Starting phenix.real_space_refine on Wed Jan 22 15:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bqv_44825/01_2025/9bqv_44825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bqv_44825/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bqv_44825/01_2025/9bqv_44825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bqv_44825/01_2025/9bqv_44825.map" model { file = "/net/cci-nas-00/data/ceres_data/9bqv_44825/01_2025/9bqv_44825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bqv_44825/01_2025/9bqv_44825.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.75, per 1000 atoms: 0.63 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: 4.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.39 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: 7.26 Time building geometry restraints manager: 5.26 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 42.780 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- 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= 1.365 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (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 TRP 0.036 0.005 TRP A 707 HIS 0.035 0.004 HIS F 238 PHE 0.057 0.005 PHE F1033 TYR 0.030 0.004 TYR F 559 ARG 0.039 0.002 ARG A 305 *********************** 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 : 2.024 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: 0.3860 time to fit residues: 93.4531 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 : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 238 HIS A 522 ASN A 923 ASN F 238 HIS F 522 ASN F 592 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.111189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072368 restraints weight = 47511.841| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.50 r_work: 0.3015 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19065 Z= 0.212 Angle : 0.571 8.673 25767 Z= 0.303 Chirality : 0.041 0.174 2847 Planarity : 0.004 0.051 3349 Dihedral : 5.350 45.384 2536 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.22 % Rotamer: Outliers : 0.83 % Allowed : 5.06 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2300 helix: 0.59 (0.15), residues: 1142 sheet: -1.21 (0.31), residues: 279 loop : -1.11 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 707 HIS 0.009 0.001 HIS F 623 PHE 0.026 0.002 PHE A 362 TYR 0.014 0.001 TYR A1081 ARG 0.004 0.001 ARG A 863 *********************** 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 155 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLN cc_start: 0.8741 (mt0) cc_final: 0.8518 (tt0) REVERT: A 629 TYR cc_start: 0.8671 (m-80) cc_final: 0.8364 (m-80) REVERT: A 648 LEU cc_start: 0.8923 (mt) cc_final: 0.8554 (mt) REVERT: A 1023 TYR cc_start: 0.8842 (m-80) cc_final: 0.8163 (m-80) REVERT: F 1 MET cc_start: 0.8186 (pmm) cc_final: 0.7752 (pmm) REVERT: F 168 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8696 (mm-30) REVERT: F 453 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8616 (mm-40) REVERT: F 629 TYR cc_start: 0.8476 (m-80) cc_final: 0.8139 (m-80) REVERT: F 641 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.7653 (mtp-110) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.3510 time to fit residues: 80.0529 Evaluate side-chains 108 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 623 HIS 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 7 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 169 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 938 HIS ** 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 = 0.3965 r_free = 0.3965 target = 0.109786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071758 restraints weight = 48509.872| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.40 r_work: 0.3051 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2787 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= 0.266 Angle : 0.538 8.078 25767 Z= 0.282 Chirality : 0.040 0.175 2847 Planarity : 0.004 0.041 3349 Dihedral : 4.923 42.859 2536 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 0.97 % Allowed : 7.34 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2300 helix: 1.33 (0.15), residues: 1148 sheet: -0.94 (0.31), residues: 270 loop : -0.89 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.016 0.001 HIS F 238 PHE 0.026 0.002 PHE A 362 TYR 0.016 0.001 TYR F1133 ARG 0.003 0.000 ARG F 828 *********************** 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 138 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8673 (tp30) REVERT: A 453 GLN cc_start: 0.8545 (mt0) cc_final: 0.8212 (mt0) REVERT: A 629 TYR cc_start: 0.8513 (m-80) cc_final: 0.8217 (m-80) REVERT: A 648 LEU cc_start: 0.9025 (mt) cc_final: 0.8694 (mt) REVERT: A 826 MET cc_start: 0.8915 (ttp) cc_final: 0.8568 (ttm) REVERT: A 875 LYS cc_start: 0.8945 (tttt) cc_final: 0.8453 (tptp) REVERT: A 1023 TYR cc_start: 0.8837 (m-80) cc_final: 0.8239 (m-80) REVERT: F 1 MET cc_start: 0.8148 (pmm) cc_final: 0.7624 (pmm) REVERT: F 158 ASN cc_start: 0.9015 (t0) cc_final: 0.8713 (t0) REVERT: F 168 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8801 (mm-30) REVERT: F 331 GLU cc_start: 0.8187 (tp30) cc_final: 0.7859 (tp30) REVERT: F 508 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7902 (pp30) REVERT: F 608 LEU cc_start: 0.8414 (tp) cc_final: 0.7485 (pp) REVERT: F 629 TYR cc_start: 0.8572 (m-80) cc_final: 0.8210 (m-80) REVERT: F 641 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.7701 (mtp-110) outliers start: 20 outliers final: 7 residues processed: 133 average time/residue: 0.3380 time to fit residues: 69.6681 Evaluate side-chains 99 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 947 ILE Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain F residue 947 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS F 291 GLN F 453 GLN ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.110750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072561 restraints weight = 48329.973| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.42 r_work: 0.3074 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19065 Z= 0.192 Angle : 0.487 8.134 25767 Z= 0.257 Chirality : 0.039 0.166 2847 Planarity : 0.003 0.035 3349 Dihedral : 4.563 42.486 2536 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.65 % Favored : 97.17 % Rotamer: Outliers : 1.22 % Allowed : 8.27 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2300 helix: 1.72 (0.15), residues: 1156 sheet: -0.83 (0.30), residues: 310 loop : -0.58 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.013 0.001 HIS A 238 PHE 0.024 0.001 PHE A 362 TYR 0.013 0.001 TYR F1081 ARG 0.003 0.000 ARG A1087 *********************** 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 137 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8519 (mm-30) REVERT: A 629 TYR cc_start: 0.8468 (m-80) cc_final: 0.8176 (m-80) REVERT: A 648 LEU cc_start: 0.8946 (mt) cc_final: 0.8602 (mt) REVERT: A 826 MET cc_start: 0.8875 (ttp) cc_final: 0.8557 (ttm) REVERT: A 875 LYS cc_start: 0.8959 (tttt) cc_final: 0.8444 (tptp) REVERT: A 927 MET cc_start: 0.8861 (ttm) cc_final: 0.8545 (mtm) REVERT: A 1023 TYR cc_start: 0.8837 (m-80) cc_final: 0.8293 (m-80) REVERT: F 1 MET cc_start: 0.8166 (pmm) cc_final: 0.7746 (pmm) REVERT: F 2 ASN cc_start: 0.8477 (m-40) cc_final: 0.7652 (p0) REVERT: F 158 ASN cc_start: 0.8982 (t0) cc_final: 0.8457 (t0) REVERT: F 168 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8787 (mm-30) REVERT: F 331 GLU cc_start: 0.8288 (tp30) cc_final: 0.7951 (tp30) REVERT: F 608 LEU cc_start: 0.8175 (tp) cc_final: 0.7586 (pp) REVERT: F 629 TYR cc_start: 0.8544 (m-80) cc_final: 0.8165 (m-80) REVERT: F 648 LEU cc_start: 0.8881 (mt) cc_final: 0.8654 (mt) REVERT: F 1007 MET cc_start: 0.8341 (tpt) cc_final: 0.8136 (tpt) REVERT: F 1059 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8618 (tm-30) outliers start: 25 outliers final: 15 residues processed: 130 average time/residue: 0.3558 time to fit residues: 72.0392 Evaluate side-chains 112 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 608 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 947 ILE 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 187 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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 938 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 HIS ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.109765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071558 restraints weight = 48824.355| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.45 r_work: 0.3060 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19065 Z= 0.218 Angle : 0.486 7.834 25767 Z= 0.257 Chirality : 0.039 0.167 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.485 41.741 2536 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 1.46 % Allowed : 9.14 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 2300 helix: 1.98 (0.15), residues: 1153 sheet: -0.69 (0.31), residues: 306 loop : -0.42 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 643 HIS 0.021 0.001 HIS A1188 PHE 0.024 0.002 PHE A 362 TYR 0.015 0.001 TYR F1133 ARG 0.003 0.000 ARG A 475 *********************** 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 134 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 2.240 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8582 (mm-30) REVERT: A 629 TYR cc_start: 0.8454 (m-80) cc_final: 0.8132 (m-80) REVERT: A 648 LEU cc_start: 0.8953 (mt) cc_final: 0.8613 (mt) REVERT: A 826 MET cc_start: 0.8823 (ttp) cc_final: 0.8498 (ttm) REVERT: A 875 LYS cc_start: 0.8935 (tttt) cc_final: 0.8364 (tptp) REVERT: A 927 MET cc_start: 0.8880 (ttm) cc_final: 0.8551 (mtm) REVERT: A 1023 TYR cc_start: 0.8848 (m-80) cc_final: 0.8167 (m-80) REVERT: F 1 MET cc_start: 0.8185 (pmm) cc_final: 0.7779 (pmm) REVERT: F 2 ASN cc_start: 0.8507 (m-40) cc_final: 0.7662 (p0) REVERT: F 158 ASN cc_start: 0.8867 (t0) cc_final: 0.8523 (t0) REVERT: F 168 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8810 (mm-30) REVERT: F 331 GLU cc_start: 0.8358 (tp30) cc_final: 0.8022 (tp30) REVERT: F 608 LEU cc_start: 0.8130 (tp) cc_final: 0.7647 (pp) REVERT: F 629 TYR cc_start: 0.8526 (m-80) cc_final: 0.8132 (m-80) REVERT: F 648 LEU cc_start: 0.8887 (mt) cc_final: 0.8639 (mt) REVERT: F 1059 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8580 (tm-30) outliers start: 30 outliers final: 22 residues processed: 128 average time/residue: 0.3048 time to fit residues: 63.3612 Evaluate side-chains 113 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 463 GLU Chi-restraints excluded: chain A residue 608 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 A residue 1043 VAL 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 973 LEU Chi-restraints excluded: chain F residue 997 GLU Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1044 MET 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 174 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 592 ASN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 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 = 0.3975 r_free = 0.3975 target = 0.110220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.073104 restraints weight = 48762.999| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.46 r_work: 0.3040 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19065 Z= 0.187 Angle : 0.483 8.289 25767 Z= 0.252 Chirality : 0.039 0.168 2847 Planarity : 0.003 0.033 3349 Dihedral : 4.400 41.196 2536 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 1.51 % Allowed : 9.92 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2300 helix: 2.18 (0.15), residues: 1156 sheet: -0.64 (0.31), residues: 310 loop : -0.29 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 643 HIS 0.008 0.001 HIS F 238 PHE 0.029 0.001 PHE F1071 TYR 0.012 0.001 TYR A1081 ARG 0.002 0.000 ARG F 959 *********************** 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 136 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 2.029 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8676 (mm-30) REVERT: A 629 TYR cc_start: 0.8390 (m-80) cc_final: 0.8102 (m-80) REVERT: A 648 LEU cc_start: 0.8965 (mt) cc_final: 0.8639 (mt) REVERT: A 826 MET cc_start: 0.8798 (ttp) cc_final: 0.8486 (ttm) REVERT: A 875 LYS cc_start: 0.8930 (tttt) cc_final: 0.8375 (tptp) REVERT: A 927 MET cc_start: 0.8887 (ttm) cc_final: 0.8585 (mtm) REVERT: A 1023 TYR cc_start: 0.8816 (m-80) cc_final: 0.8174 (m-80) REVERT: F 1 MET cc_start: 0.8232 (pmm) cc_final: 0.7924 (pmm) REVERT: F 2 ASN cc_start: 0.8482 (m-40) cc_final: 0.7626 (p0) REVERT: F 158 ASN cc_start: 0.8868 (t0) cc_final: 0.8541 (t0) REVERT: F 168 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8825 (mm-30) REVERT: F 331 GLU cc_start: 0.8394 (tp30) cc_final: 0.8069 (tp30) REVERT: F 608 LEU cc_start: 0.8066 (tp) cc_final: 0.7573 (pp) REVERT: F 629 TYR cc_start: 0.8502 (m-80) cc_final: 0.8100 (m-80) REVERT: F 648 LEU cc_start: 0.8877 (mt) cc_final: 0.8629 (mt) REVERT: F 787 ASP cc_start: 0.8943 (p0) cc_final: 0.8727 (p0) REVERT: F 1059 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8541 (tm-30) REVERT: F 1084 PHE cc_start: 0.8668 (m-80) cc_final: 0.8406 (m-10) outliers start: 31 outliers final: 20 residues processed: 132 average time/residue: 0.3299 time to fit residues: 68.2106 Evaluate side-chains 112 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE 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 608 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 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 463 GLU 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 17 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 291 GLN A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.108579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071166 restraints weight = 48667.462| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.46 r_work: 0.3008 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19065 Z= 0.291 Angle : 0.529 7.246 25767 Z= 0.274 Chirality : 0.040 0.171 2847 Planarity : 0.003 0.034 3349 Dihedral : 4.482 38.830 2536 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 1.75 % Allowed : 10.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2300 helix: 2.19 (0.15), residues: 1151 sheet: -0.53 (0.31), residues: 295 loop : -0.32 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 643 HIS 0.005 0.001 HIS A1188 PHE 0.026 0.002 PHE A1071 TYR 0.017 0.001 TYR F1133 ARG 0.004 0.000 ARG F1145 *********************** 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 131 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 2.090 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8807 (mm-30) REVERT: A 629 TYR cc_start: 0.8375 (m-80) cc_final: 0.8085 (m-80) REVERT: A 641 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7857 (mtp85) REVERT: A 648 LEU cc_start: 0.8941 (mt) cc_final: 0.8618 (mt) REVERT: A 666 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 1023 TYR cc_start: 0.8831 (m-80) cc_final: 0.8158 (m-80) REVERT: F 1 MET cc_start: 0.8352 (pmm) cc_final: 0.8003 (pmm) REVERT: F 2 ASN cc_start: 0.8552 (m-40) cc_final: 0.7678 (p0) REVERT: F 158 ASN cc_start: 0.8933 (t0) cc_final: 0.8596 (t0) REVERT: F 168 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8863 (mm-30) REVERT: F 331 GLU cc_start: 0.8482 (tp30) cc_final: 0.8170 (tp30) REVERT: F 608 LEU cc_start: 0.8179 (tp) cc_final: 0.7653 (pp) REVERT: F 629 TYR cc_start: 0.8506 (m-80) cc_final: 0.8090 (m-80) REVERT: F 648 LEU cc_start: 0.8877 (mt) cc_final: 0.8633 (mt) REVERT: F 1059 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8620 (tm-30) REVERT: F 1084 PHE cc_start: 0.8748 (m-80) cc_final: 0.8455 (m-10) outliers start: 36 outliers final: 26 residues processed: 126 average time/residue: 0.3003 time to fit residues: 61.5455 Evaluate side-chains 116 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 374 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 724 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 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 947 ILE Chi-restraints excluded: chain F residue 996 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 147 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 164 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.110282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073207 restraints weight = 48712.562| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.50 r_work: 0.3037 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19065 Z= 0.174 Angle : 0.472 7.021 25767 Z= 0.247 Chirality : 0.039 0.161 2847 Planarity : 0.003 0.032 3349 Dihedral : 4.286 39.419 2536 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.52 % Favored : 97.30 % Rotamer: Outliers : 1.65 % Allowed : 10.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2300 helix: 2.37 (0.15), residues: 1154 sheet: -0.58 (0.31), residues: 310 loop : -0.23 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 643 HIS 0.005 0.001 HIS A 238 PHE 0.021 0.001 PHE A 362 TYR 0.011 0.001 TYR A1081 ARG 0.002 0.000 ARG F1145 *********************** 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 129 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8798 (mm-30) REVERT: A 629 TYR cc_start: 0.8372 (m-80) cc_final: 0.8123 (m-80) REVERT: A 648 LEU cc_start: 0.8942 (mt) cc_final: 0.8618 (mt) REVERT: A 708 MET cc_start: 0.5141 (mpp) cc_final: 0.4933 (mpp) REVERT: A 927 MET cc_start: 0.8849 (ttm) cc_final: 0.8524 (mtm) REVERT: A 1023 TYR cc_start: 0.8853 (m-80) cc_final: 0.8192 (m-80) REVERT: F 2 ASN cc_start: 0.8539 (m-40) cc_final: 0.7662 (p0) REVERT: F 158 ASN cc_start: 0.8918 (t0) cc_final: 0.8498 (t0) REVERT: F 331 GLU cc_start: 0.8471 (tp30) cc_final: 0.8140 (tp30) REVERT: F 608 LEU cc_start: 0.8062 (tp) cc_final: 0.7603 (pp) REVERT: F 629 TYR cc_start: 0.8487 (m-80) cc_final: 0.8097 (m-80) REVERT: F 648 LEU cc_start: 0.8847 (mt) cc_final: 0.8602 (mt) REVERT: F 669 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8058 (ptp-110) REVERT: F 787 ASP cc_start: 0.9008 (p0) cc_final: 0.8780 (p0) REVERT: F 1007 MET cc_start: 0.8382 (tpt) cc_final: 0.8131 (tpp) REVERT: F 1059 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8543 (tm-30) outliers start: 34 outliers final: 22 residues processed: 126 average time/residue: 0.3021 time to fit residues: 61.3158 Evaluate side-chains 109 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE 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 608 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 A residue 999 PHE 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 370 HIS Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 669 ARG 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 996 PHE Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1066 LEU Chi-restraints excluded: chain F residue 1099 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 107 optimal weight: 0.0870 chunk 223 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN A 584 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.108036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070489 restraints weight = 49017.758| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.47 r_work: 0.2988 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19065 Z= 0.335 Angle : 0.556 8.659 25767 Z= 0.284 Chirality : 0.041 0.170 2847 Planarity : 0.003 0.031 3349 Dihedral : 4.492 37.479 2536 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 1.61 % Allowed : 10.75 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2300 helix: 2.27 (0.15), residues: 1153 sheet: -0.48 (0.32), residues: 287 loop : -0.33 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1186 HIS 0.005 0.001 HIS A1188 PHE 0.025 0.002 PHE F 362 TYR 0.017 0.001 TYR A1081 ARG 0.005 0.000 ARG A1083 *********************** 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 121 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 2.276 Fit side-chains revert: symmetry clash REVERT: A 629 TYR cc_start: 0.8334 (m-80) cc_final: 0.8108 (m-80) REVERT: A 641 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7863 (mtp85) REVERT: A 648 LEU cc_start: 0.8973 (mt) cc_final: 0.8641 (mt) REVERT: A 708 MET cc_start: 0.5565 (mpp) cc_final: 0.5264 (mpp) REVERT: A 826 MET cc_start: 0.8401 (ttp) cc_final: 0.8129 (ttm) REVERT: A 1023 TYR cc_start: 0.8851 (m-80) cc_final: 0.8184 (m-80) REVERT: A 1071 PHE cc_start: 0.8281 (t80) cc_final: 0.7988 (t80) REVERT: F 2 ASN cc_start: 0.8487 (m-40) cc_final: 0.7640 (p0) REVERT: F 158 ASN cc_start: 0.8844 (t0) cc_final: 0.8537 (t0) REVERT: F 168 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8853 (mm-30) REVERT: F 331 GLU cc_start: 0.8428 (tp30) cc_final: 0.8100 (tp30) REVERT: F 432 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8230 (mtp-110) REVERT: F 608 LEU cc_start: 0.8176 (tp) cc_final: 0.7671 (pp) REVERT: F 629 TYR cc_start: 0.8502 (m-80) cc_final: 0.8143 (m-80) REVERT: F 648 LEU cc_start: 0.8911 (mt) cc_final: 0.8660 (mt) REVERT: F 669 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8056 (ptp-110) REVERT: F 1059 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8604 (tm-30) REVERT: F 1071 PHE cc_start: 0.8360 (t80) cc_final: 0.8114 (t80) outliers start: 33 outliers final: 26 residues processed: 116 average time/residue: 0.3096 time to fit residues: 57.1610 Evaluate side-chains 112 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE 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 608 LEU Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 724 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 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 403 THR Chi-restraints excluded: chain F residue 432 ARG Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 669 ARG 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 996 PHE Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1043 VAL Chi-restraints excluded: chain F residue 1066 LEU Chi-restraints excluded: chain F residue 1099 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 201 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 181 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.110417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073285 restraints weight = 48688.906| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.53 r_work: 0.3042 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4112 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= 0.159 Angle : 0.481 8.497 25767 Z= 0.249 Chirality : 0.038 0.158 2847 Planarity : 0.003 0.034 3349 Dihedral : 4.259 39.699 2536 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.26 % Favored : 97.57 % Rotamer: Outliers : 1.41 % Allowed : 10.85 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2300 helix: 2.48 (0.15), residues: 1154 sheet: -0.60 (0.31), residues: 313 loop : -0.13 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1186 HIS 0.005 0.001 HIS A 238 PHE 0.023 0.001 PHE F 362 TYR 0.013 0.001 TYR A1081 ARG 0.002 0.000 ARG F 190 ********************** 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 125 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 2.291 Fit side-chains revert: symmetry clash REVERT: A 629 TYR cc_start: 0.8317 (m-80) cc_final: 0.8107 (m-80) REVERT: A 648 LEU cc_start: 0.8939 (mt) cc_final: 0.8608 (mt) REVERT: A 708 MET cc_start: 0.5609 (mpp) cc_final: 0.5322 (mpp) REVERT: A 952 ASP cc_start: 0.9444 (m-30) cc_final: 0.9119 (m-30) REVERT: A 1023 TYR cc_start: 0.8842 (m-80) cc_final: 0.8172 (m-80) REVERT: F 2 ASN cc_start: 0.8453 (m-40) cc_final: 0.7606 (p0) REVERT: F 158 ASN cc_start: 0.8782 (t0) cc_final: 0.8491 (t0) REVERT: F 331 GLU cc_start: 0.8436 (tp30) cc_final: 0.8132 (tp30) REVERT: F 432 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8190 (mtp180) REVERT: F 629 TYR cc_start: 0.8431 (m-80) cc_final: 0.8097 (m-80) REVERT: F 648 LEU cc_start: 0.8878 (mt) cc_final: 0.8571 (mt) REVERT: F 669 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8046 (ptp-110) REVERT: F 1059 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8600 (tm-30) outliers start: 29 outliers final: 20 residues processed: 121 average time/residue: 0.3373 time to fit residues: 63.9331 Evaluate side-chains 113 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE 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 608 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 A residue 999 PHE 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 432 ARG Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain F residue 669 ARG Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 947 ILE Chi-restraints excluded: chain F residue 996 PHE 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 140 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 238 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.109649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071783 restraints weight = 48792.485| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.84 r_work: 0.3020 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19065 Z= 0.206 Angle : 0.502 9.131 25767 Z= 0.258 Chirality : 0.039 0.161 2847 Planarity : 0.003 0.032 3349 Dihedral : 4.254 37.559 2536 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.70 % Favored : 97.13 % Rotamer: Outliers : 1.26 % Allowed : 11.24 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2300 helix: 2.48 (0.15), residues: 1154 sheet: -0.50 (0.32), residues: 302 loop : -0.16 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1186 HIS 0.005 0.001 HIS A 238 PHE 0.030 0.001 PHE A1071 TYR 0.013 0.001 TYR A1081 ARG 0.004 0.000 ARG F 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9086.79 seconds wall clock time: 162 minutes 28.40 seconds (9748.40 seconds total)