 (m-80) REVERT: F 2 ASN cc_start: 0.8487 (m-40) cc_final: 0.7637 (p0) REVERT: F 158 ASN cc_start: 0.8884 (t0) cc_final: 0.8530 (t0) REVERT: F 331 GLU cc_start: 0.8440 (tp30) cc_final: 0.8157 (tp30) REVERT: F 432 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8086 (mtp180) REVERT: F 629 TYR cc_start: 0.8360 (m-80) cc_final: 0.8009 (m-80) REVERT: F 648 LEU cc_start: 0.8883 (mt) cc_final: 0.8561 (mt) REVERT: F 787 ASP cc_start: 0.8929 (p0) cc_final: 0.8693 (p0) REVERT: F 997 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: F 1071 PHE cc_start: 0.8202 (t80) cc_final: 0.7969 (t80) REVERT: F 1084 PHE cc_start: 0.8492 (m-80) cc_final: 0.8192 (m-10) outliers start: 25 outliers final: 17 residues processed: 125 average time/residue: 0.1352 time to fit residues: 26.7276 Evaluate side-chains 114 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 370 HIS Chi-restraints excluded: chain F residue 432 ARG Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 138 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.109979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072965 restraints weight = 48942.571| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.44 r_work: 0.3035 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19065 Z= 0.146 Angle : 0.505 12.818 25767 Z= 0.258 Chirality : 0.039 0.158 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.201 36.893 2536 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.57 % Favored : 97.26 % Rotamer: Outliers : 1.12 % Allowed : 11.04 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.18), residues: 2300 helix: 2.51 (0.15), residues: 1157 sheet: -0.38 (0.32), residues: 300 loop : -0.12 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 475 TYR 0.016 0.001 TYR A1081 PHE 0.025 0.001 PHE A 639 TRP 0.013 0.001 TRP A 643 HIS 0.009 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00337 (19065) covalent geometry : angle 0.50493 (25767) hydrogen bonds : bond 0.03425 ( 916) hydrogen bonds : angle 4.10494 ( 2613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4697.69 seconds wall clock time: 81 minutes 37.05 seconds (4897.05 seconds total)