Starting phenix.real_space_refine on Sat Jul 4 21:59:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwm_23550/07_2026/7lwm_23550.cif" } resolution = 2.83 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= -0.001 sd= 0.098 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 102 5.16 5 C 15046 2.51 5 N 3879 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23571 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7685 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7697 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7671 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.17, per 1000 atoms: 0.22 Number of scatterers: 23571 At special positions: 0 Unit cell: (127.211, 134.694, 194.558, 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 102 16.00 O 4544 8.00 N 3879 7.00 C 15046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.06 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 61 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 61 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN B1098 " " NAG F 1 " - " ASN C1098 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 27.7% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.040A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.689A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.741A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.691A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.550A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.519A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.269A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.906A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.212A pdb=" N GLY B 142 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.195A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.662A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.619A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.811A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.139A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.553A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.022A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.449A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.897A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.110A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.861A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.053A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.736A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.580A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.795A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.939A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.500A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.640A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.716A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.382A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.805A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.716A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.381A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.544A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.823A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.463A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.530A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.346A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.182A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.671A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.200A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.860A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.652A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.917A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.348A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.756A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.525A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.813A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.580A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.604A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.469A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.691A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.379A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.156A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.851A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.525A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.546A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.409A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.724A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2865 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: 5.53 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5994 1.33 - 1.45: 4625 1.45 - 1.58: 13334 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 24079 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.67e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.48e+01 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 24193 1.97 - 3.94: 7676 3.94 - 5.92: 836 5.92 - 7.89: 58 7.89 - 9.86: 4 Bond angle restraints: 32767 Sorted by residual: angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.35 -6.75 1.00e+00 1.00e+00 4.56e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.90e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.87 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.55 -5.75 1.00e+00 1.00e+00 3.30e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 117.17 5.43 1.00e+00 1.00e+00 2.95e+01 ... (remaining 32762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13037 17.91 - 35.81: 759 35.81 - 53.72: 136 53.72 - 71.62: 50 71.62 - 89.53: 26 Dihedral angle restraints: 14008 sinusoidal: 5354 harmonic: 8654 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -163.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.46 75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -158.84 72.84 1 1.00e+01 1.00e-02 6.77e+01 ... (remaining 14005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2945 0.110 - 0.219: 846 0.219 - 0.328: 79 0.328 - 0.438: 5 0.438 - 0.547: 3 Chirality restraints: 3878 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.99e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.74e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.31e+01 ... (remaining 3875 not shown) Planarity restraints: 4211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.378 2.00e-02 2.50e+03 2.05e-01 1.05e+03 pdb=" CG TRP C 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.199 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.140 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.306 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.215 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.069 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.140 2.00e-02 2.50e+03 1.46e-01 2.67e+02 pdb=" CG ASN B 709 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.220 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " -0.124 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN C 61 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " 0.196 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " -0.157 2.00e-02 2.50e+03 ... (remaining 4208 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11247 2.99 - 3.47: 22004 3.47 - 3.95: 39373 3.95 - 4.42: 43391 4.42 - 4.90: 73750 Nonbonded interactions: 189765 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.518 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.520 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.524 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.529 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.532 3.040 ... (remaining 189760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 through 215 and (name N or name CA or name C or name \ O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 through 487 or (resid 488 and (name N or name CA or name C or name \ O or name CB )) or resid 489 through 527 or (resid 528 and (name N or name CA o \ r name C or name O or name CB )) or resid 529 through 810 or (resid 811 and (nam \ e N or name CA or name C or name O or name CB )) or resid 813 through 827 or res \ id 855 through 866 or (resid 867 through 868 and (name N or name CA or name C or \ name O or name CB )) or resid 869 through 1141 or (resid 1142 and (name N or na \ me CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 114 \ 5 through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1310)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or resid 16 \ 6 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 195 or (resid 196 through 197 and (nam \ e N or name CA or name C or name O or name CB )) or resid 198 through 241 or (re \ sid 242 through 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 280 or (resid 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 through 483 or resid 485 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 582 o \ r (resid 583 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 84 through 585 or (resid 586 and (name N or name CA or name C or name O or name \ CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C or \ name O or name CB )) or resid 620 through 676 or resid 690 through 744 or (resi \ d 745 and (name N or name CA or name C or name O or name CB )) or resid 746 thro \ ugh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) o \ r resid 749 through 810 or (resid 811 and (name N or name CA or name C or name O \ or name CB )) or resid 813 or (resid 814 and (name N or name CA or name C or na \ me O or name CB )) or resid 815 through 827 or resid 855 through 866 or (resid 8 \ 67 through 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 1091 or (resid 1092 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1093 through 1143 or (resid 1144 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 through 195 or (resid 196 th \ rough 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 213 or (resid 214 through 215 and (name N or name CA or name C or name O \ or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or \ name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (name \ N or name CA or name C or name O or name CB )) or resid 240 through 308 or (resi \ d 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thro \ ugh 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) o \ r resid 481 through 483 or resid 485 through 487 or (resid 488 and (name N or na \ me CA or name C or name O or name CB )) or resid 489 through 527 or (resid 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 582 or (resid 583 and (name N or name CA or name C or name O or nam \ e CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or name C \ or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N or na \ me CA or name C or name O or name CB )) or resid 620 through 813 or (resid 814 a \ nd (name N or name CA or name C or name O or name CB )) or resid 815 through 109 \ 1 or (resid 1092 and (name N or name CA or name C or name O or name CB )) or res \ id 1093 through 1141 or (resid 1142 and (name N or name CA or name C or name O o \ r name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.013 0.077 24154 Z= 0.773 Angle : 1.796 9.859 32954 Z= 1.198 Chirality : 0.095 0.547 3878 Planarity : 0.013 0.235 4177 Dihedral : 12.975 89.530 8318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.27 % Favored : 94.36 % Rotamer: Outliers : 0.59 % Allowed : 2.24 % Favored : 97.17 % Cbeta Deviations : 0.14 % 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: -0.71 (0.14), residues: 2924 helix: -0.88 (0.17), residues: 687 sheet: 0.86 (0.20), residues: 577 loop : -0.74 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 273 TYR 0.125 0.019 TYR B 495 PHE 0.095 0.013 PHE A 718 TRP 0.378 0.029 TRP C 886 HIS 0.015 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01340 / 0.77 (24079) covalent geometry : angle 1.77934 / 1.20 (32767) SS BOND : bond 0.01470 / 0.91 ( 38) SS BOND : angle 2.22132 / 1.45 ( 76) hydrogen bonds : bond 0.16343 / 10.76 ( 1042) hydrogen bonds : angle 8.21025 / 5.74 ( 2865) link_BETA1-4 : bond 0.02128 / 0.95 ( 3) link_BETA1-4 : angle 4.42229 / 2.70 ( 9) link_NAG-ASN : bond 0.01365 / 0.80 ( 34) link_NAG-ASN : angle 4.40146 / 3.06 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 358 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7610 (t60) cc_final: 0.7302 (t60) REVERT: A 114 THR cc_start: 0.8237 (m) cc_final: 0.8014 (p) REVERT: A 116 SER cc_start: 0.7964 (p) cc_final: 0.7670 (m) REVERT: A 126 VAL cc_start: 0.7561 (t) cc_final: 0.7269 (p) REVERT: A 207 HIS cc_start: 0.7383 (m170) cc_final: 0.7011 (t70) REVERT: A 230 PRO cc_start: 0.8923 (Cg_endo) cc_final: 0.8720 (Cg_exo) REVERT: A 378 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7481 (mmtp) REVERT: A 563 GLN cc_start: 0.7608 (mt0) cc_final: 0.6939 (mp10) REVERT: B 271 GLN cc_start: 0.8599 (mt0) cc_final: 0.8090 (mt0) REVERT: B 304 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7590 (mtmm) REVERT: B 319 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7209 (ttp-110) REVERT: B 569 ILE cc_start: 0.8088 (mm) cc_final: 0.7754 (tp) REVERT: B 935 GLN cc_start: 0.7822 (tt0) cc_final: 0.7513 (tt0) REVERT: C 117 LEU cc_start: 0.7440 (mp) cc_final: 0.6857 (tt) REVERT: C 129 LYS cc_start: 0.6725 (mttt) cc_final: 0.5941 (mppt) REVERT: C 321 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7469 (mm-40) REVERT: C 370 ASN cc_start: 0.7268 (m-40) cc_final: 0.6962 (p0) REVERT: C 378 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7212 (mmmm) REVERT: C 455 LEU cc_start: 0.8128 (tp) cc_final: 0.7909 (tp) outliers start: 15 outliers final: 4 residues processed: 372 average time/residue: 0.5475 time to fit residues: 238.4984 Evaluate side-chains 202 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 1094 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 954 GLN A1101 HIS B 334 ASN B 764 ASN B 957 GLN B1002 GLN B1088 HIS C 81 ASN C 360 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 481 ASN C 564 GLN C 603 ASN C 607 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115134 restraints weight = 27718.453| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.23 r_work: 0.3099 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24154 Z= 0.137 Angle : 0.658 11.036 32954 Z= 0.344 Chirality : 0.047 0.467 3878 Planarity : 0.004 0.034 4177 Dihedral : 5.855 48.843 3179 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 2.00 % Allowed : 7.43 % Favored : 90.57 % 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: 0.38 (0.15), residues: 2924 helix: 1.54 (0.21), residues: 649 sheet: 0.70 (0.18), residues: 714 loop : -0.49 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.025 0.002 TYR B 369 PHE 0.026 0.002 PHE B 201 TRP 0.023 0.002 TRP C 886 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (24079) covalent geometry : angle 0.63159 / 0.34 (32767) SS BOND : bond 0.00826 / 0.60 ( 38) SS BOND : angle 1.70625 / 1.08 ( 76) hydrogen bonds : bond 0.05138 / 3.39 ( 1042) hydrogen bonds : angle 6.35559 / 4.45 ( 2865) link_BETA1-4 : bond 0.00706 / 0.34 ( 3) link_BETA1-4 : angle 2.09788 / 1.26 ( 9) link_NAG-ASN : bond 0.00431 / 0.24 ( 34) link_NAG-ASN : angle 3.00284 / 1.94 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7902 (t60) cc_final: 0.7668 (t60) REVERT: A 114 THR cc_start: 0.8330 (m) cc_final: 0.8026 (p) REVERT: A 207 HIS cc_start: 0.7245 (m-70) cc_final: 0.6930 (t70) REVERT: A 314 GLN cc_start: 0.8441 (mt0) cc_final: 0.8156 (tt0) REVERT: A 347 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: A 378 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7781 (mmtp) REVERT: A 394 ASN cc_start: 0.7598 (m-40) cc_final: 0.7231 (m-40) REVERT: A 465 GLU cc_start: 0.7060 (tt0) cc_final: 0.6690 (tt0) REVERT: A 563 GLN cc_start: 0.7711 (mt0) cc_final: 0.6801 (mp10) REVERT: A 790 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8358 (mmtt) REVERT: A 988 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7809 (pt0) REVERT: A 994 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: B 200 TYR cc_start: 0.4826 (m-10) cc_final: 0.4321 (m-10) REVERT: B 319 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7510 (ttp-110) REVERT: B 321 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7590 (mm-40) REVERT: B 569 ILE cc_start: 0.8401 (mm) cc_final: 0.7706 (tp) REVERT: B 764 ASN cc_start: 0.8305 (t0) cc_final: 0.8068 (m110) REVERT: B 969 ASN cc_start: 0.8577 (m-40) cc_final: 0.8349 (m-40) REVERT: B 995 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7920 (mtp180) REVERT: C 28 TYR cc_start: 0.7642 (m-80) cc_final: 0.7377 (m-80) REVERT: C 117 LEU cc_start: 0.7046 (mp) cc_final: 0.6560 (tt) REVERT: C 271 GLN cc_start: 0.8064 (mt0) cc_final: 0.7805 (mt0) REVERT: C 370 ASN cc_start: 0.7415 (m-40) cc_final: 0.6959 (p0) REVERT: C 376 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7154 (p) REVERT: C 455 LEU cc_start: 0.7900 (tp) cc_final: 0.7213 (pt) REVERT: C 514 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8152 (p) REVERT: C 780 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8337 (pt0) REVERT: C 950 ASP cc_start: 0.8484 (m-30) cc_final: 0.8161 (m-30) REVERT: C 985 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7231 (p0) outliers start: 51 outliers final: 15 residues processed: 285 average time/residue: 0.5056 time to fit residues: 170.1054 Evaluate side-chains 210 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 178 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 223 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN A1048 HIS B 49 HIS B 804 GLN B 901 GLN B1010 GLN B1048 HIS C 81 ASN C 165 ASN C 360 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 440 ASN C 901 GLN C1048 HIS ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.183301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115081 restraints weight = 27682.688| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.42 r_work: 0.3047 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24154 Z= 0.190 Angle : 0.630 11.159 32954 Z= 0.327 Chirality : 0.047 0.315 3878 Planarity : 0.004 0.039 4177 Dihedral : 5.416 51.264 3177 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.36 % Allowed : 8.84 % Favored : 88.80 % 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: 0.37 (0.15), residues: 2924 helix: 1.63 (0.21), residues: 655 sheet: 0.67 (0.18), residues: 701 loop : -0.55 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1039 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE C 453 TRP 0.019 0.002 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (24079) covalent geometry : angle 0.60739 / 0.32 (32767) SS BOND : bond 0.00362 / 0.23 ( 38) SS BOND : angle 1.44476 / 0.90 ( 76) hydrogen bonds : bond 0.05245 / 3.43 ( 1042) hydrogen bonds : angle 6.11232 / 4.27 ( 2865) link_BETA1-4 : bond 0.00269 / 0.12 ( 3) link_BETA1-4 : angle 1.49694 / 0.87 ( 9) link_NAG-ASN : bond 0.00534 / 0.22 ( 34) link_NAG-ASN : angle 2.83992 / 1.83 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8405 (m) cc_final: 0.7927 (p) REVERT: A 207 HIS cc_start: 0.7155 (m-70) cc_final: 0.6892 (t70) REVERT: A 347 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: A 378 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7790 (mmtp) REVERT: A 394 ASN cc_start: 0.7619 (m-40) cc_final: 0.7358 (m-40) REVERT: A 559 PHE cc_start: 0.6801 (m-80) cc_final: 0.6501 (m-80) REVERT: A 577 ARG cc_start: 0.6027 (ttp-170) cc_final: 0.5622 (ttm-80) REVERT: A 702 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: A 790 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8366 (mmtt) REVERT: A 988 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7682 (pt0) REVERT: A 994 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: B 271 GLN cc_start: 0.8656 (mt0) cc_final: 0.8320 (mt0) REVERT: B 319 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7773 (ttm170) REVERT: B 321 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7690 (mm-40) REVERT: B 569 ILE cc_start: 0.8207 (mm) cc_final: 0.7590 (tp) REVERT: B 764 ASN cc_start: 0.8273 (t0) cc_final: 0.7988 (m110) REVERT: B 995 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7839 (mtp180) REVERT: C 28 TYR cc_start: 0.7758 (m-80) cc_final: 0.7278 (m-80) REVERT: C 52 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: C 117 LEU cc_start: 0.6988 (mp) cc_final: 0.6482 (tt) REVERT: C 271 GLN cc_start: 0.8015 (mt0) cc_final: 0.7707 (OUTLIER) REVERT: C 324 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: C 356 LYS cc_start: 0.7941 (tptt) cc_final: 0.7496 (tptt) REVERT: C 370 ASN cc_start: 0.7452 (m-40) cc_final: 0.6930 (p0) REVERT: C 376 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7163 (p) REVERT: C 455 LEU cc_start: 0.7809 (tp) cc_final: 0.7091 (pt) REVERT: C 619 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: C 780 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8310 (pt0) REVERT: C 950 ASP cc_start: 0.8453 (m-30) cc_final: 0.8012 (m-30) REVERT: C 985 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7062 (p0) outliers start: 60 outliers final: 25 residues processed: 253 average time/residue: 0.5164 time to fit residues: 155.3124 Evaluate side-chains 229 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 104 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 GLN A 901 GLN B1010 GLN C 321 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117830 restraints weight = 27609.668| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.44 r_work: 0.3048 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24154 Z= 0.150 Angle : 0.578 11.008 32954 Z= 0.299 Chirality : 0.045 0.314 3878 Planarity : 0.004 0.041 4177 Dihedral : 5.074 51.789 3176 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 2.24 % Allowed : 10.22 % Favored : 87.54 % 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: 0.43 (0.15), residues: 2924 helix: 1.75 (0.21), residues: 661 sheet: 0.69 (0.18), residues: 709 loop : -0.53 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.020 0.001 TYR C 170 PHE 0.026 0.001 PHE A 140 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (24079) covalent geometry : angle 0.55567 / 0.29 (32767) SS BOND : bond 0.00288 / 0.19 ( 38) SS BOND : angle 1.45991 / 0.90 ( 76) hydrogen bonds : bond 0.04640 / 3.04 ( 1042) hydrogen bonds : angle 5.90658 / 4.13 ( 2865) link_BETA1-4 : bond 0.00419 / 0.20 ( 3) link_BETA1-4 : angle 1.31409 / 0.76 ( 9) link_NAG-ASN : bond 0.00339 / 0.17 ( 34) link_NAG-ASN : angle 2.61385 / 1.70 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8276 (m) cc_final: 0.7871 (p) REVERT: A 205 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8914 (t) REVERT: A 207 HIS cc_start: 0.7141 (m-70) cc_final: 0.6848 (t-90) REVERT: A 347 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: A 378 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7365 (mtpp) REVERT: A 394 ASN cc_start: 0.7662 (m-40) cc_final: 0.7334 (m-40) REVERT: A 702 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: A 790 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8400 (mmtt) REVERT: A 988 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7732 (pt0) REVERT: A 994 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: B 227 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7210 (p) REVERT: B 271 GLN cc_start: 0.8634 (mt0) cc_final: 0.8369 (mt0) REVERT: B 319 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7747 (ttm170) REVERT: B 321 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7686 (mm-40) REVERT: B 558 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7682 (mmtp) REVERT: B 569 ILE cc_start: 0.8216 (mm) cc_final: 0.7562 (tp) REVERT: B 764 ASN cc_start: 0.8320 (t0) cc_final: 0.8108 (m110) REVERT: B 995 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7830 (mtp180) REVERT: C 28 TYR cc_start: 0.7782 (m-80) cc_final: 0.7210 (m-80) REVERT: C 52 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: C 117 LEU cc_start: 0.6950 (mp) cc_final: 0.6481 (tt) REVERT: C 271 GLN cc_start: 0.8050 (mt0) cc_final: 0.7740 (OUTLIER) REVERT: C 324 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: C 356 LYS cc_start: 0.7865 (tptt) cc_final: 0.7496 (tptt) REVERT: C 370 ASN cc_start: 0.7513 (m-40) cc_final: 0.7024 (p0) REVERT: C 455 LEU cc_start: 0.7815 (tp) cc_final: 0.7090 (pt) REVERT: C 619 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: C 661 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8480 (pt0) REVERT: C 780 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8336 (pt0) REVERT: C 950 ASP cc_start: 0.8503 (m-30) cc_final: 0.8083 (m-30) REVERT: C 983 ARG cc_start: 0.6797 (mtt180) cc_final: 0.6496 (mpt180) REVERT: C 985 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6962 (p0) REVERT: C 994 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8189 (m-30) outliers start: 57 outliers final: 21 residues processed: 236 average time/residue: 0.4709 time to fit residues: 132.1148 Evaluate side-chains 222 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 779 GLN B 935 GLN B1010 GLN B1106 GLN C 81 ASN C 165 ASN C 321 GLN C 439 ASN C 440 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.183437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117790 restraints weight = 27429.441| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.43 r_work: 0.3042 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24154 Z= 0.163 Angle : 0.577 12.795 32954 Z= 0.297 Chirality : 0.046 0.300 3878 Planarity : 0.004 0.051 4177 Dihedral : 4.984 51.709 3176 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 2.71 % Allowed : 10.89 % Favored : 86.40 % 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: 0.41 (0.15), residues: 2924 helix: 1.69 (0.21), residues: 674 sheet: 0.72 (0.18), residues: 698 loop : -0.56 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.020 0.001 TYR C1067 PHE 0.031 0.002 PHE B 392 TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (24079) covalent geometry : angle 0.55705 / 0.29 (32767) SS BOND : bond 0.00402 / 0.23 ( 38) SS BOND : angle 1.28762 / 0.81 ( 76) hydrogen bonds : bond 0.04683 / 3.07 ( 1042) hydrogen bonds : angle 5.82752 / 4.07 ( 2865) link_BETA1-4 : bond 0.00415 / 0.19 ( 3) link_BETA1-4 : angle 1.25095 / 0.70 ( 9) link_NAG-ASN : bond 0.00322 / 0.16 ( 34) link_NAG-ASN : angle 2.53344 / 1.65 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8294 (m) cc_final: 0.7896 (p) REVERT: A 207 HIS cc_start: 0.7140 (m-70) cc_final: 0.6910 (t70) REVERT: A 347 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6573 (OUTLIER) REVERT: A 357 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7426 (mmm-85) REVERT: A 378 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7735 (mmtp) REVERT: A 394 ASN cc_start: 0.7620 (m-40) cc_final: 0.7312 (m-40) REVERT: A 569 ILE cc_start: 0.8345 (tp) cc_final: 0.8123 (mp) REVERT: A 702 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: A 750 SER cc_start: 0.8938 (t) cc_final: 0.8659 (m) REVERT: A 780 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8178 (tt0) REVERT: A 790 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8412 (mmtt) REVERT: A 988 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7669 (pt0) REVERT: A 994 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: B 271 GLN cc_start: 0.8660 (mt0) cc_final: 0.8388 (mt0) REVERT: B 314 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: B 319 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7677 (ttm170) REVERT: B 321 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 558 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7740 (mmtp) REVERT: B 569 ILE cc_start: 0.8227 (mm) cc_final: 0.7549 (tp) REVERT: B 764 ASN cc_start: 0.8350 (t0) cc_final: 0.8055 (m110) REVERT: B 779 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: B 995 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7817 (mtp180) REVERT: C 28 TYR cc_start: 0.7795 (m-80) cc_final: 0.7178 (m-80) REVERT: C 102 ARG cc_start: 0.7617 (tpp80) cc_final: 0.6810 (tpp-160) REVERT: C 117 LEU cc_start: 0.6895 (mp) cc_final: 0.6446 (tt) REVERT: C 129 LYS cc_start: 0.6805 (mttt) cc_final: 0.5798 (mppt) REVERT: C 271 GLN cc_start: 0.8049 (mt0) cc_final: 0.7779 (mt0) REVERT: C 356 LYS cc_start: 0.7878 (tptt) cc_final: 0.7502 (tttm) REVERT: C 370 ASN cc_start: 0.7626 (m-40) cc_final: 0.7058 (p0) REVERT: C 376 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7288 (p) REVERT: C 386 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7314 (mmmt) REVERT: C 455 LEU cc_start: 0.7820 (tp) cc_final: 0.7093 (pt) REVERT: C 506 GLN cc_start: 0.7458 (mt0) cc_final: 0.6973 (mp10) REVERT: C 619 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: C 661 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: C 780 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8316 (pt0) REVERT: C 950 ASP cc_start: 0.8563 (m-30) cc_final: 0.8134 (m-30) REVERT: C 983 ARG cc_start: 0.6836 (mtt180) cc_final: 0.6596 (mpt180) REVERT: C 994 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8196 (m-30) outliers start: 69 outliers final: 25 residues processed: 252 average time/residue: 0.5467 time to fit residues: 162.9303 Evaluate side-chains 231 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 237 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 GLN B 66 HIS B 935 GLN B1010 GLN B1106 GLN C 81 ASN C 165 ASN C 321 GLN C 440 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117145 restraints weight = 27568.801| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.41 r_work: 0.3051 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24154 Z= 0.151 Angle : 0.561 10.201 32954 Z= 0.288 Chirality : 0.045 0.282 3878 Planarity : 0.004 0.043 4177 Dihedral : 4.820 51.547 3176 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 2.32 % Allowed : 11.87 % Favored : 85.81 % 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: 0.43 (0.15), residues: 2924 helix: 1.83 (0.21), residues: 669 sheet: 0.65 (0.18), residues: 699 loop : -0.56 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.020 0.001 TYR A 170 PHE 0.027 0.001 PHE C 453 TRP 0.013 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (24079) covalent geometry : angle 0.54042 / 0.28 (32767) SS BOND : bond 0.00384 / 0.23 ( 38) SS BOND : angle 1.41495 / 0.90 ( 76) hydrogen bonds : bond 0.04467 / 2.93 ( 1042) hydrogen bonds : angle 5.74771 / 4.01 ( 2865) link_BETA1-4 : bond 0.00333 / 0.17 ( 3) link_BETA1-4 : angle 1.14946 / 0.65 ( 9) link_NAG-ASN : bond 0.00396 / 0.17 ( 34) link_NAG-ASN : angle 2.48445 / 1.64 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8221 (m) cc_final: 0.7859 (p) REVERT: A 207 HIS cc_start: 0.7153 (m-70) cc_final: 0.6923 (t-90) REVERT: A 347 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: A 357 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: A 378 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7799 (mmtp) REVERT: A 394 ASN cc_start: 0.7582 (m-40) cc_final: 0.7243 (m-40) REVERT: A 569 ILE cc_start: 0.8448 (tp) cc_final: 0.8245 (mp) REVERT: A 577 ARG cc_start: 0.5949 (ttp-170) cc_final: 0.5728 (ttm-80) REVERT: A 702 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: A 747 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8634 (p) REVERT: A 750 SER cc_start: 0.8985 (t) cc_final: 0.8721 (m) REVERT: A 780 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8190 (tt0) REVERT: A 790 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8416 (mmtt) REVERT: A 804 GLN cc_start: 0.8643 (mp10) cc_final: 0.8256 (mm110) REVERT: A 988 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7673 (pt0) REVERT: A 994 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: B 227 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7041 (p) REVERT: B 271 GLN cc_start: 0.8666 (mt0) cc_final: 0.8406 (mt0) REVERT: B 319 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7657 (ttm170) REVERT: B 321 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7752 (mm-40) REVERT: B 558 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7732 (mmtp) REVERT: B 569 ILE cc_start: 0.8246 (mm) cc_final: 0.7575 (tp) REVERT: B 583 GLU cc_start: 0.8056 (mp0) cc_final: 0.7837 (pm20) REVERT: B 764 ASN cc_start: 0.8323 (t0) cc_final: 0.8030 (m110) REVERT: B 779 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: B 916 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8787 (tt) REVERT: B 995 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7787 (mtp180) REVERT: C 28 TYR cc_start: 0.7774 (m-80) cc_final: 0.7214 (m-80) REVERT: C 102 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7024 (tpp-160) REVERT: C 117 LEU cc_start: 0.6733 (mp) cc_final: 0.6448 (tm) REVERT: C 129 LYS cc_start: 0.6740 (mttt) cc_final: 0.5607 (mppt) REVERT: C 190 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6320 (mtt90) REVERT: C 356 LYS cc_start: 0.7808 (tptt) cc_final: 0.7390 (tttm) REVERT: C 370 ASN cc_start: 0.7498 (m-40) cc_final: 0.6980 (p0) REVERT: C 386 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7224 (mmmt) REVERT: C 403 ARG cc_start: 0.7041 (ttp80) cc_final: 0.6771 (ttm170) REVERT: C 455 LEU cc_start: 0.7767 (tp) cc_final: 0.7073 (pt) REVERT: C 619 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: C 661 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: C 780 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8287 (pt0) REVERT: C 886 TRP cc_start: 0.8078 (p90) cc_final: 0.7367 (p90) REVERT: C 950 ASP cc_start: 0.8567 (m-30) cc_final: 0.8129 (m-30) REVERT: C 994 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8187 (m-30) outliers start: 59 outliers final: 23 residues processed: 249 average time/residue: 0.5445 time to fit residues: 159.5586 Evaluate side-chains 240 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 261 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 255 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 269 optimal weight: 0.6980 chunk 128 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 GLN B 935 GLN B 957 GLN C 165 ASN C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.183131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116173 restraints weight = 27298.298| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.53 r_work: 0.3038 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 24154 Z= 0.129 Angle : 0.554 13.882 32954 Z= 0.283 Chirality : 0.044 0.289 3878 Planarity : 0.004 0.044 4177 Dihedral : 4.685 50.804 3176 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.32 % Allowed : 12.54 % Favored : 85.14 % 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: 0.49 (0.15), residues: 2924 helix: 1.88 (0.21), residues: 676 sheet: 0.65 (0.19), residues: 691 loop : -0.52 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.021 0.001 TYR A 170 PHE 0.027 0.001 PHE C 453 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (24079) covalent geometry : angle 0.53116 / 0.28 (32767) SS BOND : bond 0.00319 / 0.19 ( 38) SS BOND : angle 1.84526 / 1.11 ( 76) hydrogen bonds : bond 0.04204 / 2.74 ( 1042) hydrogen bonds : angle 5.64549 / 3.94 ( 2865) link_BETA1-4 : bond 0.00328 / 0.16 ( 3) link_BETA1-4 : angle 1.10781 / 0.62 ( 9) link_NAG-ASN : bond 0.00325 / 0.16 ( 34) link_NAG-ASN : angle 2.41196 / 1.60 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8181 (m) cc_final: 0.7834 (p) REVERT: A 207 HIS cc_start: 0.7144 (m-70) cc_final: 0.6908 (t-90) REVERT: A 347 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: A 357 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7498 (mmm-85) REVERT: A 378 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7767 (mmtp) REVERT: A 394 ASN cc_start: 0.7645 (m-40) cc_final: 0.7287 (m-40) REVERT: A 702 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: A 747 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 750 SER cc_start: 0.8942 (t) cc_final: 0.8679 (m) REVERT: A 780 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8148 (tt0) REVERT: A 790 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8428 (mmtt) REVERT: A 804 GLN cc_start: 0.8604 (mp10) cc_final: 0.8255 (mm110) REVERT: A 988 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7670 (pt0) REVERT: A 994 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: B 227 VAL cc_start: 0.7510 (OUTLIER) cc_final: 0.7214 (p) REVERT: B 271 GLN cc_start: 0.8648 (mt0) cc_final: 0.8378 (mt0) REVERT: B 319 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7678 (ttm170) REVERT: B 321 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7721 (mm-40) REVERT: B 347 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5720 (t80) REVERT: B 558 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7741 (mmtp) REVERT: B 569 ILE cc_start: 0.8210 (mm) cc_final: 0.7458 (tp) REVERT: B 583 GLU cc_start: 0.8127 (mp0) cc_final: 0.7910 (pm20) REVERT: B 764 ASN cc_start: 0.8275 (t0) cc_final: 0.7980 (m110) REVERT: B 779 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8317 (tm-30) REVERT: B 995 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7751 (mtp180) REVERT: B 1094 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8560 (t) REVERT: C 28 TYR cc_start: 0.7735 (m-80) cc_final: 0.7231 (m-80) REVERT: C 81 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.7073 (p0) REVERT: C 102 ARG cc_start: 0.7683 (tpp80) cc_final: 0.6975 (tpp-160) REVERT: C 129 LYS cc_start: 0.6688 (mttt) cc_final: 0.5658 (mppt) REVERT: C 190 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6347 (mtt90) REVERT: C 356 LYS cc_start: 0.7772 (tptt) cc_final: 0.7348 (tttm) REVERT: C 370 ASN cc_start: 0.7772 (m-40) cc_final: 0.7045 (p0) REVERT: C 455 LEU cc_start: 0.7762 (tp) cc_final: 0.7053 (pt) REVERT: C 619 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: C 661 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: C 780 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8276 (pt0) REVERT: C 886 TRP cc_start: 0.8080 (p90) cc_final: 0.7399 (p90) REVERT: C 904 TYR cc_start: 0.8429 (m-10) cc_final: 0.8120 (m-10) REVERT: C 950 ASP cc_start: 0.8524 (m-30) cc_final: 0.8064 (m-30) REVERT: C 994 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8189 (m-30) outliers start: 59 outliers final: 20 residues processed: 258 average time/residue: 0.4664 time to fit residues: 144.0562 Evaluate side-chains 243 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 172 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 226 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 935 GLN B 957 GLN B1010 GLN C 81 ASN C 165 ASN C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115284 restraints weight = 27352.668| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.59 r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24154 Z= 0.139 Angle : 0.553 10.039 32954 Z= 0.282 Chirality : 0.045 0.294 3878 Planarity : 0.004 0.043 4177 Dihedral : 4.616 49.996 3176 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 12.85 % Favored : 85.02 % 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: 0.49 (0.15), residues: 2924 helix: 1.85 (0.21), residues: 676 sheet: 0.67 (0.19), residues: 678 loop : -0.50 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.022 0.001 TYR A 170 PHE 0.030 0.001 PHE C 453 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (24079) covalent geometry : angle 0.53275 / 0.28 (32767) SS BOND : bond 0.00357 / 0.23 ( 38) SS BOND : angle 1.59719 / 0.97 ( 76) hydrogen bonds : bond 0.04298 / 2.81 ( 1042) hydrogen bonds : angle 5.60222 / 3.90 ( 2865) link_BETA1-4 : bond 0.00331 / 0.17 ( 3) link_BETA1-4 : angle 1.07383 / 0.59 ( 9) link_NAG-ASN : bond 0.00316 / 0.16 ( 34) link_NAG-ASN : angle 2.35694 / 1.56 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8106 (m) cc_final: 0.7759 (p) REVERT: A 207 HIS cc_start: 0.7241 (m-70) cc_final: 0.7019 (t-90) REVERT: A 347 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6436 (m-80) REVERT: A 357 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7574 (mmm-85) REVERT: A 378 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7822 (mmtp) REVERT: A 393 THR cc_start: 0.8247 (m) cc_final: 0.7961 (t) REVERT: A 394 ASN cc_start: 0.7672 (m-40) cc_final: 0.7191 (m-40) REVERT: A 702 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: A 747 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8581 (p) REVERT: A 750 SER cc_start: 0.8930 (t) cc_final: 0.8675 (m) REVERT: A 780 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8176 (tt0) REVERT: A 790 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8440 (mmtt) REVERT: A 804 GLN cc_start: 0.8611 (mp10) cc_final: 0.8285 (mm110) REVERT: A 988 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7671 (pt0) REVERT: A 994 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: B 227 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7167 (p) REVERT: B 271 GLN cc_start: 0.8619 (mt0) cc_final: 0.8291 (mt0) REVERT: B 319 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7874 (ttm170) REVERT: B 321 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7749 (mm-40) REVERT: B 569 ILE cc_start: 0.8193 (mm) cc_final: 0.7570 (tp) REVERT: B 583 GLU cc_start: 0.8138 (mp0) cc_final: 0.7921 (pm20) REVERT: B 764 ASN cc_start: 0.8308 (t0) cc_final: 0.7999 (m110) REVERT: B 779 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: B 995 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7751 (mtp180) REVERT: C 28 TYR cc_start: 0.7735 (m-80) cc_final: 0.7221 (m-80) REVERT: C 81 ASN cc_start: 0.7083 (OUTLIER) cc_final: 0.6757 (p0) REVERT: C 102 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7363 (tpp-160) REVERT: C 129 LYS cc_start: 0.6519 (mttt) cc_final: 0.5625 (mppt) REVERT: C 190 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6420 (mtt90) REVERT: C 356 LYS cc_start: 0.7806 (tptt) cc_final: 0.7364 (tttp) REVERT: C 370 ASN cc_start: 0.7870 (m-40) cc_final: 0.7012 (p0) REVERT: C 455 LEU cc_start: 0.7751 (tp) cc_final: 0.7043 (pt) REVERT: C 619 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: C 661 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: C 780 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8262 (pt0) REVERT: C 886 TRP cc_start: 0.8154 (p90) cc_final: 0.7522 (p90) REVERT: C 950 ASP cc_start: 0.8576 (m-30) cc_final: 0.8126 (m-30) REVERT: C 994 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8199 (m-30) outliers start: 54 outliers final: 24 residues processed: 255 average time/residue: 0.5081 time to fit residues: 154.1715 Evaluate side-chains 250 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 153 optimal weight: 0.3980 chunk 171 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN B 935 GLN B 957 GLN C 165 ASN C 321 GLN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112069 restraints weight = 27337.426| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.35 r_work: 0.3019 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24154 Z= 0.179 Angle : 0.577 10.354 32954 Z= 0.295 Chirality : 0.046 0.294 3878 Planarity : 0.004 0.043 4177 Dihedral : 4.632 50.061 3174 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.08 % Allowed : 13.17 % Favored : 84.75 % 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: 0.41 (0.15), residues: 2924 helix: 1.75 (0.21), residues: 672 sheet: 0.59 (0.18), residues: 708 loop : -0.53 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.022 0.002 TYR A 170 PHE 0.031 0.002 PHE C 453 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (24079) covalent geometry : angle 0.55479 / 0.29 (32767) SS BOND : bond 0.00410 / 0.28 ( 38) SS BOND : angle 1.86551 / 1.12 ( 76) hydrogen bonds : bond 0.04649 / 3.04 ( 1042) hydrogen bonds : angle 5.68677 / 3.96 ( 2865) link_BETA1-4 : bond 0.00263 / 0.13 ( 3) link_BETA1-4 : angle 1.10463 / 0.61 ( 9) link_NAG-ASN : bond 0.00338 / 0.17 ( 34) link_NAG-ASN : angle 2.44321 / 1.64 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8123 (m) cc_final: 0.7796 (p) REVERT: A 357 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7624 (mmm-85) REVERT: A 378 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7885 (mmtp) REVERT: A 393 THR cc_start: 0.8261 (m) cc_final: 0.7995 (t) REVERT: A 394 ASN cc_start: 0.7664 (m-40) cc_final: 0.7377 (m-40) REVERT: A 702 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: A 747 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8639 (p) REVERT: A 750 SER cc_start: 0.8987 (t) cc_final: 0.8725 (m) REVERT: A 780 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8189 (tt0) REVERT: A 790 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8467 (mmtt) REVERT: A 804 GLN cc_start: 0.8615 (mp10) cc_final: 0.8309 (mm110) REVERT: A 994 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: B 271 GLN cc_start: 0.8700 (mt0) cc_final: 0.8407 (mt0) REVERT: B 319 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7937 (ttm170) REVERT: B 321 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7753 (mm-40) REVERT: B 569 ILE cc_start: 0.8290 (mm) cc_final: 0.7672 (tp) REVERT: B 583 GLU cc_start: 0.8212 (mp0) cc_final: 0.7986 (pm20) REVERT: B 764 ASN cc_start: 0.8341 (t0) cc_final: 0.8021 (m110) REVERT: B 779 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 995 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7804 (mtp180) REVERT: C 28 TYR cc_start: 0.7759 (m-80) cc_final: 0.7261 (m-80) REVERT: C 102 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7408 (tpp-160) REVERT: C 129 LYS cc_start: 0.6540 (mttt) cc_final: 0.5768 (mppt) REVERT: C 356 LYS cc_start: 0.7908 (tptt) cc_final: 0.7435 (tttp) REVERT: C 370 ASN cc_start: 0.7862 (m-40) cc_final: 0.7018 (p0) REVERT: C 387 LEU cc_start: 0.8887 (mm) cc_final: 0.8668 (mp) REVERT: C 455 LEU cc_start: 0.7791 (tp) cc_final: 0.7074 (pt) REVERT: C 619 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: C 661 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: C 780 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8280 (pt0) REVERT: C 855 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6636 (m-10) REVERT: C 886 TRP cc_start: 0.8118 (p90) cc_final: 0.7436 (p90) REVERT: C 950 ASP cc_start: 0.8590 (m-30) cc_final: 0.8135 (m-30) REVERT: C 994 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8211 (m-30) outliers start: 53 outliers final: 32 residues processed: 239 average time/residue: 0.5133 time to fit residues: 146.1760 Evaluate side-chains 248 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 935 GLN B 957 GLN C 165 ASN C 321 GLN C 603 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112349 restraints weight = 27281.123| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.39 r_work: 0.3000 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 24154 Z= 0.187 Angle : 0.588 10.349 32954 Z= 0.301 Chirality : 0.046 0.297 3878 Planarity : 0.004 0.043 4177 Dihedral : 4.673 50.222 3174 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.97 % Allowed : 13.29 % Favored : 84.75 % 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: 0.35 (0.15), residues: 2924 helix: 1.72 (0.21), residues: 668 sheet: 0.54 (0.18), residues: 706 loop : -0.57 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.022 0.002 TYR C 904 PHE 0.032 0.002 PHE C 453 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (24079) covalent geometry : angle 0.56563 / 0.29 (32767) SS BOND : bond 0.00374 / 0.24 ( 38) SS BOND : angle 1.87745 / 1.13 ( 76) hydrogen bonds : bond 0.04741 / 3.09 ( 1042) hydrogen bonds : angle 5.72185 / 3.98 ( 2865) link_BETA1-4 : bond 0.00295 / 0.15 ( 3) link_BETA1-4 : angle 1.07532 / 0.60 ( 9) link_NAG-ASN : bond 0.00336 / 0.17 ( 34) link_NAG-ASN : angle 2.45670 / 1.64 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8067 (m) cc_final: 0.7777 (p) REVERT: A 170 TYR cc_start: 0.8158 (t80) cc_final: 0.7941 (t80) REVERT: A 347 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6416 (m-10) REVERT: A 357 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7608 (mmm-85) REVERT: A 378 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7883 (mmtp) REVERT: A 394 ASN cc_start: 0.7564 (m-40) cc_final: 0.7298 (m-40) REVERT: A 702 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: A 747 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 750 SER cc_start: 0.8986 (t) cc_final: 0.8711 (m) REVERT: A 780 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8187 (tt0) REVERT: A 790 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8477 (mmtt) REVERT: A 804 GLN cc_start: 0.8610 (mp10) cc_final: 0.8306 (mm110) REVERT: A 985 ASP cc_start: 0.7717 (p0) cc_final: 0.7385 (p0) REVERT: A 988 GLU cc_start: 0.8212 (mp0) cc_final: 0.7697 (pt0) REVERT: A 994 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: B 200 TYR cc_start: 0.4799 (m-10) cc_final: 0.4555 (m-10) REVERT: B 271 GLN cc_start: 0.8690 (mt0) cc_final: 0.8402 (mt0) REVERT: B 321 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7761 (mm-40) REVERT: B 569 ILE cc_start: 0.8281 (mm) cc_final: 0.7683 (tp) REVERT: B 583 GLU cc_start: 0.8271 (mp0) cc_final: 0.7966 (pm20) REVERT: B 764 ASN cc_start: 0.8387 (t0) cc_final: 0.8047 (m110) REVERT: B 779 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: B 869 MET cc_start: 0.9104 (mtt) cc_final: 0.8816 (mtt) REVERT: B 995 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7826 (mtp180) REVERT: C 28 TYR cc_start: 0.7779 (m-80) cc_final: 0.7278 (m-80) REVERT: C 102 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7341 (tpp-160) REVERT: C 129 LYS cc_start: 0.6470 (mttt) cc_final: 0.5726 (mppt) REVERT: C 190 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6469 (mtt90) REVERT: C 192 PHE cc_start: 0.8123 (m-80) cc_final: 0.7915 (m-80) REVERT: C 356 LYS cc_start: 0.7907 (tptt) cc_final: 0.7436 (tttp) REVERT: C 370 ASN cc_start: 0.7905 (m-40) cc_final: 0.7069 (p0) REVERT: C 387 LEU cc_start: 0.8868 (mm) cc_final: 0.8655 (mp) REVERT: C 455 LEU cc_start: 0.7775 (tp) cc_final: 0.6919 (pt) REVERT: C 619 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: C 661 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8503 (pt0) REVERT: C 780 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8270 (pt0) REVERT: C 855 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6706 (m-10) REVERT: C 886 TRP cc_start: 0.8129 (p90) cc_final: 0.7403 (p90) REVERT: C 950 ASP cc_start: 0.8604 (m-30) cc_final: 0.8142 (m-30) REVERT: C 994 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8214 (m-30) outliers start: 50 outliers final: 30 residues processed: 234 average time/residue: 0.4773 time to fit residues: 132.8310 Evaluate side-chains 244 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 194 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 127 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 935 GLN B 957 GLN B1106 GLN C 165 ASN C 321 GLN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.183890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115450 restraints weight = 27233.261| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.45 r_work: 0.3051 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24154 Z= 0.111 Angle : 0.526 9.293 32954 Z= 0.270 Chirality : 0.044 0.289 3878 Planarity : 0.004 0.043 4177 Dihedral : 4.381 48.383 3174 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.38 % Allowed : 14.11 % Favored : 84.51 % 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: 0.57 (0.15), residues: 2924 helix: 2.01 (0.21), residues: 671 sheet: 0.68 (0.19), residues: 675 loop : -0.47 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.020 0.001 TYR C 170 PHE 0.030 0.001 PHE C 453 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24079) covalent geometry : angle 0.50688 / 0.26 (32767) SS BOND : bond 0.00344 / 0.23 ( 38) SS BOND : angle 1.50144 / 0.91 ( 76) hydrogen bonds : bond 0.03888 / 2.54 ( 1042) hydrogen bonds : angle 5.51098 / 3.84 ( 2865) link_BETA1-4 : bond 0.00360 / 0.18 ( 3) link_BETA1-4 : angle 1.05254 / 0.58 ( 9) link_NAG-ASN : bond 0.00340 / 0.17 ( 34) link_NAG-ASN : angle 2.27028 / 1.53 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9694.47 seconds wall clock time: 165 minutes 26.76 seconds (9926.76 seconds total)