Starting phenix.real_space_refine on Thu Mar 5 15:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwo_23552/03_2026/7lwo_23552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwo_23552/03_2026/7lwo_23552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lwo_23552/03_2026/7lwo_23552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwo_23552/03_2026/7lwo_23552.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwo_23552/03_2026/7lwo_23552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwo_23552/03_2026/7lwo_23552.map" } resolution = 2.85 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= 0.100 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 101 5.16 5 C 15038 2.51 5 N 3878 2.21 5 O 4539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23556 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.28, per 1000 atoms: 0.22 Number of scatterers: 23556 At special positions: 0 Unit cell: (128.28, 135.763, 193.489, 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 101 16.00 O 4539 8.00 N 3878 7.00 C 15038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.03 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=2.03 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=1.92 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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 717 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 801 " " 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 282 " " NAG B1310 " - " ASN B 234 " " 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 331 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN B1098 " " NAG F 1 " - " ASN C1098 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.0 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: 73 helices and 44 sheets defined 27.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.686A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.449A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.320A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.566A 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: 3.922A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A 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: 3.733A 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 918 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: 3.710A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.111A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.706A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.097A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.616A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 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: 3.750A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.797A 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 891 removed outlier: 3.780A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.077A 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: 3.636A 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: 4.037A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.160A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) 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 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.004A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.670A 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 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.564A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.707A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (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 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.597A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.506A 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: 3.679A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.341A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.934A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.512A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.804A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.631A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.372A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.533A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.754A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.585A 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: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.262A 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: 4.627A 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: 8.373A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.741A 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: 3.603A 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: 7.007A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.856A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.393A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.206A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.466A 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: 3.773A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.481A 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: 5.969A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.671A 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: 4.431A 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: 4.707A 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: 8.600A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.758A 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: 7.490A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.799A 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 removed outlier: 3.735A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.550A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.791A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.057A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.755A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.988A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.454A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.632A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2868 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: 6.01 Time building geometry restraints manager: 2.65 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: 6176 1.33 - 1.46: 4484 1.46 - 1.58: 13279 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24064 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.62e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.41e+01 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 24059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 23060 1.82 - 3.64: 8284 3.64 - 5.46: 1278 5.46 - 7.28: 115 7.28 - 9.10: 10 Bond angle restraints: 32747 Sorted by residual: angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 116.43 6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 116.87 5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " pdb=" CG PHE A 58 " ideal model delta sigma weight residual 113.80 119.53 -5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 118.28 -5.68 1.00e+00 1.00e+00 3.23e+01 ... (remaining 32742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13835 17.97 - 35.94: 734 35.94 - 53.91: 123 53.91 - 71.88: 44 71.88 - 89.85: 24 Dihedral angle restraints: 14760 sinusoidal: 6106 harmonic: 8654 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.05 79.05 1 1.00e+01 1.00e-02 7.78e+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 -150.73 64.73 1 1.00e+01 1.00e-02 5.50e+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 93.00 154.73 -61.73 1 1.00e+01 1.00e-02 5.05e+01 ... (remaining 14757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2820 0.103 - 0.205: 955 0.205 - 0.308: 80 0.308 - 0.410: 16 0.410 - 0.513: 2 Chirality restraints: 3873 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 -2.56 0.16 2.00e-02 2.50e+03 6.27e+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 -2.55 0.15 2.00e-02 2.50e+03 5.80e+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 -2.52 0.12 2.00e-02 2.50e+03 3.60e+01 ... (remaining 3870 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.371 2.00e-02 2.50e+03 2.01e-01 1.01e+03 pdb=" CG TRP C 886 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.190 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.138 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.303 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.212 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.070 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.251 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.140 2.00e-02 2.50e+03 1.52e-01 2.89e+02 pdb=" CG ASN A 331 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.237 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.140 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN B1074 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.228 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.176 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11011 2.99 - 3.47: 22005 3.47 - 3.94: 39116 3.94 - 4.42: 43250 4.42 - 4.90: 73642 Nonbonded interactions: 189024 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.511 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.523 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.527 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.531 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.546 3.040 ... (remaining 189019 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 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 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 na \ me 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 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 479 or (resid 480 and (name N or name CA or name C or name O o \ r name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or na \ me C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 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 name CA or name C or name O or name CB )) or resid 1143 through 1144 o \ r (resid 1145 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 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 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 or 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 or (resid \ 583 and (name N or name CA or name C or name O or name CB )) or resid 584 throug \ h 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 o \ r name CB )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 through 747 o \ r (resid 748 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 49 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 name O or n \ ame CB )) or resid 815 through 827 or resid 855 through 866 or (resid 867 throug \ h 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thro \ ugh 1091 or (resid 1092 and (name N or name CA or name C or name O or name CB )) \ or resid 1093 through 1143 or (resid 1144 through 1146 and (name N or name CA o \ r 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 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r 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 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 483 or resid 485 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 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 n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A 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 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N o \ r 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: 1.640 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.530 Find NCS groups from input model: 0.730 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.111 24137 Z= 0.779 Angle : 1.804 11.287 32929 Z= 1.203 Chirality : 0.095 0.513 3873 Planarity : 0.013 0.201 4176 Dihedral : 12.476 89.855 9073 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.55 % Favored : 95.14 % Rotamer: Outliers : 0.59 % Allowed : 1.81 % Favored : 97.60 % Cbeta Deviations : 0.22 % 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: -0.78 (0.14), residues: 2924 helix: -0.98 (0.17), residues: 692 sheet: 0.67 (0.20), residues: 581 loop : -0.70 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 905 TYR 0.111 0.019 TYR B 707 PHE 0.090 0.013 PHE C 718 TRP 0.371 0.030 TRP C 886 HIS 0.013 0.003 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01345 (24064) covalent geometry : angle 1.78685 (32747) SS BOND : bond 0.02200 ( 37) SS BOND : angle 2.23175 ( 74) hydrogen bonds : bond 0.16304 ( 1042) hydrogen bonds : angle 8.14966 ( 2868) link_BETA1-4 : bond 0.02026 ( 3) link_BETA1-4 : angle 4.10217 ( 9) link_NAG-ASN : bond 0.01327 ( 33) link_NAG-ASN : angle 4.60763 ( 99) *********************** 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 407 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8035 (p-90) cc_final: 0.7822 (p-90) REVERT: A 389 ASP cc_start: 0.6933 (m-30) cc_final: 0.6615 (m-30) REVERT: A 859 THR cc_start: 0.8492 (p) cc_final: 0.8270 (t) REVERT: B 731 MET cc_start: 0.9084 (mtm) cc_final: 0.8713 (mtp) REVERT: B 859 THR cc_start: 0.8706 (p) cc_final: 0.8494 (t) REVERT: B 960 ASN cc_start: 0.7719 (m-40) cc_final: 0.7509 (m110) REVERT: C 238 PHE cc_start: 0.8139 (p90) cc_final: 0.7923 (p90) REVERT: C 434 ILE cc_start: 0.8649 (mt) cc_final: 0.8390 (mt) outliers start: 15 outliers final: 7 residues processed: 405 average time/residue: 0.5816 time to fit residues: 273.7224 Evaluate side-chains 253 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 246 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0010 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 532 ASN A 703 ASN A 779 GLN A 954 GLN B 540 ASN B 764 ASN B1048 HIS B1125 ASN B1135 ASN C 211 ASN C 239 GLN C 394 ASN C1005 GLN C1048 HIS C1119 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117138 restraints weight = 27335.141| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.05 r_work: 0.3045 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24137 Z= 0.161 Angle : 0.679 10.555 32929 Z= 0.351 Chirality : 0.048 0.450 3873 Planarity : 0.004 0.062 4176 Dihedral : 6.429 57.075 3938 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 2.36 % Allowed : 7.83 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.23 (0.15), residues: 2924 helix: 1.18 (0.20), residues: 667 sheet: 0.64 (0.18), residues: 693 loop : -0.49 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 190 TYR 0.022 0.002 TYR A 369 PHE 0.018 0.002 PHE A 464 TRP 0.023 0.002 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00374 (24064) covalent geometry : angle 0.65426 (32747) SS BOND : bond 0.00499 ( 37) SS BOND : angle 1.21076 ( 74) hydrogen bonds : bond 0.05249 ( 1042) hydrogen bonds : angle 6.31218 ( 2868) link_BETA1-4 : bond 0.00623 ( 3) link_BETA1-4 : angle 2.07431 ( 9) link_NAG-ASN : bond 0.00358 ( 33) link_NAG-ASN : angle 3.20458 ( 99) *********************** 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 327 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: A 316 SER cc_start: 0.8539 (m) cc_final: 0.8331 (m) REVERT: A 364 ASP cc_start: 0.7045 (t0) cc_final: 0.6807 (t0) REVERT: A 408 ARG cc_start: 0.8047 (ppt90) cc_final: 0.7674 (ppt90) REVERT: A 1143 PRO cc_start: 0.7828 (Cg_exo) cc_final: 0.7603 (Cg_endo) REVERT: B 190 ARG cc_start: 0.6904 (mtt-85) cc_final: 0.6554 (mmt90) REVERT: B 569 ILE cc_start: 0.8534 (mt) cc_final: 0.8181 (tt) REVERT: B 646 ARG cc_start: 0.8562 (mtp180) cc_final: 0.7815 (mmp80) REVERT: B 654 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7828 (tt0) REVERT: B 656 VAL cc_start: 0.8074 (t) cc_final: 0.7733 (m) REVERT: B 814 LYS cc_start: 0.7659 (mttm) cc_final: 0.7372 (mtmm) REVERT: B 988 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 994 ASP cc_start: 0.8025 (m-30) cc_final: 0.7766 (m-30) REVERT: B 1038 LYS cc_start: 0.8942 (tttm) cc_final: 0.8363 (mmtp) REVERT: C 129 LYS cc_start: 0.7317 (mtpt) cc_final: 0.7075 (tttm) REVERT: C 271 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6875 (tp-100) REVERT: C 347 PHE cc_start: 0.6435 (m-10) cc_final: 0.5750 (m-80) REVERT: C 378 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6462 (tppt) REVERT: C 564 GLN cc_start: 0.7776 (tp40) cc_final: 0.7328 (tt0) REVERT: C 583 GLU cc_start: 0.8525 (pt0) cc_final: 0.8316 (pm20) REVERT: C 656 VAL cc_start: 0.7516 (t) cc_final: 0.7173 (m) REVERT: C 702 GLU cc_start: 0.7994 (pt0) cc_final: 0.7536 (tm-30) REVERT: C 855 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.5802 (m-80) REVERT: C 935 GLN cc_start: 0.7592 (mt0) cc_final: 0.7364 (mt0) REVERT: C 957 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7349 (pt0) REVERT: C 1038 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8317 (mmpt) outliers start: 60 outliers final: 25 residues processed: 302 average time/residue: 0.5002 time to fit residues: 179.2593 Evaluate side-chains 240 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 129 optimal weight: 40.0000 chunk 93 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1048 HIS C 239 GLN C 314 GLN C 394 ASN C 901 GLN C1005 GLN C1010 GLN C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.190151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130421 restraints weight = 27464.221| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.85 r_work: 0.3142 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24137 Z= 0.109 Angle : 0.573 10.652 32929 Z= 0.296 Chirality : 0.044 0.393 3873 Planarity : 0.004 0.038 4176 Dihedral : 5.794 56.354 3935 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 2.44 % Allowed : 8.89 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.55 (0.15), residues: 2924 helix: 1.77 (0.21), residues: 663 sheet: 0.71 (0.19), residues: 675 loop : -0.37 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.020 0.001 TYR A 170 PHE 0.021 0.001 PHE C 106 TRP 0.016 0.001 TRP C 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00233 (24064) covalent geometry : angle 0.55271 (32747) SS BOND : bond 0.00306 ( 37) SS BOND : angle 1.02970 ( 74) hydrogen bonds : bond 0.04332 ( 1042) hydrogen bonds : angle 5.89164 ( 2868) link_BETA1-4 : bond 0.00331 ( 3) link_BETA1-4 : angle 1.47782 ( 9) link_NAG-ASN : bond 0.00344 ( 33) link_NAG-ASN : angle 2.70055 ( 99) *********************** 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 306 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: A 287 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: A 319 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7342 (ttm-80) REVERT: A 408 ARG cc_start: 0.8170 (ppt90) cc_final: 0.7861 (ppt90) REVERT: A 454 ARG cc_start: 0.6329 (ttm-80) cc_final: 0.5830 (mmm-85) REVERT: A 574 ASP cc_start: 0.7405 (t0) cc_final: 0.7073 (t0) REVERT: A 780 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7741 (pt0) REVERT: A 787 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: A 825 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7852 (mmmt) REVERT: B 190 ARG cc_start: 0.7045 (mtt-85) cc_final: 0.6656 (mmt90) REVERT: B 564 GLN cc_start: 0.7066 (mm110) cc_final: 0.6769 (mm110) REVERT: B 568 ASP cc_start: 0.7700 (t0) cc_final: 0.7475 (t0) REVERT: B 569 ILE cc_start: 0.8556 (mt) cc_final: 0.8222 (tt) REVERT: B 656 VAL cc_start: 0.8234 (t) cc_final: 0.7910 (m) REVERT: B 814 LYS cc_start: 0.7688 (mttm) cc_final: 0.7385 (mtmt) REVERT: B 988 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 1038 LYS cc_start: 0.8968 (tttm) cc_final: 0.8517 (mptt) REVERT: C 271 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6911 (tp-100) REVERT: C 309 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7157 (mp0) REVERT: C 347 PHE cc_start: 0.6629 (m-10) cc_final: 0.6072 (m-80) REVERT: C 378 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6956 (mppt) REVERT: C 434 ILE cc_start: 0.8317 (mt) cc_final: 0.8098 (mp) REVERT: C 564 GLN cc_start: 0.7711 (tp40) cc_final: 0.7298 (tt0) REVERT: C 702 GLU cc_start: 0.7946 (pt0) cc_final: 0.7649 (tm-30) REVERT: C 780 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7759 (pt0) REVERT: C 855 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: C 935 GLN cc_start: 0.7796 (mt0) cc_final: 0.7593 (mt0) REVERT: C 957 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7484 (pt0) outliers start: 62 outliers final: 25 residues processed: 283 average time/residue: 0.5728 time to fit residues: 189.6595 Evaluate side-chains 236 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 35 optimal weight: 0.0270 chunk 248 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 39 optimal weight: 0.0010 overall best weight: 1.6050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 544 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1010 GLN B 901 GLN B1010 GLN C 239 GLN C 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.187827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116491 restraints weight = 27201.631| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.03 r_work: 0.3031 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24137 Z= 0.160 Angle : 0.592 9.919 32929 Z= 0.302 Chirality : 0.046 0.284 3873 Planarity : 0.004 0.041 4176 Dihedral : 5.575 56.218 3930 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 2.83 % Allowed : 9.95 % Favored : 87.22 % 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: 0.47 (0.15), residues: 2924 helix: 1.74 (0.21), residues: 668 sheet: 0.55 (0.18), residues: 698 loop : -0.39 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 190 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.002 PHE C 643 TRP 0.019 0.002 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00382 (24064) covalent geometry : angle 0.57232 (32747) SS BOND : bond 0.00447 ( 37) SS BOND : angle 1.01856 ( 74) hydrogen bonds : bond 0.04686 ( 1042) hydrogen bonds : angle 5.82412 ( 2868) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 1.27841 ( 9) link_NAG-ASN : bond 0.00368 ( 33) link_NAG-ASN : angle 2.66569 ( 99) *********************** 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 294 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 222 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: A 309 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: A 319 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7140 (ttm-80) REVERT: A 389 ASP cc_start: 0.8200 (m-30) cc_final: 0.7756 (m-30) REVERT: A 408 ARG cc_start: 0.8011 (ppt90) cc_final: 0.7699 (ppt90) REVERT: A 454 ARG cc_start: 0.6362 (ttm-80) cc_final: 0.5862 (mmm-85) REVERT: A 574 ASP cc_start: 0.7542 (t0) cc_final: 0.7230 (t0) REVERT: A 780 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7630 (pt0) REVERT: A 787 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8166 (mm-40) REVERT: A 825 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7746 (mmmt) REVERT: A 935 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: B 190 ARG cc_start: 0.6821 (mtt-85) cc_final: 0.6475 (mmt90) REVERT: B 314 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: B 532 ASN cc_start: 0.7586 (t0) cc_final: 0.7349 (t160) REVERT: B 564 GLN cc_start: 0.7037 (mm110) cc_final: 0.6786 (mm110) REVERT: B 568 ASP cc_start: 0.7632 (t0) cc_final: 0.7420 (t0) REVERT: B 569 ILE cc_start: 0.8497 (mt) cc_final: 0.8133 (tt) REVERT: B 619 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8112 (mp0) REVERT: B 656 VAL cc_start: 0.8067 (t) cc_final: 0.7814 (m) REVERT: B 790 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8091 (mmtt) REVERT: B 814 LYS cc_start: 0.7685 (mttm) cc_final: 0.7335 (mtmt) REVERT: B 1038 LYS cc_start: 0.8985 (tttm) cc_final: 0.8393 (mmtp) REVERT: C 45 SER cc_start: 0.8164 (p) cc_final: 0.7819 (t) REVERT: C 271 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6758 (tp-100) REVERT: C 309 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7087 (mp0) REVERT: C 347 PHE cc_start: 0.6532 (m-10) cc_final: 0.5939 (m-80) REVERT: C 357 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7300 (ttm110) REVERT: C 378 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6916 (mppt) REVERT: C 564 GLN cc_start: 0.7666 (tp40) cc_final: 0.7232 (tt0) REVERT: C 702 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: C 780 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7789 (pt0) REVERT: C 855 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6084 (m-80) REVERT: C 935 GLN cc_start: 0.7548 (mt0) cc_final: 0.7327 (mt0) REVERT: C 957 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7241 (pt0) outliers start: 72 outliers final: 32 residues processed: 266 average time/residue: 0.5729 time to fit residues: 177.5635 Evaluate side-chains 252 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 234 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 49 HIS A 52 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 901 GLN C 239 GLN C 394 ASN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115574 restraints weight = 27123.316| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.44 r_work: 0.3025 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 24137 Z= 0.272 Angle : 0.671 11.209 32929 Z= 0.343 Chirality : 0.050 0.611 3873 Planarity : 0.004 0.051 4176 Dihedral : 5.833 56.944 3930 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.08 % Favored : 96.82 % Rotamer: Outliers : 3.19 % Allowed : 10.46 % Favored : 86.35 % 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: 0.12 (0.15), residues: 2924 helix: 1.29 (0.21), residues: 670 sheet: 0.40 (0.18), residues: 670 loop : -0.57 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.019 0.002 TYR A1067 PHE 0.020 0.002 PHE A 464 TRP 0.025 0.002 TRP C 886 HIS 0.006 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00671 (24064) covalent geometry : angle 0.64983 (32747) SS BOND : bond 0.00705 ( 37) SS BOND : angle 1.39879 ( 74) hydrogen bonds : bond 0.05617 ( 1042) hydrogen bonds : angle 6.03561 ( 2868) link_BETA1-4 : bond 0.00134 ( 3) link_BETA1-4 : angle 1.30256 ( 9) link_NAG-ASN : bond 0.00403 ( 33) link_NAG-ASN : angle 2.93093 ( 99) *********************** 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 295 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 214 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6892 (tt0) REVERT: A 309 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: A 319 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7267 (ttm-80) REVERT: A 389 ASP cc_start: 0.8277 (m-30) cc_final: 0.7901 (m-30) REVERT: A 408 ARG cc_start: 0.7984 (ppt90) cc_final: 0.7690 (ppt90) REVERT: A 454 ARG cc_start: 0.6488 (ttm-80) cc_final: 0.6248 (mmm-85) REVERT: A 574 ASP cc_start: 0.7550 (t0) cc_final: 0.7333 (t0) REVERT: A 780 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7609 (pt0) REVERT: A 787 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: A 935 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: A 1139 ASP cc_start: 0.8326 (t0) cc_final: 0.7167 (p0) REVERT: B 190 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6624 (mmt90) REVERT: B 314 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: B 532 ASN cc_start: 0.7652 (t0) cc_final: 0.7376 (t160) REVERT: B 569 ILE cc_start: 0.8517 (mt) cc_final: 0.8122 (tt) REVERT: B 619 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8108 (mp0) REVERT: B 790 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8107 (mmtt) REVERT: B 814 LYS cc_start: 0.7765 (mttm) cc_final: 0.7425 (mtmt) REVERT: B 855 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.4733 (m-80) REVERT: B 950 ASP cc_start: 0.8071 (m-30) cc_final: 0.7679 (m-30) REVERT: B 964 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7822 (tppt) REVERT: C 41 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7066 (mmtt) REVERT: C 45 SER cc_start: 0.8200 (p) cc_final: 0.7976 (t) REVERT: C 271 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6903 (tp-100) REVERT: C 309 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7153 (mp0) REVERT: C 347 PHE cc_start: 0.6237 (m-10) cc_final: 0.5511 (m-80) REVERT: C 394 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7379 (m-40) REVERT: C 453 PHE cc_start: 0.5392 (p90) cc_final: 0.4121 (p90) REVERT: C 564 GLN cc_start: 0.7697 (tp40) cc_final: 0.7292 (tt0) REVERT: C 855 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: C 935 GLN cc_start: 0.7678 (mt0) cc_final: 0.7429 (mt0) REVERT: C 957 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7271 (pt0) REVERT: C 1038 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8371 (mmpt) REVERT: C 1144 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8134 (mm-30) outliers start: 81 outliers final: 45 residues processed: 263 average time/residue: 0.5508 time to fit residues: 169.3139 Evaluate side-chains 259 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 170 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 263 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 38 optimal weight: 30.0000 chunk 256 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 675 GLN A1005 GLN B 804 GLN B 901 GLN C 239 GLN C 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.188689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115653 restraints weight = 27203.094| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.06 r_work: 0.3047 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24137 Z= 0.109 Angle : 0.538 11.410 32929 Z= 0.276 Chirality : 0.044 0.349 3873 Planarity : 0.004 0.056 4176 Dihedral : 5.349 56.299 3930 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 2.12 % Allowed : 11.84 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 2924 helix: 1.83 (0.21), residues: 666 sheet: 0.46 (0.18), residues: 685 loop : -0.42 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.024 0.001 TYR C 508 PHE 0.019 0.001 PHE B 192 TRP 0.013 0.001 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (24064) covalent geometry : angle 0.52091 (32747) SS BOND : bond 0.00305 ( 37) SS BOND : angle 0.97027 ( 74) hydrogen bonds : bond 0.04039 ( 1042) hydrogen bonds : angle 5.65943 ( 2868) link_BETA1-4 : bond 0.00472 ( 3) link_BETA1-4 : angle 1.01195 ( 9) link_NAG-ASN : bond 0.00389 ( 33) link_NAG-ASN : angle 2.37114 ( 99) *********************** 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 271 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7387 (mtp85) cc_final: 0.7130 (mtp85) REVERT: A 309 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: A 319 ARG cc_start: 0.7742 (ttm170) cc_final: 0.7292 (ttm-80) REVERT: A 389 ASP cc_start: 0.8217 (m-30) cc_final: 0.7840 (m-30) REVERT: A 565 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6829 (p90) REVERT: A 574 ASP cc_start: 0.7625 (t0) cc_final: 0.7372 (t0) REVERT: A 780 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7649 (pt0) REVERT: A 935 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: A 1139 ASP cc_start: 0.8242 (t0) cc_final: 0.6993 (p0) REVERT: B 190 ARG cc_start: 0.6883 (mtt-85) cc_final: 0.6502 (mmt90) REVERT: B 191 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: B 532 ASN cc_start: 0.7609 (t0) cc_final: 0.7356 (t160) REVERT: B 569 ILE cc_start: 0.8445 (mt) cc_final: 0.8101 (tt) REVERT: B 619 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8034 (mp0) REVERT: B 790 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8123 (mmtt) REVERT: B 935 GLN cc_start: 0.8137 (tt0) cc_final: 0.7933 (tt0) REVERT: B 950 ASP cc_start: 0.8049 (m-30) cc_final: 0.7659 (m-30) REVERT: B 964 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7727 (tppt) REVERT: B 1038 LYS cc_start: 0.9053 (tttm) cc_final: 0.8462 (mmtp) REVERT: C 45 SER cc_start: 0.8112 (p) cc_final: 0.7893 (t) REVERT: C 271 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6906 (tp-100) REVERT: C 309 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7163 (mp0) REVERT: C 347 PHE cc_start: 0.6469 (m-10) cc_final: 0.5860 (m-80) REVERT: C 378 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6922 (mppt) REVERT: C 564 GLN cc_start: 0.7693 (tp40) cc_final: 0.7275 (tt0) REVERT: C 957 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7275 (pt0) outliers start: 54 outliers final: 27 residues processed: 253 average time/residue: 0.5471 time to fit residues: 162.1620 Evaluate side-chains 239 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 175 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 95 optimal weight: 0.0570 chunk 131 optimal weight: 20.0000 chunk 235 optimal weight: 0.0770 overall best weight: 1.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 675 GLN A 954 GLN C 239 GLN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116689 restraints weight = 27101.494| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.18 r_work: 0.2998 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24137 Z= 0.167 Angle : 0.576 10.453 32929 Z= 0.293 Chirality : 0.045 0.349 3873 Planarity : 0.004 0.057 4176 Dihedral : 5.398 56.376 3930 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.74 % Favored : 97.13 % Rotamer: Outliers : 2.52 % Allowed : 12.11 % Favored : 85.37 % 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: 1.67 (0.21), residues: 677 sheet: 0.43 (0.18), residues: 693 loop : -0.45 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.028 0.002 TYR C 508 PHE 0.019 0.002 PHE C 643 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00403 (24064) covalent geometry : angle 0.55734 (32747) SS BOND : bond 0.00470 ( 37) SS BOND : angle 0.99849 ( 74) hydrogen bonds : bond 0.04593 ( 1042) hydrogen bonds : angle 5.68907 ( 2868) link_BETA1-4 : bond 0.00345 ( 3) link_BETA1-4 : angle 1.14246 ( 9) link_NAG-ASN : bond 0.00334 ( 33) link_NAG-ASN : angle 2.58464 ( 99) *********************** 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: 64 poor density : 216 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7191 (mm-40) REVERT: A 237 ARG cc_start: 0.7406 (mtp85) cc_final: 0.7183 (mtp85) REVERT: A 309 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: A 319 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7293 (ttm-80) REVERT: A 389 ASP cc_start: 0.8244 (m-30) cc_final: 0.7912 (m-30) REVERT: A 408 ARG cc_start: 0.7835 (ppt90) cc_final: 0.7449 (ppt90) REVERT: A 565 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6857 (p90) REVERT: A 574 ASP cc_start: 0.7680 (t0) cc_final: 0.7457 (t0) REVERT: A 780 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7725 (pt0) REVERT: A 1139 ASP cc_start: 0.8331 (t0) cc_final: 0.7059 (p0) REVERT: B 190 ARG cc_start: 0.6971 (mtt-85) cc_final: 0.6572 (mmt90) REVERT: B 314 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: B 532 ASN cc_start: 0.7650 (t0) cc_final: 0.7384 (t160) REVERT: B 569 ILE cc_start: 0.8462 (mt) cc_final: 0.8107 (tt) REVERT: B 619 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8149 (mp0) REVERT: B 790 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8159 (mmtt) REVERT: B 935 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: B 950 ASP cc_start: 0.8120 (m-30) cc_final: 0.7754 (m-30) REVERT: B 964 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7827 (tppt) REVERT: B 1038 LYS cc_start: 0.9006 (tttm) cc_final: 0.8465 (mmtp) REVERT: C 271 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7022 (tp-100) REVERT: C 309 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7221 (mp0) REVERT: C 347 PHE cc_start: 0.6349 (m-10) cc_final: 0.5688 (m-80) REVERT: C 378 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6732 (mppt) REVERT: C 564 GLN cc_start: 0.7731 (tp40) cc_final: 0.7317 (tt0) REVERT: C 957 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7367 (pt0) outliers start: 64 outliers final: 38 residues processed: 257 average time/residue: 0.5802 time to fit residues: 174.0812 Evaluate side-chains 254 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 72 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 751 ASN C 239 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116984 restraints weight = 27096.724| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.96 r_work: 0.3045 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24137 Z= 0.181 Angle : 0.580 10.358 32929 Z= 0.296 Chirality : 0.046 0.331 3873 Planarity : 0.004 0.059 4176 Dihedral : 5.402 56.598 3930 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.80 % Favored : 97.06 % Rotamer: Outliers : 2.40 % Allowed : 12.74 % Favored : 84.86 % 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: 0.31 (0.15), residues: 2924 helix: 1.57 (0.21), residues: 682 sheet: 0.39 (0.18), residues: 703 loop : -0.47 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.021 0.002 TYR C 508 PHE 0.021 0.002 PHE C 643 TRP 0.018 0.002 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00440 (24064) covalent geometry : angle 0.56210 (32747) SS BOND : bond 0.00477 ( 37) SS BOND : angle 1.00818 ( 74) hydrogen bonds : bond 0.04667 ( 1042) hydrogen bonds : angle 5.70039 ( 2868) link_BETA1-4 : bond 0.00348 ( 3) link_BETA1-4 : angle 1.09451 ( 9) link_NAG-ASN : bond 0.00332 ( 33) link_NAG-ASN : angle 2.52397 ( 99) *********************** 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 275 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: A 237 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7079 (mtp85) REVERT: A 309 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: A 319 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7248 (ttm-80) REVERT: A 389 ASP cc_start: 0.8209 (m-30) cc_final: 0.7875 (m-30) REVERT: A 565 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6827 (p90) REVERT: A 574 ASP cc_start: 0.7734 (t0) cc_final: 0.7532 (t0) REVERT: A 780 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7623 (pt0) REVERT: A 1139 ASP cc_start: 0.8205 (t0) cc_final: 0.6875 (p0) REVERT: B 190 ARG cc_start: 0.7186 (mtt-85) cc_final: 0.6756 (mmt90) REVERT: B 314 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: B 532 ASN cc_start: 0.7655 (t0) cc_final: 0.7391 (t160) REVERT: B 569 ILE cc_start: 0.8483 (mt) cc_final: 0.8128 (tt) REVERT: B 599 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9064 (p) REVERT: B 619 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8155 (mp0) REVERT: B 740 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8552 (ttt) REVERT: B 790 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8143 (mmtt) REVERT: B 935 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: B 950 ASP cc_start: 0.8041 (m-30) cc_final: 0.7656 (m-30) REVERT: B 964 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7760 (tppt) REVERT: B 1038 LYS cc_start: 0.9035 (tttm) cc_final: 0.8468 (mmtp) REVERT: C 190 ARG cc_start: 0.6780 (mpt180) cc_final: 0.6324 (mmp-170) REVERT: C 271 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7021 (tp-100) REVERT: C 309 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7185 (mp0) REVERT: C 347 PHE cc_start: 0.6403 (m-10) cc_final: 0.5653 (m-80) REVERT: C 378 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6733 (mppt) REVERT: C 564 GLN cc_start: 0.7706 (tp40) cc_final: 0.7279 (tt0) REVERT: C 957 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7257 (pt0) outliers start: 61 outliers final: 40 residues processed: 255 average time/residue: 0.5588 time to fit residues: 166.8459 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 : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 166 optimal weight: 0.5980 chunk 136 optimal weight: 20.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.187882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115500 restraints weight = 27109.689| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.02 r_work: 0.3015 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24137 Z= 0.146 Angle : 0.555 10.568 32929 Z= 0.283 Chirality : 0.045 0.305 3873 Planarity : 0.004 0.056 4176 Dihedral : 5.271 56.320 3930 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 2.28 % Allowed : 12.82 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2924 helix: 1.68 (0.21), residues: 682 sheet: 0.45 (0.18), residues: 693 loop : -0.43 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.022 0.001 TYR A 170 PHE 0.043 0.001 PHE C 453 TRP 0.016 0.001 TRP C 886 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00348 (24064) covalent geometry : angle 0.53931 (32747) SS BOND : bond 0.00390 ( 37) SS BOND : angle 0.91660 ( 74) hydrogen bonds : bond 0.04307 ( 1042) hydrogen bonds : angle 5.59126 ( 2868) link_BETA1-4 : bond 0.00344 ( 3) link_BETA1-4 : angle 1.02591 ( 9) link_NAG-ASN : bond 0.00324 ( 33) link_NAG-ASN : angle 2.35775 ( 99) *********************** 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 267 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: A 237 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7167 (mtp85) REVERT: A 309 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: A 319 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7083 (ttm-80) REVERT: A 389 ASP cc_start: 0.8183 (m-30) cc_final: 0.7854 (m-30) REVERT: A 565 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6844 (p90) REVERT: A 780 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7661 (pt0) REVERT: A 1139 ASP cc_start: 0.8251 (t0) cc_final: 0.6886 (p0) REVERT: B 190 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.6748 (mmt90) REVERT: B 191 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: B 314 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8413 (tm-30) REVERT: B 532 ASN cc_start: 0.7647 (t0) cc_final: 0.7416 (t160) REVERT: B 569 ILE cc_start: 0.8425 (mt) cc_final: 0.8096 (tt) REVERT: B 599 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9087 (p) REVERT: B 619 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8140 (mp0) REVERT: B 740 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8580 (ttt) REVERT: B 790 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8146 (mmtt) REVERT: B 814 LYS cc_start: 0.7832 (mttm) cc_final: 0.7484 (mtmt) REVERT: B 935 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: B 950 ASP cc_start: 0.8093 (m-30) cc_final: 0.7708 (m-30) REVERT: B 964 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7778 (tppt) REVERT: B 1038 LYS cc_start: 0.9013 (tttm) cc_final: 0.8480 (mmtp) REVERT: C 190 ARG cc_start: 0.6734 (mpt180) cc_final: 0.6272 (mmp-170) REVERT: C 271 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6998 (tp-100) REVERT: C 309 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7200 (mp0) REVERT: C 347 PHE cc_start: 0.6417 (m-10) cc_final: 0.5673 (m-80) REVERT: C 453 PHE cc_start: 0.5746 (p90) cc_final: 0.4387 (p90) REVERT: C 564 GLN cc_start: 0.7721 (tp40) cc_final: 0.7304 (tt0) REVERT: C 583 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: C 808 ASP cc_start: 0.7349 (t0) cc_final: 0.7115 (t0) REVERT: C 957 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7310 (pt0) REVERT: C 1118 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8035 (m-30) outliers start: 58 outliers final: 39 residues processed: 248 average time/residue: 0.5746 time to fit residues: 166.8003 Evaluate side-chains 251 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 chunk 75 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 169 optimal weight: 0.3980 chunk 292 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 179 optimal weight: 0.4980 chunk 296 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 273 optimal weight: 1.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 188 ASN C 239 GLN C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.191798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122101 restraints weight = 27243.772| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.29 r_work: 0.3104 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24137 Z= 0.094 Angle : 0.508 11.286 32929 Z= 0.260 Chirality : 0.043 0.266 3873 Planarity : 0.003 0.048 4176 Dihedral : 4.936 55.780 3930 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 1.45 % Allowed : 13.80 % Favored : 84.74 % 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: 0.66 (0.15), residues: 2924 helix: 1.99 (0.21), residues: 679 sheet: 0.57 (0.18), residues: 683 loop : -0.28 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.023 0.001 TYR A 170 PHE 0.037 0.001 PHE C 453 TRP 0.037 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00204 (24064) covalent geometry : angle 0.49438 (32747) SS BOND : bond 0.00242 ( 37) SS BOND : angle 0.74659 ( 74) hydrogen bonds : bond 0.03473 ( 1042) hydrogen bonds : angle 5.33536 ( 2868) link_BETA1-4 : bond 0.00430 ( 3) link_BETA1-4 : angle 0.91353 ( 9) link_NAG-ASN : bond 0.00338 ( 33) link_NAG-ASN : angle 2.09888 ( 99) ********************** 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 249 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7323 (mm-40) REVERT: A 309 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: A 319 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7295 (ttm-80) REVERT: A 389 ASP cc_start: 0.8070 (m-30) cc_final: 0.7755 (m-30) REVERT: A 408 ARG cc_start: 0.8040 (ppt90) cc_final: 0.7814 (ppt90) REVERT: A 656 VAL cc_start: 0.8452 (t) cc_final: 0.8225 (m) REVERT: A 780 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7809 (pt0) REVERT: B 190 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6769 (mmt90) REVERT: B 191 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: B 271 GLN cc_start: 0.8718 (mt0) cc_final: 0.8365 (mp10) REVERT: B 532 ASN cc_start: 0.7680 (t0) cc_final: 0.7409 (t160) REVERT: B 569 ILE cc_start: 0.8367 (mt) cc_final: 0.8084 (tt) REVERT: B 619 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8097 (mp0) REVERT: B 814 LYS cc_start: 0.7913 (mttm) cc_final: 0.7628 (mtmt) REVERT: B 950 ASP cc_start: 0.8320 (m-30) cc_final: 0.8027 (m-30) REVERT: B 964 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7935 (tppt) REVERT: B 1038 LYS cc_start: 0.9012 (tttm) cc_final: 0.8558 (mmtp) REVERT: C 190 ARG cc_start: 0.6858 (mpt180) cc_final: 0.6507 (mmp-170) REVERT: C 271 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7095 (tp-100) REVERT: C 309 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7373 (mp0) REVERT: C 347 PHE cc_start: 0.6424 (m-10) cc_final: 0.5775 (m-80) REVERT: C 453 PHE cc_start: 0.5858 (p90) cc_final: 0.4487 (p90) REVERT: C 564 GLN cc_start: 0.7767 (tp40) cc_final: 0.7373 (tt0) REVERT: C 583 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: C 646 ARG cc_start: 0.8525 (tpp-160) cc_final: 0.7786 (ttt180) REVERT: C 957 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7563 (pt0) outliers start: 37 outliers final: 20 residues processed: 237 average time/residue: 0.5661 time to fit residues: 156.9491 Evaluate side-chains 237 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 108 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.188605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116590 restraints weight = 27156.847| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.18 r_work: 0.3052 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24137 Z= 0.176 Angle : 0.569 11.214 32929 Z= 0.291 Chirality : 0.045 0.292 3873 Planarity : 0.004 0.051 4176 Dihedral : 5.141 56.303 3930 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 1.38 % Allowed : 14.12 % 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: 0.51 (0.15), residues: 2924 helix: 1.74 (0.21), residues: 682 sheet: 0.53 (0.18), residues: 680 loop : -0.35 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.019 0.002 TYR A 170 PHE 0.038 0.002 PHE C 453 TRP 0.041 0.002 TRP A 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00428 (24064) covalent geometry : angle 0.55471 (32747) SS BOND : bond 0.00484 ( 37) SS BOND : angle 0.93674 ( 74) hydrogen bonds : bond 0.04544 ( 1042) hydrogen bonds : angle 5.55445 ( 2868) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.08108 ( 9) link_NAG-ASN : bond 0.00300 ( 33) link_NAG-ASN : angle 2.26668 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10238.99 seconds wall clock time: 174 minutes 29.91 seconds (10469.91 seconds total)