Starting phenix.real_space_refine on Sat Feb 7 08:58:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mta_48604/02_2026/9mta_48604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mta_48604/02_2026/9mta_48604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mta_48604/02_2026/9mta_48604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mta_48604/02_2026/9mta_48604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mta_48604/02_2026/9mta_48604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mta_48604/02_2026/9mta_48604.map" } resolution = 2.78 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= 0.006 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20132 2.51 5 N 5488 2.21 5 O 5440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s 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: 31228 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7807 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 43, 'TRANS': 937} Chain breaks: 9 Restraints were copied for chains: B, C, D Time building chain proxies: 9.69, per 1000 atoms: 0.31 Number of scatterers: 31228 At special positions: 0 Unit cell: (149.814, 149.814, 160.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 5440 8.00 N 5488 7.00 C 20132 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 12 sheets defined 69.9% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.821A pdb=" N ILE A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.932A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.895A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.509A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.572A pdb=" N ASP A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.653A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.052A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 405 through 415 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 512 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 removed outlier: 3.807A pdb=" N ARG A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 644 Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.578A pdb=" N GLY A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.719A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) 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: 3.602A 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 835 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.969A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 904 removed outlier: 3.541A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 4.358A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.714A pdb=" N ILE A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.952A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.531A pdb=" N GLN A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' 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 1033 Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 5.406A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1087 removed outlier: 4.291A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 4.248A 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 1176 removed outlier: 3.739A pdb=" N GLU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.821A pdb=" N ILE B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.932A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.895A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.509A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.572A pdb=" N ASP B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.653A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.052A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 395 through 404 Processing helix chain 'B' and resid 405 through 415 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 512 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 removed outlier: 3.807A pdb=" N ARG B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.578A pdb=" N GLY B 650 " --> pdb=" O PRO B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.719A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) 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: 3.602A 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 835 Processing helix chain 'B' and resid 852 through 862 removed outlier: 3.969A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 904 removed outlier: 3.541A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 removed outlier: 4.358A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 916 through 924 removed outlier: 3.714A pdb=" N ILE B 922 " --> pdb=" O PRO B 918 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 973 removed outlier: 4.952A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.531A pdb=" N GLN B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' 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 1033 Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 5.406A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1087 removed outlier: 4.291A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 4.248A 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 1176 removed outlier: 3.739A pdb=" N GLU B1176 " --> pdb=" O LEU B1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.821A pdb=" N ILE C 14 " --> pdb=" O TRP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.932A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.895A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.509A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 318 removed outlier: 3.572A pdb=" N ASP C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.653A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 4.052A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 386 Processing helix chain 'C' and resid 395 through 404 Processing helix chain 'C' and resid 405 through 415 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 512 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 removed outlier: 3.807A pdb=" N ARG C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 644 Processing helix chain 'C' and resid 646 through 650 removed outlier: 3.578A pdb=" N GLY C 650 " --> pdb=" O PRO C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.719A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) 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: 3.602A 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 835 Processing helix chain 'C' and resid 852 through 862 removed outlier: 3.969A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 904 removed outlier: 3.541A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 removed outlier: 4.358A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 916 through 924 removed outlier: 3.714A pdb=" N ILE C 922 " --> pdb=" O PRO C 918 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 973 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: 3.531A pdb=" N GLN C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' 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 1033 Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 5.406A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1087 removed outlier: 4.291A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 4.248A 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 1176 removed outlier: 3.739A pdb=" N GLU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.821A pdb=" N ILE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.932A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 178 removed outlier: 3.895A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.508A pdb=" N LEU D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.572A pdb=" N ASP D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.654A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 removed outlier: 4.052A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 395 through 404 Processing helix chain 'D' and resid 405 through 415 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 512 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 removed outlier: 3.808A pdb=" N ARG D 601 " --> pdb=" O ARG D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 644 Processing helix chain 'D' and resid 646 through 650 removed outlier: 3.546A pdb=" N GLY D 650 " --> pdb=" O PRO D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.719A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) 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: 3.602A 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 835 Processing helix chain 'D' and resid 852 through 862 removed outlier: 3.969A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 904 removed outlier: 3.541A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 removed outlier: 4.358A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 916 through 924 removed outlier: 3.714A pdb=" N ILE D 922 " --> pdb=" O PRO D 918 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 973 removed outlier: 4.952A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.531A pdb=" N GLN D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' 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 1033 Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 5.406A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1087 removed outlier: 4.292A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 4.248A 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 1176 removed outlier: 3.739A pdb=" N GLU D1176 " --> pdb=" O LEU D1172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.856A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 989 through 990 removed outlier: 3.912A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 20 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.856A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 989 through 990 removed outlier: 3.912A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 16 through 20 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.856A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 removed outlier: 3.912A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 20 Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.856A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 989 through 990 removed outlier: 3.912A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1916 hydrogen bonds defined for protein. 5616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 3.78 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: 10140 1.34 - 1.46: 7213 1.46 - 1.58: 14343 1.58 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 31952 Sorted by residual: bond pdb=" C ARG D 953 " pdb=" O ARG D 953 " ideal model delta sigma weight residual 1.235 1.242 -0.007 4.70e-03 4.53e+04 2.39e+00 bond pdb=" CG LEU C 626 " pdb=" CD2 LEU C 626 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CG LEU A 626 " pdb=" CD2 LEU A 626 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CG LEU B 626 " pdb=" CD2 LEU B 626 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CG LEU D 626 " pdb=" CD2 LEU D 626 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.77e-01 ... (remaining 31947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 42562 1.31 - 2.62: 539 2.62 - 3.92: 155 3.92 - 5.23: 24 5.23 - 6.54: 8 Bond angle restraints: 43288 Sorted by residual: angle pdb=" N PRO A1077 " pdb=" CA PRO A1077 " pdb=" C PRO A1077 " ideal model delta sigma weight residual 110.70 114.02 -3.32 1.22e+00 6.72e-01 7.43e+00 angle pdb=" N PRO B1077 " pdb=" CA PRO B1077 " pdb=" C PRO B1077 " ideal model delta sigma weight residual 110.70 114.02 -3.32 1.22e+00 6.72e-01 7.43e+00 angle pdb=" N PRO C1077 " pdb=" CA PRO C1077 " pdb=" C PRO C1077 " ideal model delta sigma weight residual 110.70 114.02 -3.32 1.22e+00 6.72e-01 7.43e+00 angle pdb=" N PRO D1077 " pdb=" CA PRO D1077 " pdb=" C PRO D1077 " ideal model delta sigma weight residual 110.70 113.96 -3.26 1.22e+00 6.72e-01 7.14e+00 angle pdb=" N PRO C 700 " pdb=" CA PRO C 700 " pdb=" C PRO C 700 " ideal model delta sigma weight residual 110.70 113.32 -2.62 1.22e+00 6.72e-01 4.60e+00 ... (remaining 43283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.89: 17639 13.89 - 27.78: 1009 27.78 - 41.68: 172 41.68 - 55.57: 80 55.57 - 69.46: 8 Dihedral angle restraints: 18908 sinusoidal: 7648 harmonic: 11260 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N PRO B 208 " pdb=" CA PRO B 208 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 18905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2884 0.025 - 0.049: 1237 0.049 - 0.074: 482 0.074 - 0.098: 173 0.098 - 0.123: 64 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ILE C 708 " pdb=" N ILE C 708 " pdb=" C ILE C 708 " pdb=" CB ILE C 708 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE A 708 " pdb=" N ILE A 708 " pdb=" C ILE A 708 " pdb=" CB ILE A 708 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE B 708 " pdb=" N ILE B 708 " pdb=" C ILE B 708 " pdb=" CB ILE B 708 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 4837 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1076 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO D1077 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D1077 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D1077 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1076 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO C1077 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C1077 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C1077 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1076 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO B1077 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B1077 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1077 " 0.028 5.00e-02 4.00e+02 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 17802 3.02 - 3.49: 31826 3.49 - 3.96: 50149 3.96 - 4.43: 59595 4.43 - 4.90: 93851 Nonbonded interactions: 253223 Sorted by model distance: nonbonded pdb=" N THR D 155 " pdb=" OG1 THR D 155 " model vdw 2.551 2.496 nonbonded pdb=" N THR B 155 " pdb=" OG1 THR B 155 " model vdw 2.552 2.496 nonbonded pdb=" N THR A 155 " pdb=" OG1 THR A 155 " model vdw 2.552 2.496 nonbonded pdb=" N THR C 155 " pdb=" OG1 THR C 155 " model vdw 2.552 2.496 nonbonded pdb=" C SER D 789 " pdb=" OG SER D 789 " model vdw 2.603 2.616 ... (remaining 253218 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.060 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.850 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.002 0.028 31952 Z= 0.106 Angle : 0.436 6.541 43288 Z= 0.234 Chirality : 0.034 0.123 4840 Planarity : 0.004 0.052 5476 Dihedral : 9.625 69.459 11628 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.48 % Allowed : 3.04 % Favored : 96.48 % 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: 1.70 (0.14), residues: 3844 helix: 1.87 (0.11), residues: 2448 sheet: -0.77 (0.30), residues: 264 loop : 0.07 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1138 TYR 0.007 0.001 TYR D 968 PHE 0.017 0.001 PHE B 423 TRP 0.014 0.001 TRP A1124 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00222 (31952) covalent geometry : angle 0.43554 (43288) hydrogen bonds : bond 0.12416 ( 1916) hydrogen bonds : angle 5.26650 ( 5616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 413 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.7726 (p90) cc_final: 0.7524 (p90) REVERT: A 122 LEU cc_start: 0.7791 (mp) cc_final: 0.7464 (mp) REVERT: A 196 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6686 (t0) REVERT: A 371 GLU cc_start: 0.7065 (mp0) cc_final: 0.6865 (mm-30) REVERT: A 573 GLN cc_start: 0.8192 (mt0) cc_final: 0.7904 (mm-40) REVERT: A 662 ASP cc_start: 0.8211 (t0) cc_final: 0.7975 (m-30) REVERT: A 860 LEU cc_start: 0.6878 (mp) cc_final: 0.6564 (tt) REVERT: A 928 LYS cc_start: 0.8443 (mtmm) cc_final: 0.7853 (mmpt) REVERT: A 1110 ARG cc_start: 0.7097 (mtt180) cc_final: 0.5902 (mpt180) REVERT: A 1116 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6767 (tm-30) REVERT: B 90 PHE cc_start: 0.7717 (p90) cc_final: 0.7515 (p90) REVERT: B 122 LEU cc_start: 0.7785 (mp) cc_final: 0.7458 (mp) REVERT: B 196 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6690 (t0) REVERT: B 371 GLU cc_start: 0.7063 (mp0) cc_final: 0.6861 (mm-30) REVERT: B 573 GLN cc_start: 0.8194 (mt0) cc_final: 0.7904 (mm-40) REVERT: B 662 ASP cc_start: 0.8212 (t0) cc_final: 0.7977 (m-30) REVERT: B 860 LEU cc_start: 0.6877 (mp) cc_final: 0.6563 (tt) REVERT: B 928 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7851 (mmpt) REVERT: B 1110 ARG cc_start: 0.7097 (mtt180) cc_final: 0.5900 (mpt180) REVERT: B 1116 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6768 (tm-30) REVERT: C 90 PHE cc_start: 0.7720 (p90) cc_final: 0.7517 (p90) REVERT: C 122 LEU cc_start: 0.7789 (mp) cc_final: 0.7463 (mp) REVERT: C 196 ASN cc_start: 0.7132 (OUTLIER) cc_final: 0.6690 (t0) REVERT: C 573 GLN cc_start: 0.8192 (mt0) cc_final: 0.7903 (mm-40) REVERT: C 662 ASP cc_start: 0.8209 (t0) cc_final: 0.7976 (m-30) REVERT: C 860 LEU cc_start: 0.6877 (mp) cc_final: 0.6562 (tt) REVERT: C 928 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7852 (mmpt) REVERT: C 1110 ARG cc_start: 0.7099 (mtt180) cc_final: 0.5902 (mpt180) REVERT: C 1116 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6768 (tm-30) REVERT: D 90 PHE cc_start: 0.7721 (p90) cc_final: 0.7519 (p90) REVERT: D 122 LEU cc_start: 0.7794 (mp) cc_final: 0.7468 (mp) REVERT: D 196 ASN cc_start: 0.7132 (OUTLIER) cc_final: 0.6689 (t0) REVERT: D 573 GLN cc_start: 0.8192 (mt0) cc_final: 0.7904 (mm-40) REVERT: D 662 ASP cc_start: 0.8210 (t0) cc_final: 0.7974 (m-30) REVERT: D 860 LEU cc_start: 0.6877 (mp) cc_final: 0.6563 (tt) REVERT: D 928 LYS cc_start: 0.8443 (mtmm) cc_final: 0.7851 (mmpt) REVERT: D 1110 ARG cc_start: 0.7098 (mtt180) cc_final: 0.5902 (mpt180) REVERT: D 1116 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6765 (tm-30) outliers start: 16 outliers final: 0 residues processed: 429 average time/residue: 0.7198 time to fit residues: 362.7213 Evaluate side-chains 297 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 293 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain D residue 196 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1014 GLN ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.203685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151263 restraints weight = 37878.482| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.17 r_work: 0.3436 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.004 0.045 31952 Z= 0.181 Angle : 0.536 8.295 43288 Z= 0.276 Chirality : 0.038 0.121 4840 Planarity : 0.005 0.066 5476 Dihedral : 3.862 37.393 4300 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.56 % Allowed : 6.51 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.14), residues: 3844 helix: 1.88 (0.10), residues: 2488 sheet: -0.72 (0.31), residues: 272 loop : -0.03 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.012 0.002 TYR D 968 PHE 0.017 0.002 PHE D 423 TRP 0.013 0.002 TRP D 691 HIS 0.012 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00442 (31952) covalent geometry : angle 0.53570 (43288) hydrogen bonds : bond 0.05020 ( 1916) hydrogen bonds : angle 4.17677 ( 5616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 294 time to evaluate : 1.176 Fit side-chains REVERT: A 186 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: A 379 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8163 (ttpt) REVERT: A 453 HIS cc_start: 0.7620 (m-70) cc_final: 0.7139 (t-170) REVERT: A 573 GLN cc_start: 0.8211 (mt0) cc_final: 0.7952 (mm-40) REVERT: A 770 ARG cc_start: 0.6550 (mtp85) cc_final: 0.5771 (ptp90) REVERT: A 860 LEU cc_start: 0.7104 (mp) cc_final: 0.6734 (tt) REVERT: A 1110 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6115 (mpt180) REVERT: A 1116 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6950 (tm-30) REVERT: B 186 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: B 379 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8164 (ttpt) REVERT: B 453 HIS cc_start: 0.7619 (m-70) cc_final: 0.7160 (t-170) REVERT: B 573 GLN cc_start: 0.8214 (mt0) cc_final: 0.7962 (mm-40) REVERT: B 770 ARG cc_start: 0.6571 (mtp85) cc_final: 0.5791 (ptp90) REVERT: B 860 LEU cc_start: 0.7108 (mp) cc_final: 0.6746 (tt) REVERT: B 1110 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6129 (mpt180) REVERT: B 1116 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6988 (tm-30) REVERT: C 186 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7300 (mpt) REVERT: C 379 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8158 (ttpt) REVERT: C 453 HIS cc_start: 0.7603 (m-70) cc_final: 0.7144 (t-170) REVERT: C 573 GLN cc_start: 0.8200 (mt0) cc_final: 0.7951 (mm-40) REVERT: C 770 ARG cc_start: 0.6563 (mtp85) cc_final: 0.5772 (ptp90) REVERT: C 860 LEU cc_start: 0.7110 (mp) cc_final: 0.6741 (tt) REVERT: C 1110 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6119 (mpt180) REVERT: C 1116 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6977 (tm-30) REVERT: D 186 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7316 (mpt) REVERT: D 379 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8151 (ttpt) REVERT: D 453 HIS cc_start: 0.7616 (m-70) cc_final: 0.7149 (t-170) REVERT: D 573 GLN cc_start: 0.8196 (mt0) cc_final: 0.7936 (mm-40) REVERT: D 770 ARG cc_start: 0.6559 (mtp85) cc_final: 0.5782 (ptp90) REVERT: D 860 LEU cc_start: 0.7095 (mp) cc_final: 0.6727 (tt) REVERT: D 1110 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6130 (mpt180) REVERT: D 1116 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6984 (tm-30) outliers start: 85 outliers final: 20 residues processed: 343 average time/residue: 0.5690 time to fit residues: 235.4233 Evaluate side-chains 298 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 789 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 75 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 237 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 383 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.203656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151610 restraints weight = 38052.410| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.25 r_work: 0.3433 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31952 Z= 0.139 Angle : 0.494 8.126 43288 Z= 0.253 Chirality : 0.037 0.120 4840 Planarity : 0.005 0.069 5476 Dihedral : 3.635 25.891 4292 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.68 % Allowed : 7.23 % Favored : 90.09 % 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 (0.14), residues: 3844 helix: 2.03 (0.10), residues: 2496 sheet: -0.91 (0.30), residues: 264 loop : 0.01 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 857 TYR 0.017 0.001 TYR D 103 PHE 0.017 0.001 PHE C 423 TRP 0.017 0.001 TRP D 691 HIS 0.008 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00333 (31952) covalent geometry : angle 0.49411 (43288) hydrogen bonds : bond 0.04469 ( 1916) hydrogen bonds : angle 3.98956 ( 5616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 268 time to evaluate : 1.217 Fit side-chains REVERT: A 186 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7344 (mpt) REVERT: A 284 MET cc_start: 0.6660 (ttm) cc_final: 0.6273 (mtm) REVERT: A 379 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8153 (tmmt) REVERT: A 453 HIS cc_start: 0.7607 (m-70) cc_final: 0.7126 (t-170) REVERT: A 573 GLN cc_start: 0.8167 (mt0) cc_final: 0.7904 (mm-40) REVERT: A 770 ARG cc_start: 0.6583 (mtp85) cc_final: 0.5789 (ptp90) REVERT: A 857 ARG cc_start: 0.5067 (mtt-85) cc_final: 0.4511 (ptp-110) REVERT: A 860 LEU cc_start: 0.7029 (mp) cc_final: 0.6671 (tt) REVERT: A 1110 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6057 (mpt180) REVERT: A 1116 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6983 (tm-30) REVERT: B 186 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7322 (mpt) REVERT: B 284 MET cc_start: 0.6676 (ttm) cc_final: 0.6282 (mtm) REVERT: B 379 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8155 (tmmt) REVERT: B 453 HIS cc_start: 0.7608 (m-70) cc_final: 0.7142 (t-170) REVERT: B 573 GLN cc_start: 0.8153 (mt0) cc_final: 0.7899 (mm-40) REVERT: B 770 ARG cc_start: 0.6583 (mtp85) cc_final: 0.5793 (ptp90) REVERT: B 857 ARG cc_start: 0.5057 (mtt-85) cc_final: 0.4499 (ptp-110) REVERT: B 860 LEU cc_start: 0.7018 (mp) cc_final: 0.6664 (tt) REVERT: B 1110 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6062 (mpt180) REVERT: B 1116 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7014 (tm-30) REVERT: C 186 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7313 (mpt) REVERT: C 284 MET cc_start: 0.6672 (ttm) cc_final: 0.6285 (mtm) REVERT: C 379 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8157 (tmmt) REVERT: C 453 HIS cc_start: 0.7586 (m-70) cc_final: 0.7118 (t-170) REVERT: C 573 GLN cc_start: 0.8157 (mt0) cc_final: 0.7901 (mm-40) REVERT: C 770 ARG cc_start: 0.6593 (mtp85) cc_final: 0.5783 (ptp90) REVERT: C 857 ARG cc_start: 0.5055 (mtt-85) cc_final: 0.4499 (ptp-110) REVERT: C 860 LEU cc_start: 0.7005 (mp) cc_final: 0.6647 (tt) REVERT: C 1110 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6049 (mpt180) REVERT: C 1116 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6990 (tm-30) REVERT: D 186 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7317 (mpt) REVERT: D 284 MET cc_start: 0.6659 (ttm) cc_final: 0.6275 (mtm) REVERT: D 379 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8144 (tmmt) REVERT: D 453 HIS cc_start: 0.7603 (m-70) cc_final: 0.7134 (t-170) REVERT: D 573 GLN cc_start: 0.8169 (mt0) cc_final: 0.7906 (mm-40) REVERT: D 770 ARG cc_start: 0.6559 (mtp85) cc_final: 0.5745 (ptp90) REVERT: D 857 ARG cc_start: 0.5051 (mtt-85) cc_final: 0.4490 (ptp-110) REVERT: D 860 LEU cc_start: 0.6999 (mp) cc_final: 0.6642 (tt) REVERT: D 1110 ARG cc_start: 0.7318 (mtt180) cc_final: 0.6072 (mpt180) REVERT: D 1116 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6990 (tm-30) outliers start: 89 outliers final: 32 residues processed: 309 average time/residue: 0.6025 time to fit residues: 224.4105 Evaluate side-chains 306 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 789 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 321 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.201678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148627 restraints weight = 37569.471| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.26 r_work: 0.3380 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 31952 Z= 0.225 Angle : 0.562 8.305 43288 Z= 0.289 Chirality : 0.040 0.127 4840 Planarity : 0.005 0.076 5476 Dihedral : 3.885 27.422 4292 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.80 % Allowed : 7.59 % Favored : 89.61 % 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: 1.59 (0.14), residues: 3844 helix: 1.77 (0.10), residues: 2492 sheet: -1.04 (0.29), residues: 268 loop : 0.06 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 857 TYR 0.013 0.002 TYR D1045 PHE 0.018 0.002 PHE D 223 TRP 0.020 0.002 TRP B 691 HIS 0.007 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00564 (31952) covalent geometry : angle 0.56220 (43288) hydrogen bonds : bond 0.05312 ( 1916) hydrogen bonds : angle 4.13119 ( 5616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 286 time to evaluate : 1.138 Fit side-chains REVERT: A 186 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7423 (mpt) REVERT: A 379 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8191 (tmmt) REVERT: A 453 HIS cc_start: 0.7682 (m-70) cc_final: 0.7320 (t-170) REVERT: A 573 GLN cc_start: 0.8303 (mt0) cc_final: 0.8091 (mm-40) REVERT: A 770 ARG cc_start: 0.6642 (mtp85) cc_final: 0.5932 (ptp90) REVERT: A 860 LEU cc_start: 0.7204 (mp) cc_final: 0.6849 (tt) REVERT: A 1110 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6238 (mpt180) REVERT: A 1116 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7167 (tm-30) REVERT: B 186 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7449 (mpt) REVERT: B 379 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8192 (tmmt) REVERT: B 453 HIS cc_start: 0.7697 (m-70) cc_final: 0.7347 (t-170) REVERT: B 573 GLN cc_start: 0.8312 (mt0) cc_final: 0.8102 (mm-40) REVERT: B 770 ARG cc_start: 0.6659 (mtp85) cc_final: 0.5948 (ptp90) REVERT: B 860 LEU cc_start: 0.7198 (mp) cc_final: 0.6844 (tt) REVERT: B 1110 ARG cc_start: 0.7410 (mtt180) cc_final: 0.6240 (mpt180) REVERT: B 1116 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7133 (tm-30) REVERT: C 186 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7419 (mpt) REVERT: C 379 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8187 (tmmt) REVERT: C 412 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7260 (tp30) REVERT: C 453 HIS cc_start: 0.7676 (m-70) cc_final: 0.7319 (t-170) REVERT: C 573 GLN cc_start: 0.8300 (mt0) cc_final: 0.8095 (mm-40) REVERT: C 770 ARG cc_start: 0.6651 (mtp85) cc_final: 0.5930 (ptp90) REVERT: C 860 LEU cc_start: 0.7190 (mp) cc_final: 0.6838 (tt) REVERT: C 1110 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6219 (mpt180) REVERT: C 1116 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7147 (tm-30) REVERT: D 186 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7408 (mpt) REVERT: D 379 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8190 (tmmt) REVERT: D 412 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7283 (tp30) REVERT: D 453 HIS cc_start: 0.7684 (m-70) cc_final: 0.7331 (t-170) REVERT: D 573 GLN cc_start: 0.8303 (mt0) cc_final: 0.8094 (mm-40) REVERT: D 770 ARG cc_start: 0.6640 (mtp85) cc_final: 0.5922 (ptp90) REVERT: D 860 LEU cc_start: 0.7196 (mp) cc_final: 0.6843 (tt) REVERT: D 1110 ARG cc_start: 0.7431 (mtt180) cc_final: 0.6243 (mpt180) REVERT: D 1116 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7175 (tm-30) outliers start: 93 outliers final: 32 residues processed: 335 average time/residue: 0.6284 time to fit residues: 250.9939 Evaluate side-chains 309 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 789 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 227 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 272 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.204301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.151513 restraints weight = 37905.928| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.21 r_work: 0.3430 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31952 Z= 0.117 Angle : 0.465 7.814 43288 Z= 0.241 Chirality : 0.036 0.121 4840 Planarity : 0.005 0.077 5476 Dihedral : 3.624 26.616 4292 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.96 % Allowed : 8.34 % Favored : 89.70 % 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: 2.01 (0.14), residues: 3844 helix: 2.15 (0.10), residues: 2492 sheet: -1.13 (0.29), residues: 256 loop : 0.14 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 857 TYR 0.008 0.001 TYR B 103 PHE 0.018 0.001 PHE C 223 TRP 0.022 0.001 TRP D 691 HIS 0.005 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00271 (31952) covalent geometry : angle 0.46466 (43288) hydrogen bonds : bond 0.04123 ( 1916) hydrogen bonds : angle 3.88822 ( 5616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 1.219 Fit side-chains REVERT: A 186 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7230 (mpt) REVERT: A 284 MET cc_start: 0.6595 (ttm) cc_final: 0.6335 (mtt) REVERT: A 287 ARG cc_start: 0.6803 (tmt170) cc_final: 0.6563 (tmt170) REVERT: A 379 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8159 (tmmt) REVERT: A 412 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7248 (tp30) REVERT: A 453 HIS cc_start: 0.7583 (m-70) cc_final: 0.7199 (t-170) REVERT: A 573 GLN cc_start: 0.8173 (mt0) cc_final: 0.7912 (mm-40) REVERT: A 770 ARG cc_start: 0.6561 (mtp85) cc_final: 0.5849 (ptp90) REVERT: A 857 ARG cc_start: 0.5055 (mtt-85) cc_final: 0.4542 (ptp-110) REVERT: A 860 LEU cc_start: 0.7056 (mp) cc_final: 0.6746 (tt) REVERT: A 1110 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6086 (mpt180) REVERT: B 186 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7249 (mpt) REVERT: B 284 MET cc_start: 0.6609 (ttm) cc_final: 0.6345 (mtt) REVERT: B 287 ARG cc_start: 0.6813 (tmt170) cc_final: 0.6571 (tmt170) REVERT: B 379 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8159 (tmmt) REVERT: B 412 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7233 (tp30) REVERT: B 453 HIS cc_start: 0.7601 (m-70) cc_final: 0.7216 (t-170) REVERT: B 573 GLN cc_start: 0.8151 (mt0) cc_final: 0.7904 (mm-40) REVERT: B 770 ARG cc_start: 0.6574 (mtp85) cc_final: 0.5866 (ptp90) REVERT: B 857 ARG cc_start: 0.5064 (mtt-85) cc_final: 0.4547 (ptp-110) REVERT: B 860 LEU cc_start: 0.7059 (mp) cc_final: 0.6749 (tt) REVERT: B 1110 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6088 (mpt180) REVERT: B 1116 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7036 (tm-30) REVERT: C 186 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7219 (mpt) REVERT: C 284 MET cc_start: 0.6593 (ttm) cc_final: 0.6336 (mtt) REVERT: C 287 ARG cc_start: 0.6808 (tmt170) cc_final: 0.6562 (tmt170) REVERT: C 379 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8152 (tmmt) REVERT: C 412 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7236 (tp30) REVERT: C 453 HIS cc_start: 0.7579 (m-70) cc_final: 0.7202 (t-170) REVERT: C 573 GLN cc_start: 0.8151 (mt0) cc_final: 0.7900 (mm-40) REVERT: C 770 ARG cc_start: 0.6572 (mtp85) cc_final: 0.5848 (ptp90) REVERT: C 857 ARG cc_start: 0.5060 (mtt-85) cc_final: 0.4546 (ptp-110) REVERT: C 860 LEU cc_start: 0.7047 (mp) cc_final: 0.6736 (tt) REVERT: C 1110 ARG cc_start: 0.7233 (mtt180) cc_final: 0.6072 (mpt180) REVERT: C 1116 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7040 (tm-30) REVERT: D 186 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7222 (mpt) REVERT: D 284 MET cc_start: 0.6590 (ttm) cc_final: 0.6334 (mtt) REVERT: D 287 ARG cc_start: 0.6806 (tmt170) cc_final: 0.6564 (tmt170) REVERT: D 379 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8156 (tmmt) REVERT: D 412 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7244 (tp30) REVERT: D 453 HIS cc_start: 0.7579 (m-70) cc_final: 0.7201 (t-170) REVERT: D 573 GLN cc_start: 0.8160 (mt0) cc_final: 0.7897 (mm-40) REVERT: D 770 ARG cc_start: 0.6558 (mtp85) cc_final: 0.5841 (ptp90) REVERT: D 857 ARG cc_start: 0.5050 (mtt-85) cc_final: 0.4534 (ptp-110) REVERT: D 860 LEU cc_start: 0.7044 (mp) cc_final: 0.6736 (tt) REVERT: D 1110 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6084 (mpt180) REVERT: D 1116 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7055 (tm-30) outliers start: 65 outliers final: 32 residues processed: 304 average time/residue: 0.6342 time to fit residues: 228.2008 Evaluate side-chains 305 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 789 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 386 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 338 optimal weight: 7.9990 chunk 196 optimal weight: 0.0980 chunk 282 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 371 optimal weight: 0.0170 chunk 312 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.206823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155355 restraints weight = 37810.392| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.28 r_work: 0.3488 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 31952 Z= 0.088 Angle : 0.419 8.124 43288 Z= 0.218 Chirality : 0.034 0.123 4840 Planarity : 0.004 0.075 5476 Dihedral : 3.359 25.270 4292 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.90 % Allowed : 8.77 % Favored : 89.34 % 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: 2.37 (0.14), residues: 3844 helix: 2.44 (0.10), residues: 2504 sheet: -1.07 (0.30), residues: 256 loop : 0.23 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 857 TYR 0.006 0.001 TYR B 227 PHE 0.020 0.001 PHE C 223 TRP 0.030 0.001 TRP B 691 HIS 0.004 0.000 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00167 (31952) covalent geometry : angle 0.41923 (43288) hydrogen bonds : bond 0.03329 ( 1916) hydrogen bonds : angle 3.68511 ( 5616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 1.211 Fit side-chains REVERT: A 284 MET cc_start: 0.6671 (ttm) cc_final: 0.6433 (mtt) REVERT: A 300 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7455 (mp) REVERT: A 379 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8122 (tmmt) REVERT: A 412 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7262 (tp30) REVERT: A 453 HIS cc_start: 0.7608 (m-70) cc_final: 0.7175 (t-170) REVERT: A 573 GLN cc_start: 0.8101 (mt0) cc_final: 0.7834 (mm-40) REVERT: A 770 ARG cc_start: 0.6576 (mtp85) cc_final: 0.5845 (ptp90) REVERT: A 860 LEU cc_start: 0.7011 (mp) cc_final: 0.6657 (tt) REVERT: A 1110 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6045 (mpt180) REVERT: B 284 MET cc_start: 0.6677 (ttm) cc_final: 0.6438 (mtt) REVERT: B 300 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7439 (mp) REVERT: B 379 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8118 (tmmt) REVERT: B 412 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7261 (tp30) REVERT: B 453 HIS cc_start: 0.7624 (m-70) cc_final: 0.7192 (t-170) REVERT: B 573 GLN cc_start: 0.8108 (mt0) cc_final: 0.7840 (mm-40) REVERT: B 770 ARG cc_start: 0.6581 (mtp85) cc_final: 0.5846 (ptp90) REVERT: B 860 LEU cc_start: 0.7004 (mp) cc_final: 0.6653 (tt) REVERT: B 1110 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6043 (mpt180) REVERT: B 1116 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6958 (tm-30) REVERT: C 284 MET cc_start: 0.6675 (ttm) cc_final: 0.6438 (mtt) REVERT: C 300 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7446 (mp) REVERT: C 379 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8115 (tmmt) REVERT: C 412 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7251 (tp30) REVERT: C 453 HIS cc_start: 0.7600 (m-70) cc_final: 0.7177 (t-170) REVERT: C 573 GLN cc_start: 0.8107 (mt0) cc_final: 0.7838 (mm-40) REVERT: C 770 ARG cc_start: 0.6568 (mtp85) cc_final: 0.5824 (ptp90) REVERT: C 860 LEU cc_start: 0.6977 (mp) cc_final: 0.6627 (tt) REVERT: C 1110 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6034 (mpt180) REVERT: D 284 MET cc_start: 0.6674 (ttm) cc_final: 0.6442 (mtt) REVERT: D 300 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7450 (mp) REVERT: D 379 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8125 (tmmt) REVERT: D 412 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7273 (tp30) REVERT: D 453 HIS cc_start: 0.7605 (m-70) cc_final: 0.7186 (t-170) REVERT: D 573 GLN cc_start: 0.8124 (mt0) cc_final: 0.7842 (mm-40) REVERT: D 770 ARG cc_start: 0.6559 (mtp85) cc_final: 0.5814 (ptp90) REVERT: D 860 LEU cc_start: 0.6999 (mp) cc_final: 0.6644 (tt) REVERT: D 1110 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6045 (mpt180) outliers start: 63 outliers final: 21 residues processed: 328 average time/residue: 0.5872 time to fit residues: 231.8375 Evaluate side-chains 290 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 789 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 357 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 326 optimal weight: 40.0000 chunk 261 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 351 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN B1164 HIS ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 HIS ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.201292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148535 restraints weight = 37600.113| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.27 r_work: 0.3386 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 31952 Z= 0.252 Angle : 0.579 9.117 43288 Z= 0.299 Chirality : 0.042 0.145 4840 Planarity : 0.005 0.082 5476 Dihedral : 3.780 27.606 4292 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.20 % Allowed : 9.25 % Favored : 88.55 % 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: 1.73 (0.14), residues: 3844 helix: 1.90 (0.10), residues: 2496 sheet: -1.09 (0.30), residues: 264 loop : 0.09 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.015 0.002 TYR C1045 PHE 0.018 0.002 PHE B 223 TRP 0.029 0.002 TRP D 691 HIS 0.007 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00638 (31952) covalent geometry : angle 0.57940 (43288) hydrogen bonds : bond 0.05368 ( 1916) hydrogen bonds : angle 4.09597 ( 5616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 1.237 Fit side-chains REVERT: A 284 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6265 (mtm) REVERT: A 379 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8156 (tmmt) REVERT: A 412 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7257 (tp30) REVERT: A 453 HIS cc_start: 0.7626 (m-70) cc_final: 0.7250 (t-170) REVERT: A 573 GLN cc_start: 0.8244 (mt0) cc_final: 0.7980 (mm-40) REVERT: A 709 THR cc_start: 0.7652 (m) cc_final: 0.7380 (t) REVERT: A 770 ARG cc_start: 0.6603 (mtp85) cc_final: 0.5862 (ptp90) REVERT: A 860 LEU cc_start: 0.7094 (mp) cc_final: 0.6754 (tt) REVERT: A 1110 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6143 (mpt180) REVERT: B 284 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6269 (mtm) REVERT: B 379 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8146 (tmmt) REVERT: B 412 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7253 (tp30) REVERT: B 453 HIS cc_start: 0.7649 (m-70) cc_final: 0.7269 (t-170) REVERT: B 573 GLN cc_start: 0.8247 (mt0) cc_final: 0.7985 (mm-40) REVERT: B 709 THR cc_start: 0.7670 (m) cc_final: 0.7403 (t) REVERT: B 770 ARG cc_start: 0.6603 (mtp85) cc_final: 0.5865 (ptp90) REVERT: B 860 LEU cc_start: 0.7111 (mp) cc_final: 0.6774 (tt) REVERT: B 1110 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6135 (mpt180) REVERT: B 1116 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7074 (tm-30) REVERT: C 284 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6264 (mtm) REVERT: C 379 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8135 (tmmt) REVERT: C 412 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7266 (tp30) REVERT: C 453 HIS cc_start: 0.7623 (m-70) cc_final: 0.7247 (t-170) REVERT: C 573 GLN cc_start: 0.8240 (mt0) cc_final: 0.7981 (mm-40) REVERT: C 709 THR cc_start: 0.7683 (m) cc_final: 0.7415 (t) REVERT: C 770 ARG cc_start: 0.6609 (mtp85) cc_final: 0.5847 (ptp90) REVERT: C 860 LEU cc_start: 0.7082 (mp) cc_final: 0.6747 (tt) REVERT: C 1110 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6131 (mpt180) REVERT: D 284 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6270 (mtm) REVERT: D 379 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8137 (tmmt) REVERT: D 412 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7263 (tp30) REVERT: D 453 HIS cc_start: 0.7635 (m-70) cc_final: 0.7249 (t-170) REVERT: D 573 GLN cc_start: 0.8256 (mt0) cc_final: 0.7987 (mm-40) REVERT: D 709 THR cc_start: 0.7661 (m) cc_final: 0.7389 (t) REVERT: D 770 ARG cc_start: 0.6579 (mtp85) cc_final: 0.5827 (ptp90) REVERT: D 860 LEU cc_start: 0.7104 (mp) cc_final: 0.6764 (tt) REVERT: D 1110 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6145 (mpt180) outliers start: 73 outliers final: 32 residues processed: 347 average time/residue: 0.6193 time to fit residues: 257.3308 Evaluate side-chains 317 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 789 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 71 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.204778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153356 restraints weight = 37612.205| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.27 r_work: 0.3456 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31952 Z= 0.098 Angle : 0.453 7.977 43288 Z= 0.237 Chirality : 0.035 0.119 4840 Planarity : 0.004 0.078 5476 Dihedral : 3.462 26.775 4292 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.69 % Allowed : 10.27 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.20 (0.14), residues: 3844 helix: 2.31 (0.10), residues: 2496 sheet: -1.22 (0.29), residues: 256 loop : 0.20 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 857 TYR 0.005 0.001 TYR D1063 PHE 0.019 0.001 PHE C 223 TRP 0.035 0.001 TRP C 691 HIS 0.005 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00213 (31952) covalent geometry : angle 0.45312 (43288) hydrogen bonds : bond 0.03791 ( 1916) hydrogen bonds : angle 3.83772 ( 5616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 1.139 Fit side-chains REVERT: A 284 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6511 (mtt) REVERT: A 379 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8132 (tmmt) REVERT: A 412 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7297 (tp30) REVERT: A 431 ASP cc_start: 0.8383 (m-30) cc_final: 0.8059 (m-30) REVERT: A 453 HIS cc_start: 0.7586 (m-70) cc_final: 0.7231 (t-170) REVERT: A 573 GLN cc_start: 0.8171 (mt0) cc_final: 0.7932 (mm-40) REVERT: A 709 THR cc_start: 0.7667 (m) cc_final: 0.7441 (t) REVERT: A 770 ARG cc_start: 0.6623 (mtp85) cc_final: 0.5900 (ptp90) REVERT: A 852 LEU cc_start: 0.6222 (tp) cc_final: 0.5961 (tt) REVERT: A 860 LEU cc_start: 0.7100 (mp) cc_final: 0.6727 (tt) REVERT: A 1042 MET cc_start: 0.9229 (mtp) cc_final: 0.9025 (mtm) REVERT: A 1110 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6129 (mpt180) REVERT: B 284 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6525 (mtt) REVERT: B 379 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8128 (tmmt) REVERT: B 412 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7293 (tp30) REVERT: B 431 ASP cc_start: 0.8388 (m-30) cc_final: 0.8061 (m-30) REVERT: B 453 HIS cc_start: 0.7606 (m-70) cc_final: 0.7246 (t-170) REVERT: B 573 GLN cc_start: 0.8186 (mt0) cc_final: 0.7950 (mm-40) REVERT: B 709 THR cc_start: 0.7672 (m) cc_final: 0.7447 (t) REVERT: B 770 ARG cc_start: 0.6628 (mtp85) cc_final: 0.5892 (ptp90) REVERT: B 852 LEU cc_start: 0.6237 (tp) cc_final: 0.5973 (tt) REVERT: B 860 LEU cc_start: 0.7090 (mp) cc_final: 0.6723 (tt) REVERT: B 1042 MET cc_start: 0.9238 (mtp) cc_final: 0.9037 (mtm) REVERT: B 1110 ARG cc_start: 0.7216 (mtt180) cc_final: 0.6124 (mpt180) REVERT: B 1116 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7038 (tm-30) REVERT: C 284 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6526 (mtt) REVERT: C 379 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8118 (tmmt) REVERT: C 412 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7298 (tp30) REVERT: C 431 ASP cc_start: 0.8354 (m-30) cc_final: 0.8026 (m-30) REVERT: C 453 HIS cc_start: 0.7579 (m-70) cc_final: 0.7229 (t-170) REVERT: C 573 GLN cc_start: 0.8179 (mt0) cc_final: 0.7935 (mm-40) REVERT: C 709 THR cc_start: 0.7687 (m) cc_final: 0.7461 (t) REVERT: C 770 ARG cc_start: 0.6629 (mtp85) cc_final: 0.5889 (ptp90) REVERT: C 852 LEU cc_start: 0.6226 (tp) cc_final: 0.5968 (tt) REVERT: C 860 LEU cc_start: 0.7075 (mp) cc_final: 0.6704 (tt) REVERT: C 1042 MET cc_start: 0.9240 (mtp) cc_final: 0.9039 (mtm) REVERT: C 1110 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6110 (mpt180) REVERT: D 284 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6532 (mtt) REVERT: D 379 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8123 (tmmt) REVERT: D 412 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7305 (tp30) REVERT: D 431 ASP cc_start: 0.8361 (m-30) cc_final: 0.8041 (m-30) REVERT: D 453 HIS cc_start: 0.7593 (m-70) cc_final: 0.7230 (t-170) REVERT: D 573 GLN cc_start: 0.8178 (mt0) cc_final: 0.7929 (mm-40) REVERT: D 770 ARG cc_start: 0.6600 (mtp85) cc_final: 0.5871 (ptp90) REVERT: D 852 LEU cc_start: 0.6207 (tp) cc_final: 0.5950 (tt) REVERT: D 860 LEU cc_start: 0.7093 (mp) cc_final: 0.6722 (tt) REVERT: D 1042 MET cc_start: 0.9232 (mtp) cc_final: 0.9030 (mtm) REVERT: D 1110 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6121 (mpt180) outliers start: 56 outliers final: 36 residues processed: 320 average time/residue: 0.6614 time to fit residues: 251.8177 Evaluate side-chains 313 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 872 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 309 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 271 optimal weight: 0.7980 chunk 342 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.203422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151002 restraints weight = 37541.818| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.23 r_work: 0.3426 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31952 Z= 0.133 Angle : 0.494 8.401 43288 Z= 0.253 Chirality : 0.036 0.122 4840 Planarity : 0.005 0.078 5476 Dihedral : 3.516 27.110 4292 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.33 % Allowed : 10.84 % Favored : 87.83 % 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: 2.15 (0.14), residues: 3844 helix: 2.26 (0.10), residues: 2500 sheet: -1.21 (0.29), residues: 256 loop : 0.20 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 857 TYR 0.012 0.001 TYR B 103 PHE 0.019 0.001 PHE C 223 TRP 0.043 0.001 TRP C 691 HIS 0.005 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00321 (31952) covalent geometry : angle 0.49406 (43288) hydrogen bonds : bond 0.04206 ( 1916) hydrogen bonds : angle 3.89181 ( 5616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 1.456 Fit side-chains REVERT: A 379 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8111 (tmmt) REVERT: A 412 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7290 (tp30) REVERT: A 453 HIS cc_start: 0.7618 (m-70) cc_final: 0.7233 (t-170) REVERT: A 573 GLN cc_start: 0.8181 (mt0) cc_final: 0.7899 (mm-40) REVERT: A 709 THR cc_start: 0.7632 (m) cc_final: 0.7384 (t) REVERT: A 770 ARG cc_start: 0.6563 (mtp85) cc_final: 0.5781 (ptp90) REVERT: A 852 LEU cc_start: 0.6195 (tp) cc_final: 0.5948 (tt) REVERT: A 860 LEU cc_start: 0.7057 (mp) cc_final: 0.6701 (tt) REVERT: A 1110 ARG cc_start: 0.7233 (mtt180) cc_final: 0.6071 (mpt180) REVERT: B 284 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6595 (mtt) REVERT: B 379 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8122 (tmmt) REVERT: B 412 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7290 (tp30) REVERT: B 453 HIS cc_start: 0.7638 (m-70) cc_final: 0.7244 (t-170) REVERT: B 573 GLN cc_start: 0.8192 (mt0) cc_final: 0.7909 (mm-40) REVERT: B 709 THR cc_start: 0.7648 (m) cc_final: 0.7398 (t) REVERT: B 770 ARG cc_start: 0.6560 (mtp85) cc_final: 0.5777 (ptp90) REVERT: B 852 LEU cc_start: 0.6217 (tp) cc_final: 0.5967 (tt) REVERT: B 860 LEU cc_start: 0.7065 (mp) cc_final: 0.6712 (tt) REVERT: B 1110 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6065 (mpt180) REVERT: B 1116 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7004 (tm-30) REVERT: C 284 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6592 (mtt) REVERT: C 379 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8118 (tmmt) REVERT: C 412 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7303 (tp30) REVERT: C 453 HIS cc_start: 0.7610 (m-70) cc_final: 0.7229 (t-170) REVERT: C 573 GLN cc_start: 0.8177 (mt0) cc_final: 0.7895 (mm-40) REVERT: C 709 THR cc_start: 0.7659 (m) cc_final: 0.7408 (t) REVERT: C 770 ARG cc_start: 0.6577 (mtp85) cc_final: 0.5784 (ptp90) REVERT: C 852 LEU cc_start: 0.6187 (tp) cc_final: 0.5943 (tt) REVERT: C 860 LEU cc_start: 0.7040 (mp) cc_final: 0.6688 (tt) REVERT: C 1110 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6058 (mpt180) REVERT: D 379 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8115 (tmmt) REVERT: D 412 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7300 (tp30) REVERT: D 431 ASP cc_start: 0.8325 (m-30) cc_final: 0.7872 (m-30) REVERT: D 453 HIS cc_start: 0.7619 (m-70) cc_final: 0.7228 (t-170) REVERT: D 573 GLN cc_start: 0.8186 (mt0) cc_final: 0.7894 (mm-40) REVERT: D 709 THR cc_start: 0.7641 (m) cc_final: 0.7382 (t) REVERT: D 770 ARG cc_start: 0.6539 (mtp85) cc_final: 0.5755 (ptp90) REVERT: D 852 LEU cc_start: 0.6173 (tp) cc_final: 0.5930 (tt) REVERT: D 860 LEU cc_start: 0.7048 (mp) cc_final: 0.6695 (tt) REVERT: D 1110 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6069 (mpt180) outliers start: 44 outliers final: 36 residues processed: 315 average time/residue: 0.6550 time to fit residues: 248.3889 Evaluate side-chains 309 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 514 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 872 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 223 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 205 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B1014 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.205298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153775 restraints weight = 37514.907| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.26 r_work: 0.3469 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31952 Z= 0.095 Angle : 0.458 8.329 43288 Z= 0.235 Chirality : 0.035 0.123 4840 Planarity : 0.004 0.078 5476 Dihedral : 3.381 26.556 4292 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.36 % Allowed : 11.05 % Favored : 87.59 % 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: 2.35 (0.14), residues: 3844 helix: 2.43 (0.10), residues: 2500 sheet: -1.25 (0.29), residues: 256 loop : 0.27 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 857 TYR 0.006 0.001 TYR B 227 PHE 0.019 0.001 PHE D 223 TRP 0.049 0.001 TRP B 691 HIS 0.005 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00206 (31952) covalent geometry : angle 0.45844 (43288) hydrogen bonds : bond 0.03576 ( 1916) hydrogen bonds : angle 3.78454 ( 5616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 1.217 Fit side-chains REVERT: A 135 GLN cc_start: 0.6714 (tm-30) cc_final: 0.6400 (tp40) REVERT: A 287 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.5295 (ttt180) REVERT: A 412 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7341 (tp30) REVERT: A 453 HIS cc_start: 0.7604 (m-70) cc_final: 0.7198 (t-170) REVERT: A 573 GLN cc_start: 0.8136 (mt0) cc_final: 0.7922 (mm-40) REVERT: A 770 ARG cc_start: 0.6605 (mtp85) cc_final: 0.5852 (ptp90) REVERT: A 852 LEU cc_start: 0.6266 (tp) cc_final: 0.6024 (tt) REVERT: A 857 ARG cc_start: 0.5048 (mtt-85) cc_final: 0.4516 (ptp-110) REVERT: A 860 LEU cc_start: 0.7061 (mp) cc_final: 0.6692 (tt) REVERT: A 1042 MET cc_start: 0.9239 (mtp) cc_final: 0.8898 (mtm) REVERT: A 1110 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6098 (mpt180) REVERT: B 135 GLN cc_start: 0.6720 (tm-30) cc_final: 0.6408 (tp40) REVERT: B 287 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5214 (ttt180) REVERT: B 412 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7339 (tp30) REVERT: B 453 HIS cc_start: 0.7602 (m-70) cc_final: 0.7197 (t-170) REVERT: B 573 GLN cc_start: 0.8149 (mt0) cc_final: 0.7932 (mm-40) REVERT: B 770 ARG cc_start: 0.6589 (mtp85) cc_final: 0.5837 (ptp90) REVERT: B 852 LEU cc_start: 0.6290 (tp) cc_final: 0.6044 (tt) REVERT: B 857 ARG cc_start: 0.5047 (mtt-85) cc_final: 0.4516 (ptp-110) REVERT: B 860 LEU cc_start: 0.7055 (mp) cc_final: 0.6692 (tt) REVERT: B 1042 MET cc_start: 0.9239 (mtp) cc_final: 0.8901 (mtm) REVERT: B 1110 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6103 (mpt180) REVERT: C 135 GLN cc_start: 0.6704 (tm-30) cc_final: 0.6392 (tp40) REVERT: C 287 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.5199 (ttt180) REVERT: C 412 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7343 (tp30) REVERT: C 453 HIS cc_start: 0.7577 (m-70) cc_final: 0.7185 (t-170) REVERT: C 573 GLN cc_start: 0.8135 (mt0) cc_final: 0.7921 (mm-40) REVERT: C 770 ARG cc_start: 0.6612 (mtp85) cc_final: 0.5838 (ptp90) REVERT: C 852 LEU cc_start: 0.6262 (tp) cc_final: 0.6024 (tt) REVERT: C 857 ARG cc_start: 0.5042 (mtt-85) cc_final: 0.4513 (ptp-110) REVERT: C 860 LEU cc_start: 0.7049 (mp) cc_final: 0.6681 (tt) REVERT: C 1042 MET cc_start: 0.9253 (mtp) cc_final: 0.8918 (mtm) REVERT: C 1110 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6096 (mpt180) REVERT: D 135 GLN cc_start: 0.6698 (tm-30) cc_final: 0.6386 (tp40) REVERT: D 287 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5293 (ttt180) REVERT: D 412 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7335 (tp30) REVERT: D 453 HIS cc_start: 0.7601 (m-70) cc_final: 0.7194 (t-170) REVERT: D 573 GLN cc_start: 0.8156 (mt0) cc_final: 0.7923 (mm-40) REVERT: D 770 ARG cc_start: 0.6588 (mtp85) cc_final: 0.5826 (ptp90) REVERT: D 852 LEU cc_start: 0.6242 (tp) cc_final: 0.6007 (tt) REVERT: D 857 ARG cc_start: 0.5022 (mtt-85) cc_final: 0.4491 (ptp-110) REVERT: D 860 LEU cc_start: 0.7059 (mp) cc_final: 0.6691 (tt) REVERT: D 1042 MET cc_start: 0.9234 (mtp) cc_final: 0.8892 (mtm) REVERT: D 1110 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6098 (mpt180) outliers start: 45 outliers final: 26 residues processed: 300 average time/residue: 0.5982 time to fit residues: 215.4898 Evaluate side-chains 302 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 872 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 156 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 chunk 245 optimal weight: 0.0040 chunk 292 optimal weight: 7.9990 chunk 297 optimal weight: 30.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.203044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150000 restraints weight = 37599.718| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.23 r_work: 0.3414 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31952 Z= 0.156 Angle : 0.509 8.162 43288 Z= 0.260 Chirality : 0.037 0.121 4840 Planarity : 0.005 0.078 5476 Dihedral : 3.535 27.076 4292 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.11 % Allowed : 11.84 % Favored : 87.05 % 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: 2.14 (0.14), residues: 3844 helix: 2.24 (0.10), residues: 2500 sheet: -1.17 (0.30), residues: 256 loop : 0.23 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 857 TYR 0.014 0.002 TYR A 103 PHE 0.019 0.002 PHE D 223 TRP 0.053 0.002 TRP B 691 HIS 0.005 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00383 (31952) covalent geometry : angle 0.50920 (43288) hydrogen bonds : bond 0.04378 ( 1916) hydrogen bonds : angle 3.90116 ( 5616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12707.46 seconds wall clock time: 216 minutes 30.25 seconds (12990.25 seconds total)