Starting phenix.real_space_refine on Fri Feb 6 20:01:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mt8_48603/02_2026/9mt8_48603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mt8_48603/02_2026/9mt8_48603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mt8_48603/02_2026/9mt8_48603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mt8_48603/02_2026/9mt8_48603.map" model { file = "/net/cci-nas-00/data/ceres_data/9mt8_48603/02_2026/9mt8_48603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mt8_48603/02_2026/9mt8_48603.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.025 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 148 5.16 5 C 17608 2.51 5 N 4748 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27188 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 6796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6796 Classifications: {'peptide': 855} Link IDs: {'PTRANS': 35, 'TRANS': 819} Chain breaks: 9 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, B, C Time building chain proxies: 7.20, per 1000 atoms: 0.26 Number of scatterers: 27188 At special positions: 0 Unit cell: (129.15, 129.15, 152.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 148 16.00 O 4680 8.00 N 4748 7.00 C 17608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 12 sheets defined 73.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'D' and resid 98 through 108 Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 161 through 176 removed outlier: 3.541A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 4.778A pdb=" N PHE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 removed outlier: 4.189A pdb=" N THR D 267 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 268' Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 307 through 315 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 4.107A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.717A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 584 through 601 Processing helix chain 'D' and resid 605 through 632 Processing helix chain 'D' and resid 634 through 644 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 removed outlier: 3.680A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 776 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 861 Processing helix chain 'D' and resid 862 through 884 removed outlier: 3.524A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 905 removed outlier: 3.700A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 916 through 924 removed outlier: 3.743A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 974 removed outlier: 4.949A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.617A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1031 Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 5.474A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D1056 " --> pdb=" O GLY D1052 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1090 removed outlier: 4.137A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 Processing helix chain 'D' and resid 1143 through 1177 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.541A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 4.778A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 4.189A pdb=" N THR A 267 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 268' Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.107A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.717A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 584 through 601 Processing helix chain 'A' and resid 605 through 632 Processing helix chain 'A' and resid 634 through 644 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.680A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.524A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.700A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.743A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.949A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.617A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1031 Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 5.474A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1090 removed outlier: 4.137A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 Processing helix chain 'A' and resid 1143 through 1177 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.541A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 4.778A pdb=" N PHE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 removed outlier: 4.189A pdb=" N THR B 267 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 268' Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 4.107A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.717A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 584 through 601 Processing helix chain 'B' and resid 605 through 632 Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 removed outlier: 3.680A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 861 Processing helix chain 'B' and resid 862 through 884 removed outlier: 3.524A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 905 removed outlier: 3.700A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 916 through 924 removed outlier: 3.743A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 974 removed outlier: 4.949A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.617A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1031 Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 5.474A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1090 removed outlier: 4.137A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 Processing helix chain 'B' and resid 1143 through 1177 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 161 through 176 removed outlier: 3.541A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 4.779A pdb=" N PHE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 4.189A pdb=" N THR C 267 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 4.107A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 502 through 511 removed outlier: 3.716A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 584 through 601 Processing helix chain 'C' and resid 605 through 632 Processing helix chain 'C' and resid 634 through 644 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 removed outlier: 3.676A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 861 Processing helix chain 'C' and resid 862 through 884 removed outlier: 3.527A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 905 removed outlier: 3.700A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 916 through 924 removed outlier: 3.743A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 974 removed outlier: 4.951A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.615A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 5.474A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C1056 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1090 removed outlier: 4.137A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 Processing helix chain 'C' and resid 1143 through 1177 Processing sheet with id=AA1, first strand: chain 'D' and resid 231 through 234 removed outlier: 3.976A pdb=" N ALA D 231 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE D 278 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU D 122 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 645 through 646 removed outlier: 3.555A pdb=" N CYS D 646 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 652 " --> pdb=" O CYS D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 989 through 990 removed outlier: 3.820A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 234 removed outlier: 3.976A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 278 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 122 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 645 through 646 removed outlier: 3.555A pdb=" N CYS A 646 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 652 " --> pdb=" O CYS A 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 989 through 990 removed outlier: 3.820A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.976A pdb=" N ALA B 231 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 278 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU B 122 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 645 through 646 removed outlier: 3.555A pdb=" N CYS B 646 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 652 " --> pdb=" O CYS B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 989 through 990 removed outlier: 3.820A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 231 through 234 removed outlier: 3.976A pdb=" N ALA C 231 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE C 278 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU C 122 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 645 through 646 removed outlier: 3.556A pdb=" N CYS C 646 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 652 " --> pdb=" O CYS C 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 3.821A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) 1773 hydrogen bonds defined for protein. 5187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8756 1.34 - 1.46: 5913 1.46 - 1.58: 12903 1.58 - 1.69: 0 1.69 - 1.81: 232 Bond restraints: 27804 Sorted by residual: bond pdb=" N PRO C 809 " pdb=" CA PRO C 809 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.07e+00 bond pdb=" N PRO B 809 " pdb=" CA PRO B 809 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 1.01e+00 bond pdb=" N PRO A 809 " pdb=" CA PRO A 809 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 1.01e+00 bond pdb=" N PRO D 809 " pdb=" CA PRO D 809 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 1.01e+00 bond pdb=" CG LEU D 626 " pdb=" CD2 LEU D 626 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.29e-01 ... (remaining 27799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 37017 1.35 - 2.71: 519 2.71 - 4.06: 96 4.06 - 5.41: 20 5.41 - 6.77: 12 Bond angle restraints: 37664 Sorted by residual: angle pdb=" N PRO B1077 " pdb=" CA PRO B1077 " pdb=" C PRO B1077 " ideal model delta sigma weight residual 110.70 113.83 -3.13 1.22e+00 6.72e-01 6.57e+00 angle pdb=" N PRO D1077 " pdb=" CA PRO D1077 " pdb=" C PRO D1077 " ideal model delta sigma weight residual 110.70 113.83 -3.13 1.22e+00 6.72e-01 6.57e+00 angle pdb=" N PRO A1077 " pdb=" CA PRO A1077 " pdb=" C PRO A1077 " ideal model delta sigma weight residual 110.70 113.83 -3.13 1.22e+00 6.72e-01 6.57e+00 angle pdb=" N PRO C1077 " pdb=" CA PRO C1077 " pdb=" C PRO C1077 " ideal model delta sigma weight residual 110.70 113.79 -3.09 1.22e+00 6.72e-01 6.42e+00 angle pdb=" N PRO A 700 " pdb=" CA PRO A 700 " pdb=" C PRO A 700 " ideal model delta sigma weight residual 110.70 113.53 -2.83 1.22e+00 6.72e-01 5.39e+00 ... (remaining 37659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 15351 15.07 - 30.14: 817 30.14 - 45.21: 212 45.21 - 60.28: 32 60.28 - 75.35: 12 Dihedral angle restraints: 16424 sinusoidal: 6604 harmonic: 9820 Sorted by residual: dihedral pdb=" N ARG B1072 " pdb=" CA ARG B1072 " pdb=" CB ARG B1072 " pdb=" CG ARG B1072 " ideal model delta sinusoidal sigma weight residual -60.00 -119.46 59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG A1072 " pdb=" CA ARG A1072 " pdb=" CB ARG A1072 " pdb=" CG ARG A1072 " ideal model delta sinusoidal sigma weight residual -60.00 -119.46 59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG D1072 " pdb=" CA ARG D1072 " pdb=" CB ARG D1072 " pdb=" CG ARG D1072 " ideal model delta sinusoidal sigma weight residual -60.00 -119.46 59.46 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 16421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2623 0.026 - 0.053: 1096 0.053 - 0.079: 346 0.079 - 0.106: 147 0.106 - 0.132: 36 Chirality restraints: 4248 Sorted by residual: chirality pdb=" CA ILE B 271 " pdb=" N ILE B 271 " pdb=" C ILE B 271 " pdb=" CB ILE B 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE D 271 " pdb=" N ILE D 271 " pdb=" C ILE D 271 " pdb=" CB ILE D 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 4245 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1076 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO C1077 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C1077 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C1077 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A1077 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1076 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO B1077 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B1077 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1077 " 0.022 5.00e-02 4.00e+02 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5302 2.78 - 3.31: 26927 3.31 - 3.84: 44364 3.84 - 4.37: 50433 4.37 - 4.90: 89420 Nonbonded interactions: 216446 Sorted by model distance: nonbonded pdb=" OE1 GLN C 831 " pdb="CA CA C2001 " model vdw 2.251 2.510 nonbonded pdb=" OE1 GLN B 831 " pdb="CA CA B2001 " model vdw 2.251 2.510 nonbonded pdb=" OE1 GLN D 831 " pdb="CA CA D2001 " model vdw 2.251 2.510 nonbonded pdb=" OE1 GLN A 831 " pdb="CA CA A2001 " model vdw 2.251 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.407 2.510 ... (remaining 216441 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: 0.09 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.900 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: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.003 0.028 27804 Z= 0.126 Angle : 0.450 6.767 37664 Z= 0.243 Chirality : 0.035 0.132 4248 Planarity : 0.004 0.041 4728 Dihedral : 10.324 75.349 10072 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.39 % Allowed : 3.61 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.15), residues: 3340 helix: 2.06 (0.11), residues: 2348 sheet: -0.90 (0.40), residues: 164 loop : -0.19 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.008 0.001 TYR D 968 PHE 0.010 0.001 PHE B1132 TRP 0.012 0.001 TRP C1124 HIS 0.003 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00281 (27804) covalent geometry : angle 0.45048 (37664) hydrogen bonds : bond 0.13693 ( 1773) hydrogen bonds : angle 4.68805 ( 5187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.984 Fit side-chains REVERT: D 473 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6461 (tp) REVERT: D 629 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7851 (mm-30) REVERT: D 687 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7846 (p) REVERT: D 869 LEU cc_start: 0.8024 (mt) cc_final: 0.7707 (mt) REVERT: A 458 MET cc_start: 0.8004 (mmm) cc_final: 0.7747 (ttt) REVERT: A 473 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6602 (tp) REVERT: A 629 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8026 (mm-30) REVERT: A 687 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7907 (p) REVERT: A 869 LEU cc_start: 0.8039 (mt) cc_final: 0.7721 (mt) REVERT: A 1160 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7507 (pttt) REVERT: B 473 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6463 (tp) REVERT: B 629 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 687 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7821 (p) REVERT: B 869 LEU cc_start: 0.7985 (mt) cc_final: 0.7672 (mt) REVERT: C 473 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6451 (tp) REVERT: C 629 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7774 (mm-30) REVERT: C 687 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7831 (p) REVERT: C 869 LEU cc_start: 0.7999 (mt) cc_final: 0.7688 (mt) outliers start: 40 outliers final: 12 residues processed: 312 average time/residue: 0.1737 time to fit residues: 87.6443 Evaluate side-chains 232 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 860 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.6980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 ASN D 908 HIS D 973 GLN D1002 HIS D1014 GLN D1128 HIS A 247 ASN A 908 HIS A 973 GLN A1002 HIS A1014 GLN A1128 HIS B 247 ASN B 908 HIS B 973 GLN B1002 HIS B1014 GLN B1128 HIS C 159 HIS C 247 ASN C 908 HIS C 973 GLN C1002 HIS C1014 GLN C1128 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.202568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.159638 restraints weight = 35323.352| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 4.00 r_work: 0.3379 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27804 Z= 0.258 Angle : 0.595 7.426 37664 Z= 0.309 Chirality : 0.040 0.141 4248 Planarity : 0.005 0.058 4728 Dihedral : 4.362 37.727 3764 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.66 % Allowed : 5.31 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3340 helix: 1.79 (0.11), residues: 2380 sheet: -0.89 (0.38), residues: 160 loop : -0.08 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.011 0.002 TYR C1015 PHE 0.020 0.002 PHE B1109 TRP 0.018 0.002 TRP C 680 HIS 0.006 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00641 (27804) covalent geometry : angle 0.59468 (37664) hydrogen bonds : bond 0.05488 ( 1773) hydrogen bonds : angle 4.07707 ( 5187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.942 Fit side-chains REVERT: D 430 MET cc_start: 0.7201 (tpp) cc_final: 0.6915 (mmm) REVERT: D 472 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6366 (tt) REVERT: D 473 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6467 (tp) REVERT: D 687 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 430 MET cc_start: 0.7198 (tpp) cc_final: 0.6907 (mmm) REVERT: A 472 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6379 (tt) REVERT: A 473 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6469 (tp) REVERT: A 687 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 1160 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7584 (pttt) REVERT: B 430 MET cc_start: 0.7202 (tpp) cc_final: 0.6913 (mmm) REVERT: B 472 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6379 (tt) REVERT: B 473 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6478 (tp) REVERT: B 687 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7979 (p) REVERT: C 430 MET cc_start: 0.7207 (tpp) cc_final: 0.6926 (mmm) REVERT: C 472 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6374 (tt) REVERT: C 473 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6468 (tp) REVERT: C 687 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7986 (p) outliers start: 48 outliers final: 23 residues processed: 233 average time/residue: 0.1717 time to fit residues: 64.4022 Evaluate side-chains 216 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1160 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 194 optimal weight: 6.9990 chunk 175 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 10 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 327 optimal weight: 0.7980 chunk 105 optimal weight: 30.0000 chunk 251 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS D1061 GLN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1061 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1061 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS C1053 ASN C1061 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.202228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.158636 restraints weight = 35343.899| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 4.11 r_work: 0.3366 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27804 Z= 0.246 Angle : 0.575 7.368 37664 Z= 0.298 Chirality : 0.040 0.143 4248 Planarity : 0.005 0.052 4728 Dihedral : 4.378 38.936 3760 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.98 % Allowed : 7.07 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.15), residues: 3340 helix: 1.71 (0.11), residues: 2372 sheet: -0.52 (0.40), residues: 140 loop : -0.20 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 706 TYR 0.012 0.002 TYR C1015 PHE 0.019 0.002 PHE C1109 TRP 0.020 0.002 TRP D 680 HIS 0.009 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00610 (27804) covalent geometry : angle 0.57458 (37664) hydrogen bonds : bond 0.05293 ( 1773) hydrogen bonds : angle 4.05100 ( 5187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.072 Fit side-chains REVERT: D 472 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6453 (tt) REVERT: D 473 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6431 (tp) REVERT: D 687 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7946 (p) REVERT: A 472 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6461 (tt) REVERT: A 473 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6434 (tp) REVERT: A 687 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7946 (p) REVERT: B 472 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6452 (tt) REVERT: B 473 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6443 (tp) REVERT: B 687 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7949 (p) REVERT: C 472 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6444 (tt) REVERT: C 473 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6436 (tp) REVERT: C 687 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7935 (p) outliers start: 57 outliers final: 27 residues processed: 240 average time/residue: 0.1654 time to fit residues: 64.1020 Evaluate side-chains 211 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 186 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 262 optimal weight: 30.0000 chunk 242 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS D1061 GLN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1061 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1061 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.203282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.158758 restraints weight = 35272.417| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.85 r_work: 0.3419 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27804 Z= 0.179 Angle : 0.510 7.009 37664 Z= 0.265 Chirality : 0.037 0.143 4248 Planarity : 0.004 0.049 4728 Dihedral : 4.252 38.408 3756 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.46 % Allowed : 8.04 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.15), residues: 3340 helix: 1.85 (0.11), residues: 2384 sheet: -0.51 (0.38), residues: 140 loop : -0.08 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 706 TYR 0.010 0.001 TYR D 256 PHE 0.013 0.002 PHE D1132 TRP 0.017 0.002 TRP D 680 HIS 0.009 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00436 (27804) covalent geometry : angle 0.50957 (37664) hydrogen bonds : bond 0.04640 ( 1773) hydrogen bonds : angle 3.86228 ( 5187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 1.029 Fit side-chains REVERT: D 472 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6207 (tt) REVERT: D 473 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6415 (tp) REVERT: A 472 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6215 (tt) REVERT: A 473 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6409 (tp) REVERT: A 687 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 472 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6222 (tt) REVERT: B 473 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6415 (tp) REVERT: B 687 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.8021 (p) REVERT: C 472 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6230 (tt) REVERT: C 473 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6425 (tp) outliers start: 71 outliers final: 35 residues processed: 247 average time/residue: 0.1698 time to fit residues: 67.6984 Evaluate side-chains 215 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 280 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS C1053 ASN C1061 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.202097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158545 restraints weight = 35313.969| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 4.05 r_work: 0.3395 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27804 Z= 0.196 Angle : 0.529 7.132 37664 Z= 0.273 Chirality : 0.038 0.142 4248 Planarity : 0.004 0.050 4728 Dihedral : 4.176 37.504 3754 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.15 % Allowed : 8.84 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.15), residues: 3340 helix: 1.92 (0.11), residues: 2364 sheet: -0.64 (0.37), residues: 140 loop : 0.05 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 706 TYR 0.014 0.001 TYR A 859 PHE 0.015 0.002 PHE D1132 TRP 0.018 0.002 TRP B 680 HIS 0.009 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00486 (27804) covalent geometry : angle 0.52877 (37664) hydrogen bonds : bond 0.04743 ( 1773) hydrogen bonds : angle 3.85243 ( 5187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 1.059 Fit side-chains REVERT: D 472 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6294 (tt) REVERT: D 473 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6430 (tp) REVERT: D 706 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7271 (mtm-85) REVERT: A 472 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6305 (tt) REVERT: A 473 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6444 (tp) REVERT: A 687 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7997 (p) REVERT: A 706 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7254 (mtm-85) REVERT: B 472 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6315 (tt) REVERT: B 473 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6438 (tp) REVERT: B 687 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7996 (p) REVERT: B 706 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7247 (mtm-85) REVERT: C 472 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6314 (tt) REVERT: C 473 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6447 (tp) REVERT: C 706 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7264 (mtm-85) outliers start: 62 outliers final: 37 residues processed: 236 average time/residue: 0.1648 time to fit residues: 64.2177 Evaluate side-chains 214 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 308 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 249 optimal weight: 0.0470 chunk 203 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS C1053 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.203267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159306 restraints weight = 35513.203| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 4.15 r_work: 0.3406 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27804 Z= 0.150 Angle : 0.482 6.885 37664 Z= 0.250 Chirality : 0.036 0.147 4248 Planarity : 0.004 0.048 4728 Dihedral : 4.063 35.973 3754 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.15 % Allowed : 9.26 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.15), residues: 3340 helix: 2.10 (0.11), residues: 2368 sheet: -0.62 (0.35), residues: 148 loop : 0.11 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 706 TYR 0.010 0.001 TYR D 256 PHE 0.012 0.001 PHE D1132 TRP 0.015 0.001 TRP D 680 HIS 0.009 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00365 (27804) covalent geometry : angle 0.48197 (37664) hydrogen bonds : bond 0.04302 ( 1773) hydrogen bonds : angle 3.71590 ( 5187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 1.092 Fit side-chains REVERT: D 472 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6174 (tt) REVERT: D 473 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6465 (tp) REVERT: D 706 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7361 (mtm-85) REVERT: A 472 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6172 (tt) REVERT: A 473 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6474 (tp) REVERT: A 706 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7365 (mtm-85) REVERT: B 472 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6173 (tt) REVERT: B 473 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6467 (tp) REVERT: B 706 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7355 (mtm-85) REVERT: C 472 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6168 (tt) REVERT: C 473 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6474 (tp) REVERT: C 706 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7354 (mtm-85) outliers start: 62 outliers final: 39 residues processed: 231 average time/residue: 0.1636 time to fit residues: 61.8591 Evaluate side-chains 214 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 259 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1014 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.203428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159405 restraints weight = 35352.716| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.08 r_work: 0.3419 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27804 Z= 0.150 Angle : 0.481 6.901 37664 Z= 0.250 Chirality : 0.036 0.147 4248 Planarity : 0.004 0.048 4728 Dihedral : 4.052 37.466 3752 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.18 % Allowed : 9.92 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.15), residues: 3340 helix: 2.13 (0.11), residues: 2372 sheet: -0.58 (0.34), residues: 148 loop : 0.13 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 706 TYR 0.009 0.001 TYR D 256 PHE 0.013 0.001 PHE A1132 TRP 0.015 0.001 TRP C 680 HIS 0.009 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00364 (27804) covalent geometry : angle 0.48112 (37664) hydrogen bonds : bond 0.04243 ( 1773) hydrogen bonds : angle 3.68480 ( 5187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 1.022 Fit side-chains REVERT: D 472 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6283 (tt) REVERT: D 473 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6538 (tp) REVERT: D 706 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7258 (mtm-85) REVERT: A 472 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6291 (tt) REVERT: A 473 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6549 (tp) REVERT: A 614 ASP cc_start: 0.7833 (t0) cc_final: 0.7617 (t0) REVERT: A 706 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7239 (mtm-85) REVERT: B 472 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6286 (tt) REVERT: B 473 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6538 (tp) REVERT: B 614 ASP cc_start: 0.7862 (t0) cc_final: 0.7640 (t0) REVERT: B 706 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7243 (mtm-85) REVERT: C 472 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6271 (tt) REVERT: C 473 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6540 (tp) REVERT: C 614 ASP cc_start: 0.7843 (t0) cc_final: 0.7625 (t0) REVERT: C 706 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7235 (mtm-85) outliers start: 63 outliers final: 37 residues processed: 239 average time/residue: 0.1642 time to fit residues: 63.9718 Evaluate side-chains 219 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 280 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 288 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 271 optimal weight: 30.0000 chunk 168 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS D1053 ASN ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1014 GLN B1053 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS C1053 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.201025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156783 restraints weight = 35506.711| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.99 r_work: 0.3374 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 27804 Z= 0.249 Angle : 0.576 7.369 37664 Z= 0.300 Chirality : 0.040 0.149 4248 Planarity : 0.005 0.053 4728 Dihedral : 4.247 38.306 3752 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.91 % Allowed : 10.54 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3340 helix: 1.82 (0.11), residues: 2368 sheet: -0.48 (0.35), residues: 148 loop : -0.03 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 442 TYR 0.012 0.001 TYR C1015 PHE 0.018 0.002 PHE D1132 TRP 0.020 0.002 TRP C 680 HIS 0.010 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00620 (27804) covalent geometry : angle 0.57593 (37664) hydrogen bonds : bond 0.05116 ( 1773) hydrogen bonds : angle 3.93536 ( 5187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.852 Fit side-chains REVERT: D 472 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6380 (tt) REVERT: D 473 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6513 (tp) REVERT: D 706 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7298 (mtm-85) REVERT: A 472 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6380 (tt) REVERT: A 473 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6521 (tp) REVERT: A 614 ASP cc_start: 0.7899 (t0) cc_final: 0.7669 (t0) REVERT: A 706 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7292 (mtm-85) REVERT: B 472 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6374 (tt) REVERT: B 473 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6511 (tp) REVERT: B 614 ASP cc_start: 0.7918 (t0) cc_final: 0.7687 (t0) REVERT: B 706 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7278 (mtm-85) REVERT: C 472 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6375 (tt) REVERT: C 473 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6523 (tp) REVERT: C 614 ASP cc_start: 0.7907 (t0) cc_final: 0.7677 (t0) REVERT: C 706 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7286 (mtm-85) outliers start: 55 outliers final: 35 residues processed: 242 average time/residue: 0.1763 time to fit residues: 67.5350 Evaluate side-chains 237 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1002 HIS Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1002 HIS Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 303 optimal weight: 0.7980 chunk 269 optimal weight: 10.0000 chunk 232 optimal weight: 0.3980 chunk 287 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 71 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 271 optimal weight: 30.0000 chunk 78 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS D1061 GLN A 135 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1061 GLN B 135 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1061 GLN C 135 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS C1061 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.203887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.160461 restraints weight = 35420.219| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 4.00 r_work: 0.3418 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27804 Z= 0.120 Angle : 0.483 6.694 37664 Z= 0.254 Chirality : 0.036 0.155 4248 Planarity : 0.004 0.046 4728 Dihedral : 4.050 37.588 3752 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.63 % Allowed : 10.96 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.15), residues: 3340 helix: 2.13 (0.11), residues: 2372 sheet: -0.52 (0.35), residues: 148 loop : 0.09 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 706 TYR 0.014 0.001 TYR C 859 PHE 0.011 0.001 PHE C1132 TRP 0.015 0.001 TRP C1058 HIS 0.017 0.001 HIS B1002 Details of bonding type rmsd covalent geometry : bond 0.00279 (27804) covalent geometry : angle 0.48338 (37664) hydrogen bonds : bond 0.04144 ( 1773) hydrogen bonds : angle 3.74342 ( 5187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.908 Fit side-chains REVERT: D 472 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6173 (tt) REVERT: D 473 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6487 (tp) REVERT: D 509 MET cc_start: 0.8231 (mtp) cc_final: 0.7934 (mtm) REVERT: D 706 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7401 (mtm-85) REVERT: A 472 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6182 (tt) REVERT: A 473 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6446 (tp) REVERT: A 509 MET cc_start: 0.8230 (mtp) cc_final: 0.7931 (mtm) REVERT: A 706 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7399 (mtm-85) REVERT: B 472 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6178 (tt) REVERT: B 473 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6480 (tp) REVERT: B 509 MET cc_start: 0.8232 (mtp) cc_final: 0.7934 (mtm) REVERT: B 706 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7382 (mtm-85) REVERT: C 472 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6170 (tt) REVERT: C 473 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6480 (tp) REVERT: C 509 MET cc_start: 0.8238 (mtp) cc_final: 0.7938 (mtm) REVERT: C 706 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7387 (mtm-85) outliers start: 47 outliers final: 23 residues processed: 237 average time/residue: 0.1692 time to fit residues: 64.3083 Evaluate side-chains 211 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 188 optimal weight: 40.0000 chunk 279 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 322 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS D1014 GLN D1061 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS A1014 GLN A1061 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1014 GLN B1061 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS C1014 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.204392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.160838 restraints weight = 35439.422| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 4.13 r_work: 0.3440 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27804 Z= 0.122 Angle : 0.479 6.754 37664 Z= 0.251 Chirality : 0.036 0.204 4248 Planarity : 0.004 0.046 4728 Dihedral : 4.001 37.178 3752 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.35 % Allowed : 11.48 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.15), residues: 3340 helix: 2.26 (0.11), residues: 2372 sheet: -0.52 (0.35), residues: 148 loop : 0.14 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.010 0.001 TYR D 818 PHE 0.011 0.001 PHE C1132 TRP 0.013 0.001 TRP B 680 HIS 0.010 0.001 HIS B1002 Details of bonding type rmsd covalent geometry : bond 0.00288 (27804) covalent geometry : angle 0.47890 (37664) hydrogen bonds : bond 0.03928 ( 1773) hydrogen bonds : angle 3.67757 ( 5187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 472 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6292 (tt) REVERT: D 473 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6615 (tp) REVERT: D 509 MET cc_start: 0.8086 (mtp) cc_final: 0.7800 (mtm) REVERT: D 576 MET cc_start: 0.7727 (mmt) cc_final: 0.7509 (mmm) REVERT: D 622 MET cc_start: 0.8686 (mtm) cc_final: 0.8462 (mtp) REVERT: D 706 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7235 (mtm-85) REVERT: A 472 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6306 (tt) REVERT: A 473 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6621 (tp) REVERT: A 509 MET cc_start: 0.8094 (mtp) cc_final: 0.7805 (mtm) REVERT: A 576 MET cc_start: 0.7726 (mmt) cc_final: 0.7505 (mmm) REVERT: A 622 MET cc_start: 0.8704 (mtm) cc_final: 0.8476 (mtp) REVERT: A 706 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7240 (mtm-85) REVERT: B 472 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6292 (tt) REVERT: B 473 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6617 (tp) REVERT: B 509 MET cc_start: 0.8102 (mtp) cc_final: 0.7813 (mtm) REVERT: B 576 MET cc_start: 0.7716 (mmt) cc_final: 0.7495 (mmm) REVERT: B 622 MET cc_start: 0.8709 (mtm) cc_final: 0.8483 (mtp) REVERT: B 706 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7235 (mtm-85) REVERT: C 472 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6284 (tt) REVERT: C 473 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6613 (tp) REVERT: C 509 MET cc_start: 0.8101 (mtp) cc_final: 0.7815 (mtm) REVERT: C 576 MET cc_start: 0.7726 (mmt) cc_final: 0.7508 (mmm) REVERT: C 622 MET cc_start: 0.8684 (mtm) cc_final: 0.8458 (mtp) REVERT: C 706 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7220 (mtm-85) outliers start: 39 outliers final: 23 residues processed: 227 average time/residue: 0.1818 time to fit residues: 65.6181 Evaluate side-chains 215 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 1160 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1160 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 1160 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 333 optimal weight: 0.0020 chunk 31 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 128 optimal weight: 0.0770 overall best weight: 0.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 HIS ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.206144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163360 restraints weight = 35317.563| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.90 r_work: 0.3463 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 27804 Z= 0.103 Angle : 0.461 6.579 37664 Z= 0.240 Chirality : 0.036 0.215 4248 Planarity : 0.004 0.047 4728 Dihedral : 3.798 35.162 3752 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.90 % Allowed : 11.82 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.15), residues: 3340 helix: 2.42 (0.11), residues: 2380 sheet: -0.47 (0.35), residues: 148 loop : 0.16 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 706 TYR 0.009 0.001 TYR D 256 PHE 0.017 0.001 PHE D 910 TRP 0.014 0.001 TRP B1058 HIS 0.009 0.001 HIS B1002 Details of bonding type rmsd covalent geometry : bond 0.00235 (27804) covalent geometry : angle 0.46112 (37664) hydrogen bonds : bond 0.03585 ( 1773) hydrogen bonds : angle 3.59385 ( 5187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.32 seconds wall clock time: 97 minutes 52.28 seconds (5872.28 seconds total)