Starting phenix.real_space_refine on Sat Jul 4 21:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwo_23552/07_2026/7lwo_23552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwo_23552/07_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_23552/07_2026/7lwo_23552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwo_23552/07_2026/7lwo_23552.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwo_23552/07_2026/7lwo_23552.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwo_23552/07_2026/7lwo_23552.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwo_23552/07_2026/7lwo_23552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwo_23552/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.47, per 1000 atoms: 0.19 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: 1.31 Conformation dependent library (CDL) restraints added in 869.0 milliseconds 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: 0.76 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: 5.13 Time building geometry restraints manager: 1.80 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: 13118 17.97 - 35.94: 707 35.94 - 53.91: 111 53.91 - 71.88: 44 71.88 - 89.85: 24 Dihedral angle restraints: 14004 sinusoidal: 5350 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 14001 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: 2.320 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.440 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 12.725 89.855 8317 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/Z covalent geometry : bond 0.01345 / 0.78 (24064) covalent geometry : angle 1.78685 / 1.20 (32747) SS BOND : bond 0.02200 / 1.46 ( 37) SS BOND : angle 2.23175 / 1.42 ( 74) hydrogen bonds : bond 0.16304 / 10.47 ( 1042) hydrogen bonds : angle 8.14966 / 5.60 ( 2868) link_BETA1-4 : bond 0.02026 / 0.90 ( 3) link_BETA1-4 : angle 4.10217 / 2.56 ( 9) link_NAG-ASN : bond 0.01327 / 0.79 ( 33) link_NAG-ASN : angle 4.60763 / 3.20 ( 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 : 0.873 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: 0.4924 time to fit residues: 234.1388 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 : 0.717 ------------------------------------------------------------------------------- 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... 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 = 0.4112 r_free = 0.4112 target = 0.188748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115179 restraints weight = 27303.707| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.03 r_work: 0.3045 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24137 Z= 0.161 Angle : 0.687 11.620 32929 Z= 0.357 Chirality : 0.048 0.499 3873 Planarity : 0.004 0.064 4176 Dihedral : 5.943 53.631 3182 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 2.28 % Allowed : 7.86 % Favored : 89.85 % 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: 0.17 (0.15), residues: 2924 helix: 1.07 (0.20), residues: 678 sheet: 0.65 (0.19), residues: 691 loop : -0.53 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 190 TYR 0.023 0.002 TYR A 369 PHE 0.018 0.002 PHE A 464 TRP 0.027 0.002 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (24064) covalent geometry : angle 0.66167 / 0.35 (32747) SS BOND : bond 0.00521 / 0.36 ( 37) SS BOND : angle 1.29880 / 0.85 ( 74) hydrogen bonds : bond 0.05546 / 3.66 ( 1042) hydrogen bonds : angle 6.35983 / 4.39 ( 2868) link_BETA1-4 : bond 0.00618 / 0.29 ( 3) link_BETA1-4 : angle 2.00801 / 1.23 ( 9) link_NAG-ASN : bond 0.00409 / 0.25 ( 33) link_NAG-ASN : angle 3.21149 / 2.04 ( 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 322 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: A 364 ASP cc_start: 0.7024 (t0) cc_final: 0.6804 (t0) REVERT: A 408 ARG cc_start: 0.8043 (ppt90) cc_final: 0.7645 (ppt90) REVERT: A 1143 PRO cc_start: 0.7821 (Cg_exo) cc_final: 0.7593 (Cg_endo) REVERT: B 190 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6619 (mtt-85) REVERT: B 569 ILE cc_start: 0.8571 (mt) cc_final: 0.8185 (tt) REVERT: B 646 ARG cc_start: 0.8549 (mtp180) cc_final: 0.7799 (mmp80) REVERT: B 654 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7815 (tt0) REVERT: B 656 VAL cc_start: 0.8092 (t) cc_final: 0.7742 (m) REVERT: B 814 LYS cc_start: 0.7655 (mttm) cc_final: 0.7350 (mtmm) REVERT: B 825 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7551 (mtpt) REVERT: B 994 ASP cc_start: 0.8000 (m-30) cc_final: 0.7764 (m-30) REVERT: B 1038 LYS cc_start: 0.8954 (tttm) cc_final: 0.8658 (ttmm) REVERT: C 129 LYS cc_start: 0.7314 (mtpt) cc_final: 0.7089 (tttm) REVERT: C 271 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6863 (tp-100) REVERT: C 347 PHE cc_start: 0.6438 (m-10) cc_final: 0.5766 (m-80) REVERT: C 355 ARG cc_start: 0.7391 (ttm170) cc_final: 0.7143 (ttm170) REVERT: C 378 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6440 (tppt) REVERT: C 564 GLN cc_start: 0.7764 (tp40) cc_final: 0.7306 (tt0) REVERT: C 583 GLU cc_start: 0.8517 (pt0) cc_final: 0.8297 (pm20) REVERT: C 656 VAL cc_start: 0.7496 (t) cc_final: 0.7127 (m) REVERT: C 702 GLU cc_start: 0.7980 (pt0) cc_final: 0.7538 (tm-30) REVERT: C 855 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.5800 (m-80) REVERT: C 935 GLN cc_start: 0.7566 (mt0) cc_final: 0.7339 (mt0) REVERT: C 957 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7308 (pt0) REVERT: C 1038 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8299 (mmpt) outliers start: 58 outliers final: 25 residues processed: 298 average time/residue: 0.4773 time to fit residues: 169.0789 Evaluate side-chains 232 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 856 ASN 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 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: 0.5980 chunk 184 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 93 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1048 HIS B1135 ASN C 239 GLN C 314 GLN C 394 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.189767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124279 restraints weight = 27456.109| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.65 r_work: 0.3108 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24137 Z= 0.117 Angle : 0.576 9.796 32929 Z= 0.299 Chirality : 0.045 0.407 3873 Planarity : 0.004 0.038 4176 Dihedral : 5.184 48.992 3179 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 2.44 % Allowed : 8.93 % Favored : 88.64 % 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: 0.51 (0.15), residues: 2924 helix: 1.71 (0.21), residues: 667 sheet: 0.67 (0.18), residues: 679 loop : -0.39 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.021 0.001 TYR A 170 PHE 0.021 0.001 PHE B 168 TRP 0.017 0.001 TRP C 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (24064) covalent geometry : angle 0.56032 / 0.30 (32747) SS BOND : bond 0.00494 / 0.32 ( 37) SS BOND : angle 1.03512 / 0.71 ( 74) hydrogen bonds : bond 0.04417 / 2.91 ( 1042) hydrogen bonds : angle 5.90348 / 4.07 ( 2868) link_BETA1-4 : bond 0.00587 / 0.27 ( 3) link_BETA1-4 : angle 1.34097 / 0.79 ( 9) link_NAG-ASN : bond 0.00368 / 0.23 ( 33) link_NAG-ASN : angle 2.36217 / 1.50 ( 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 301 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: A 287 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 309 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: A 408 ARG cc_start: 0.8087 (ppt90) cc_final: 0.7828 (ppt90) REVERT: A 454 ARG cc_start: 0.6281 (ttm-80) cc_final: 0.5765 (mmm-85) REVERT: A 554 GLU cc_start: 0.8178 (tt0) cc_final: 0.7904 (pp20) REVERT: A 565 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6710 (p90) REVERT: A 574 ASP cc_start: 0.7338 (t0) cc_final: 0.6988 (t0) REVERT: A 675 GLN cc_start: 0.7691 (tt0) cc_final: 0.7448 (tm-30) REVERT: A 780 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7582 (pt0) REVERT: A 787 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8145 (mm-40) REVERT: A 825 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7717 (mmmt) REVERT: B 190 ARG cc_start: 0.6892 (mtt-85) cc_final: 0.6487 (mmt90) REVERT: B 564 GLN cc_start: 0.6868 (mm110) cc_final: 0.6561 (mm110) REVERT: B 569 ILE cc_start: 0.8491 (mt) cc_final: 0.8147 (tt) REVERT: B 654 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7969 (tt0) REVERT: B 656 VAL cc_start: 0.8090 (t) cc_final: 0.7766 (m) REVERT: B 814 LYS cc_start: 0.7647 (mttm) cc_final: 0.7333 (mtmt) REVERT: B 1038 LYS cc_start: 0.8948 (tttm) cc_final: 0.8456 (mptt) REVERT: C 190 ARG cc_start: 0.6622 (mpt180) cc_final: 0.6395 (mpt180) REVERT: C 271 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6822 (tp-100) REVERT: C 309 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7039 (mp0) REVERT: C 347 PHE cc_start: 0.6482 (m-10) cc_final: 0.5833 (m-80) REVERT: C 355 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7099 (ttm170) REVERT: C 378 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6851 (mppt) REVERT: C 564 GLN cc_start: 0.7587 (tp40) cc_final: 0.7169 (tt0) REVERT: C 702 GLU cc_start: 0.7919 (pt0) cc_final: 0.7539 (tm-30) REVERT: C 780 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7719 (pt0) REVERT: C 855 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5982 (m-80) REVERT: C 935 GLN cc_start: 0.7686 (mt0) cc_final: 0.7471 (mt0) REVERT: C 957 GLN cc_start: 0.7639 (tp-100) cc_final: 0.7243 (pt0) outliers start: 62 outliers final: 28 residues processed: 278 average time/residue: 0.5039 time to fit residues: 164.9895 Evaluate side-chains 235 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 557 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 856 ASN 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 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 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 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 723 THR 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: 5.9990 chunk 248 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 52 GLN A 544 ASN A1010 GLN A1119 ASN C 239 GLN C 394 ASN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125171 restraints weight = 27244.951| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.73 r_work: 0.3070 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24137 Z= 0.260 Angle : 0.667 8.980 32929 Z= 0.342 Chirality : 0.049 0.363 3873 Planarity : 0.004 0.035 4176 Dihedral : 5.285 52.711 3177 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 2.87 % Allowed : 9.87 % Favored : 87.26 % 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: 0.17 (0.15), residues: 2924 helix: 1.34 (0.21), residues: 669 sheet: 0.45 (0.18), residues: 690 loop : -0.55 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 190 TYR 0.019 0.002 TYR C1067 PHE 0.020 0.002 PHE C 643 TRP 0.025 0.002 TRP C 886 HIS 0.006 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.26 (24064) covalent geometry : angle 0.65077 / 0.34 (32747) SS BOND : bond 0.00677 / 0.46 ( 37) SS BOND : angle 1.24079 / 0.83 ( 74) hydrogen bonds : bond 0.05596 / 3.69 ( 1042) hydrogen bonds : angle 6.06051 / 4.16 ( 2868) link_BETA1-4 : bond 0.00210 / 0.10 ( 3) link_BETA1-4 : angle 1.38971 / 0.82 ( 9) link_NAG-ASN : bond 0.00356 / 0.24 ( 33) link_NAG-ASN : angle 2.56239 / 1.63 ( 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 285 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: A 319 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7366 (ttm-80) REVERT: A 389 ASP cc_start: 0.8147 (m-30) cc_final: 0.7760 (m-30) REVERT: A 408 ARG cc_start: 0.8082 (ppt90) cc_final: 0.7803 (ppt90) REVERT: A 454 ARG cc_start: 0.6603 (ttm-80) cc_final: 0.6134 (mmm-85) REVERT: A 565 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6905 (p90) REVERT: A 675 GLN cc_start: 0.7794 (tt0) cc_final: 0.7529 (tt0) REVERT: A 780 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7852 (pt0) REVERT: A 787 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: A 935 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 969 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8329 (m-40) REVERT: B 190 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6811 (mmt90) REVERT: B 314 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8543 (tm-30) REVERT: B 532 ASN cc_start: 0.7710 (t0) cc_final: 0.7440 (t160) REVERT: B 564 GLN cc_start: 0.7298 (mm110) cc_final: 0.7068 (mm110) REVERT: B 567 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7514 (mmm160) REVERT: B 569 ILE cc_start: 0.8573 (mt) cc_final: 0.8250 (tt) REVERT: B 654 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7913 (tt0) REVERT: B 790 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8250 (mmtt) REVERT: B 814 LYS cc_start: 0.7796 (mttm) cc_final: 0.7483 (mtmt) REVERT: C 45 SER cc_start: 0.8342 (p) cc_final: 0.8069 (t) REVERT: C 271 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6907 (tp-100) REVERT: C 309 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7288 (mp0) REVERT: C 347 PHE cc_start: 0.6466 (m-10) cc_final: 0.5824 (m-80) REVERT: C 355 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: C 378 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7057 (mppt) REVERT: C 564 GLN cc_start: 0.7763 (tp40) cc_final: 0.7384 (tt0) REVERT: C 583 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: C 855 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: C 935 GLN cc_start: 0.7817 (mt0) cc_final: 0.7564 (mt0) REVERT: C 957 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7588 (pt0) REVERT: C 1038 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8380 (mmpt) outliers start: 73 outliers final: 37 residues processed: 255 average time/residue: 0.5882 time to fit residues: 175.0696 Evaluate side-chains 250 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 565 PHE 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 957 GLN Chi-restraints excluded: chain A residue 969 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 314 GLN Chi-restraints excluded: chain B residue 323 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 936 ASP 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 284 THR Chi-restraints excluded: chain C residue 355 ARG 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 393 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 234 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 137 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 52 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 935 GLN C 239 GLN C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114797 restraints weight = 27115.541| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.02 r_work: 0.3004 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24137 Z= 0.231 Angle : 0.633 10.955 32929 Z= 0.325 Chirality : 0.048 0.329 3873 Planarity : 0.004 0.037 4176 Dihedral : 5.139 52.860 3177 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.02 % Rotamer: Outliers : 3.30 % Allowed : 10.34 % 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: 0.13 (0.15), residues: 2924 helix: 1.31 (0.21), residues: 669 sheet: 0.40 (0.18), residues: 679 loop : -0.57 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 190 TYR 0.018 0.002 TYR A1067 PHE 0.021 0.002 PHE A 464 TRP 0.022 0.002 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (24064) covalent geometry : angle 0.61401 / 0.32 (32747) SS BOND : bond 0.00619 / 0.42 ( 37) SS BOND : angle 1.38856 / 0.98 ( 74) hydrogen bonds : bond 0.05224 / 3.44 ( 1042) hydrogen bonds : angle 5.97882 / 4.10 ( 2868) link_BETA1-4 : bond 0.00275 / 0.13 ( 3) link_BETA1-4 : angle 1.20191 / 0.70 ( 9) link_NAG-ASN : bond 0.00299 / 0.20 ( 33) link_NAG-ASN : angle 2.66286 / 1.70 ( 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 299 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 215 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6870 (mt0) REVERT: A 309 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: A 319 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7375 (ttm-80) REVERT: A 389 ASP cc_start: 0.8276 (m-30) cc_final: 0.7884 (m-30) REVERT: A 408 ARG cc_start: 0.8009 (ppt90) cc_final: 0.7716 (ppt90) REVERT: A 454 ARG cc_start: 0.6543 (ttm-80) cc_final: 0.6303 (mmm-85) REVERT: A 565 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6696 (p90) REVERT: A 675 GLN cc_start: 0.7693 (tt0) cc_final: 0.7355 (tt0) REVERT: A 780 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7675 (pt0) REVERT: A 787 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8508 (mt0) REVERT: A 935 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: A 969 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8319 (m-40) REVERT: A 1139 ASP cc_start: 0.8360 (t0) cc_final: 0.7193 (p0) REVERT: B 190 ARG cc_start: 0.7081 (mtt-85) cc_final: 0.6703 (mmt90) REVERT: B 314 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: B 532 ASN cc_start: 0.7653 (t0) cc_final: 0.7397 (t160) REVERT: B 567 ARG cc_start: 0.7746 (mtt-85) cc_final: 0.7442 (mmm160) REVERT: B 569 ILE cc_start: 0.8510 (mt) cc_final: 0.8142 (tt) REVERT: B 619 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8160 (mp0) REVERT: B 646 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7974 (ttp-170) REVERT: B 790 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8128 (mmtt) REVERT: B 814 LYS cc_start: 0.7811 (mttm) cc_final: 0.7472 (mtmt) REVERT: B 964 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7818 (tppt) REVERT: B 1038 LYS cc_start: 0.9042 (tttm) cc_final: 0.8503 (mmtp) REVERT: C 45 SER cc_start: 0.8254 (p) cc_final: 0.8017 (t) REVERT: C 271 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6928 (tp-100) REVERT: C 309 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7206 (mp0) REVERT: C 347 PHE cc_start: 0.6307 (m-10) cc_final: 0.5677 (m-80) REVERT: C 355 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7190 (ttm170) REVERT: C 357 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7072 (ttm110) REVERT: C 564 GLN cc_start: 0.7748 (tp40) cc_final: 0.7353 (tt0) REVERT: C 571 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: C 583 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: C 855 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: C 935 GLN cc_start: 0.7691 (mt0) cc_final: 0.7468 (mt0) REVERT: C 957 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7378 (pt0) REVERT: C 1038 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8407 (mmpt) outliers start: 84 outliers final: 48 residues processed: 267 average time/residue: 0.5746 time to fit residues: 180.0080 Evaluate side-chains 267 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 239 GLN 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 529 LYS Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 969 ASN 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 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 645 THR Chi-restraints excluded: chain B residue 646 ARG 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 859 THR Chi-restraints excluded: chain B residue 936 ASP 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 284 THR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 357 ARG 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 434 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 573 THR 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 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: 0.9980 chunk 188 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 290 optimal weight: 0.0980 chunk 38 optimal weight: 30.0000 chunk 256 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 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 = 0.4112 r_free = 0.4112 target = 0.189104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119423 restraints weight = 27200.803| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.08 r_work: 0.3071 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24137 Z= 0.105 Angle : 0.531 11.251 32929 Z= 0.272 Chirality : 0.045 0.587 3873 Planarity : 0.004 0.059 4176 Dihedral : 4.617 49.998 3177 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.50 % Favored : 97.37 % Rotamer: Outliers : 1.93 % Allowed : 12.07 % Favored : 86.00 % 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: 1.83 (0.21), residues: 668 sheet: 0.42 (0.18), residues: 710 loop : -0.37 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.019 0.001 TYR C 380 PHE 0.024 0.001 PHE A 192 TRP 0.012 0.001 TRP C 886 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (24064) covalent geometry : angle 0.51615 / 0.27 (32747) SS BOND : bond 0.00264 / 0.18 ( 37) SS BOND : angle 0.93610 / 0.66 ( 74) hydrogen bonds : bond 0.03868 / 2.55 ( 1042) hydrogen bonds : angle 5.59889 / 3.84 ( 2868) link_BETA1-4 : bond 0.00330 / 0.15 ( 3) link_BETA1-4 : angle 0.93631 / 0.54 ( 9) link_NAG-ASN : bond 0.00502 / 0.36 ( 33) link_NAG-ASN : angle 2.22573 / 1.39 ( 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 275 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7377 (mtp85) cc_final: 0.7120 (mtp85) REVERT: A 309 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 319 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7317 (ttm-80) REVERT: A 389 ASP cc_start: 0.8184 (m-30) cc_final: 0.7831 (m-30) REVERT: A 408 ARG cc_start: 0.7983 (ppt90) cc_final: 0.7663 (ppt90) REVERT: A 675 GLN cc_start: 0.7536 (tt0) cc_final: 0.7267 (tt0) REVERT: A 780 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7705 (pt0) REVERT: A 935 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: A 1045 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8253 (tptt) REVERT: A 1139 ASP cc_start: 0.8266 (t0) cc_final: 0.6991 (p0) REVERT: B 190 ARG cc_start: 0.7027 (mtt-85) cc_final: 0.6659 (mmt90) REVERT: B 532 ASN cc_start: 0.7618 (t0) cc_final: 0.7337 (t160) REVERT: B 569 ILE cc_start: 0.8403 (mt) cc_final: 0.8097 (tt) REVERT: B 619 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8140 (mp0) REVERT: B 654 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7911 (tt0) REVERT: B 950 ASP cc_start: 0.8172 (m-30) cc_final: 0.7836 (m-30) REVERT: B 964 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7786 (tppt) REVERT: B 1038 LYS cc_start: 0.9030 (tttm) cc_final: 0.8491 (mmtp) REVERT: C 45 SER cc_start: 0.8177 (p) cc_final: 0.7960 (t) REVERT: C 190 ARG cc_start: 0.6737 (mpt180) cc_final: 0.6295 (mmp-170) REVERT: C 271 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6994 (tp-100) REVERT: C 309 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7237 (mp0) REVERT: C 347 PHE cc_start: 0.6512 (m-10) cc_final: 0.5931 (m-80) REVERT: C 378 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6726 (mppt) REVERT: C 564 GLN cc_start: 0.7721 (tp40) cc_final: 0.7318 (tt0) REVERT: C 583 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: C 780 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7861 (pt0) REVERT: C 957 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7363 (pt0) REVERT: C 1118 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8008 (m-30) outliers start: 49 outliers final: 22 residues processed: 256 average time/residue: 0.5782 time to fit residues: 173.0445 Evaluate side-chains 241 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 557 LYS Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 661 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 C residue 271 GLN Chi-restraints excluded: chain C residue 284 THR 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 583 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A1005 GLN B 481 ASN B 901 GLN C 239 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113627 restraints weight = 27120.433| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.30 r_work: 0.2936 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 24137 Z= 0.356 Angle : 0.719 14.205 32929 Z= 0.366 Chirality : 0.054 0.843 3873 Planarity : 0.005 0.048 4176 Dihedral : 5.084 54.006 3174 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 3.22 % Allowed : 11.52 % Favored : 85.25 % 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: -0.03 (0.15), residues: 2924 helix: 1.09 (0.21), residues: 681 sheet: 0.38 (0.18), residues: 686 loop : -0.69 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.020 0.002 TYR B 279 PHE 0.022 0.003 PHE C 43 TRP 0.028 0.003 TRP C 886 HIS 0.007 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.36 (24064) covalent geometry : angle 0.70032 / 0.36 (32747) SS BOND : bond 0.00850 / 0.58 ( 37) SS BOND : angle 1.34889 / 0.90 ( 74) hydrogen bonds : bond 0.06011 / 3.96 ( 1042) hydrogen bonds : angle 6.05797 / 4.15 ( 2868) link_BETA1-4 : bond 0.00232 / 0.08 ( 3) link_BETA1-4 : angle 1.34094 / 0.79 ( 9) link_NAG-ASN : bond 0.00366 / 0.25 ( 33) link_NAG-ASN : angle 2.89069 / 1.82 ( 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 292 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7180 (mm-40) REVERT: A 237 ARG cc_start: 0.7410 (mtp85) cc_final: 0.7176 (mtp85) REVERT: A 309 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: A 319 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7346 (ttm-80) REVERT: A 389 ASP cc_start: 0.8307 (m-30) cc_final: 0.7973 (m-30) REVERT: A 454 ARG cc_start: 0.6527 (ttm-80) cc_final: 0.5913 (ttm-80) REVERT: A 565 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6850 (p90) REVERT: A 675 GLN cc_start: 0.7609 (tt0) cc_final: 0.7368 (tt0) REVERT: A 780 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7675 (pt0) REVERT: A 787 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: A 935 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: A 1139 ASP cc_start: 0.8293 (t0) cc_final: 0.7036 (p0) REVERT: B 190 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.6775 (mmt90) REVERT: B 314 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: B 532 ASN cc_start: 0.7700 (t0) cc_final: 0.7419 (t160) REVERT: B 569 ILE cc_start: 0.8513 (mt) cc_final: 0.8151 (tt) REVERT: B 619 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8194 (mp0) REVERT: B 790 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8153 (mmtt) REVERT: B 855 PHE cc_start: 0.5621 (OUTLIER) cc_final: 0.4617 (m-80) REVERT: C 41 LYS cc_start: 0.7537 (mmtt) cc_final: 0.7206 (mmtt) REVERT: C 271 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7024 (tp-100) REVERT: C 309 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7221 (mp0) REVERT: C 347 PHE cc_start: 0.6364 (m-10) cc_final: 0.5616 (m-80) REVERT: C 453 PHE cc_start: 0.5581 (p90) cc_final: 0.4231 (p90) REVERT: C 564 GLN cc_start: 0.7817 (tp40) cc_final: 0.7417 (tt0) REVERT: C 583 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: C 855 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: C 957 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7375 (pt0) outliers start: 82 outliers final: 52 residues processed: 268 average time/residue: 0.5413 time to fit residues: 171.4032 Evaluate side-chains 264 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 546 LEU Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 565 PHE 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 286 THR 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 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 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU 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 266 TYR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 378 LYS 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 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 761 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 947 LYS 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: 0.7980 chunk 229 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B 804 GLN B 901 GLN B 907 ASN C 188 ASN C 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.188222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118153 restraints weight = 27079.440| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.02 r_work: 0.3072 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24137 Z= 0.112 Angle : 0.542 11.679 32929 Z= 0.278 Chirality : 0.045 0.592 3873 Planarity : 0.004 0.049 4176 Dihedral : 4.566 50.640 3174 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.50 % Favored : 97.37 % Rotamer: Outliers : 2.04 % Allowed : 12.98 % Favored : 84.98 % 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: 0.36 (0.15), residues: 2924 helix: 1.66 (0.21), residues: 680 sheet: 0.46 (0.18), residues: 678 loop : -0.47 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.025 0.001 TYR C 508 PHE 0.021 0.001 PHE B 192 TRP 0.014 0.001 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24064) covalent geometry : angle 0.52677 / 0.27 (32747) SS BOND : bond 0.00328 / 0.22 ( 37) SS BOND : angle 0.90314 / 0.63 ( 74) hydrogen bonds : bond 0.04045 / 2.67 ( 1042) hydrogen bonds : angle 5.65935 / 3.87 ( 2868) link_BETA1-4 : bond 0.00521 / 0.23 ( 3) link_BETA1-4 : angle 0.91752 / 0.52 ( 9) link_NAG-ASN : bond 0.00399 / 0.28 ( 33) link_NAG-ASN : angle 2.29804 / 1.44 ( 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 267 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7165 (mm-40) REVERT: A 237 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7096 (mtp85) REVERT: A 309 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: A 319 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7178 (ttm-80) REVERT: A 389 ASP cc_start: 0.8198 (m-30) cc_final: 0.7869 (m-30) REVERT: A 675 GLN cc_start: 0.7524 (tt0) cc_final: 0.7277 (tt0) REVERT: A 780 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7663 (pt0) REVERT: A 935 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: A 1139 ASP cc_start: 0.8248 (t0) cc_final: 0.6905 (p0) REVERT: B 190 ARG cc_start: 0.7169 (mtt-85) cc_final: 0.6753 (mmt90) REVERT: B 532 ASN cc_start: 0.7648 (t0) cc_final: 0.7410 (t160) REVERT: B 569 ILE cc_start: 0.8486 (mt) cc_final: 0.8142 (tt) REVERT: B 619 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8137 (mp0) REVERT: B 935 GLN cc_start: 0.8244 (tt0) cc_final: 0.8009 (tt0) REVERT: B 950 ASP cc_start: 0.8107 (m-30) cc_final: 0.7696 (m-30) REVERT: B 964 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7769 (tppt) REVERT: B 1038 LYS cc_start: 0.9048 (tttm) cc_final: 0.8516 (mmtp) REVERT: C 190 ARG cc_start: 0.6753 (mpt180) cc_final: 0.6426 (mmp-170) REVERT: C 271 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7027 (tp-100) REVERT: C 309 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7217 (mp0) REVERT: C 347 PHE cc_start: 0.6349 (m-10) cc_final: 0.5705 (m-80) REVERT: C 564 GLN cc_start: 0.7743 (tp40) cc_final: 0.7347 (tt0) REVERT: C 583 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: C 780 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7848 (pt0) REVERT: C 957 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7332 (pt0) outliers start: 52 outliers final: 33 residues processed: 252 average time/residue: 0.5549 time to fit residues: 164.1638 Evaluate side-chains 243 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 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 1136 THR 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 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 284 THR 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 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 947 LYS 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: 4.9990 chunk 34 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 260 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN B 907 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 = 0.4095 r_free = 0.4095 target = 0.187370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115853 restraints weight = 27093.367| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.05 r_work: 0.3055 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3273 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 : 0.568 11.174 32929 Z= 0.291 Chirality : 0.046 0.545 3873 Planarity : 0.004 0.044 4176 Dihedral : 4.580 50.996 3174 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 1.97 % Allowed : 13.13 % 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: 0.35 (0.15), residues: 2924 helix: 1.64 (0.21), residues: 682 sheet: 0.41 (0.18), residues: 699 loop : -0.47 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.030 0.001 TYR C 508 PHE 0.043 0.002 PHE C 453 TRP 0.025 0.002 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (24064) covalent geometry : angle 0.55391 / 0.29 (32747) SS BOND : bond 0.00444 / 0.30 ( 37) SS BOND : angle 0.93458 / 0.64 ( 74) hydrogen bonds : bond 0.04494 / 2.96 ( 1042) hydrogen bonds : angle 5.65329 / 3.87 ( 2868) link_BETA1-4 : bond 0.00336 / 0.13 ( 3) link_BETA1-4 : angle 1.05665 / 0.60 ( 9) link_NAG-ASN : bond 0.00343 / 0.25 ( 33) link_NAG-ASN : angle 2.25997 / 1.42 ( 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 263 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7177 (mm-40) REVERT: A 237 ARG cc_start: 0.7446 (mtp85) cc_final: 0.7179 (mtp85) REVERT: A 309 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: A 319 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7308 (ttm-80) REVERT: A 389 ASP cc_start: 0.8163 (m-30) cc_final: 0.7838 (m-30) REVERT: A 675 GLN cc_start: 0.7531 (tt0) cc_final: 0.7303 (tt0) REVERT: A 780 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7696 (pt0) REVERT: A 935 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: A 1139 ASP cc_start: 0.8261 (t0) cc_final: 0.6879 (p0) REVERT: B 190 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.6801 (mmt90) REVERT: B 314 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: B 532 ASN cc_start: 0.7663 (t0) cc_final: 0.7399 (t160) REVERT: B 569 ILE cc_start: 0.8461 (mt) cc_final: 0.8118 (tt) REVERT: B 599 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9080 (p) REVERT: B 619 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8179 (mp0) REVERT: B 790 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8192 (mmtt) REVERT: B 935 GLN cc_start: 0.8336 (tt0) cc_final: 0.8119 (tt0) REVERT: B 950 ASP cc_start: 0.8107 (m-30) cc_final: 0.7711 (m-30) REVERT: B 964 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7794 (tppt) REVERT: B 1038 LYS cc_start: 0.9008 (tttm) cc_final: 0.8477 (mmtp) REVERT: C 271 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7048 (tp-100) REVERT: C 309 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7236 (mp0) REVERT: C 347 PHE cc_start: 0.6398 (m-10) cc_final: 0.5656 (m-80) REVERT: C 453 PHE cc_start: 0.5845 (p90) cc_final: 0.4485 (p90) REVERT: C 564 GLN cc_start: 0.7753 (tp40) cc_final: 0.7352 (tt0) REVERT: C 583 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: C 697 MET cc_start: 0.8472 (ptm) cc_final: 0.8086 (ptm) REVERT: C 957 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7356 (pt0) outliers start: 50 outliers final: 34 residues processed: 247 average time/residue: 0.5334 time to fit residues: 155.6535 Evaluate side-chains 247 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 557 LYS 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 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1096 VAL 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 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 790 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU 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 284 THR Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR 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 855 PHE Chi-restraints excluded: chain C residue 1092 GLU 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: 0.6980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 292 optimal weight: 0.2980 chunk 221 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 chunk 251 optimal weight: 0.2980 chunk 273 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4137 r_free = 0.4137 target = 0.190448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116623 restraints weight = 27251.374| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.95 r_work: 0.3111 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24137 Z= 0.096 Angle : 0.513 11.666 32929 Z= 0.263 Chirality : 0.044 0.442 3873 Planarity : 0.004 0.061 4176 Dihedral : 4.267 48.523 3174 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.44 % Rotamer: Outliers : 1.45 % Allowed : 13.72 % Favored : 84.82 % 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: 0.60 (0.15), residues: 2924 helix: 1.93 (0.21), residues: 680 sheet: 0.54 (0.18), residues: 680 loop : -0.32 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.018 0.001 TYR A1067 PHE 0.038 0.001 PHE C 453 TRP 0.039 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (24064) covalent geometry : angle 0.50128 / 0.26 (32747) SS BOND : bond 0.00246 / 0.16 ( 37) SS BOND : angle 0.76990 / 0.52 ( 74) hydrogen bonds : bond 0.03578 / 2.36 ( 1042) hydrogen bonds : angle 5.39306 / 3.69 ( 2868) link_BETA1-4 : bond 0.00348 / 0.14 ( 3) link_BETA1-4 : angle 0.82591 / 0.46 ( 9) link_NAG-ASN : bond 0.00386 / 0.27 ( 33) link_NAG-ASN : angle 1.99648 / 1.25 ( 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 256 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: A 169 GLU cc_start: 0.7573 (tt0) cc_final: 0.7301 (mt-10) REVERT: A 309 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: A 319 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7252 (ttm-80) REVERT: A 324 GLU cc_start: 0.7184 (mp0) cc_final: 0.6858 (mp0) REVERT: A 389 ASP cc_start: 0.8083 (m-30) cc_final: 0.7787 (m-30) REVERT: A 780 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7840 (pt0) REVERT: B 190 ARG cc_start: 0.7129 (mtt-85) cc_final: 0.6704 (mmt90) REVERT: B 205 SER cc_start: 0.8762 (p) cc_final: 0.8392 (m) REVERT: B 271 GLN cc_start: 0.8793 (mt0) cc_final: 0.8462 (mp10) REVERT: B 532 ASN cc_start: 0.7661 (t0) cc_final: 0.7378 (t160) REVERT: B 569 ILE cc_start: 0.8383 (mt) cc_final: 0.8099 (tt) REVERT: B 599 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9134 (p) REVERT: B 654 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8095 (tt0) REVERT: B 935 GLN cc_start: 0.8354 (tt0) cc_final: 0.8130 (tt0) REVERT: B 950 ASP cc_start: 0.8368 (m-30) cc_final: 0.8086 (m-30) REVERT: B 964 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7941 (tppt) REVERT: B 1038 LYS cc_start: 0.8964 (tttm) cc_final: 0.8528 (mmtp) REVERT: C 271 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7135 (tp-100) REVERT: C 309 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7365 (mp0) REVERT: C 347 PHE cc_start: 0.6507 (m-10) cc_final: 0.5856 (m-80) REVERT: C 453 PHE cc_start: 0.5762 (p90) cc_final: 0.4378 (p90) REVERT: C 564 GLN cc_start: 0.7805 (tp40) cc_final: 0.7436 (tt0) REVERT: C 583 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: C 646 ARG cc_start: 0.8560 (tpp-160) cc_final: 0.7766 (ttp-170) REVERT: C 697 MET cc_start: 0.8550 (ptm) cc_final: 0.8208 (ptm) REVERT: C 780 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8011 (pt0) REVERT: C 957 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7639 (pt0) outliers start: 37 outliers final: 23 residues processed: 245 average time/residue: 0.5397 time to fit residues: 155.5691 Evaluate side-chains 242 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 430 THR 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 1136 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU 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 284 THR 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 731 MET 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: 4.9990 chunk 126 optimal weight: 30.0000 chunk 236 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 360 ASN B 901 GLN B 913 GLN B1010 GLN C 239 GLN C 394 ASN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123221 restraints weight = 27045.230| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.76 r_work: 0.3028 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 24137 Z= 0.387 Angle : 0.741 13.128 32929 Z= 0.378 Chirality : 0.054 0.577 3873 Planarity : 0.005 0.111 4176 Dihedral : 4.986 53.448 3174 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 1.81 % Allowed : 13.45 % 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: -0.06 (0.15), residues: 2924 helix: 1.07 (0.20), residues: 686 sheet: 0.34 (0.18), residues: 690 loop : -0.70 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 190 TYR 0.025 0.003 TYR C 508 PHE 0.040 0.003 PHE C 453 TRP 0.036 0.003 TRP A 436 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00957 / 0.39 (24064) covalent geometry : angle 0.72322 / 0.37 (32747) SS BOND : bond 0.00986 / 0.67 ( 37) SS BOND : angle 1.94839 / 1.39 ( 74) hydrogen bonds : bond 0.06160 / 4.06 ( 1042) hydrogen bonds : angle 6.01622 / 4.12 ( 2868) link_BETA1-4 : bond 0.00187 / 0.07 ( 3) link_BETA1-4 : angle 1.41337 / 0.82 ( 9) link_NAG-ASN : bond 0.00384 / 0.26 ( 33) link_NAG-ASN : angle 2.58818 / 1.65 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9410.21 seconds wall clock time: 160 minutes 47.17 seconds (9647.17 seconds total)