Starting phenix.real_space_refine on Mon Aug 25 03:03:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uk1_42342/08_2025/8uk1_42342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uk1_42342/08_2025/8uk1_42342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uk1_42342/08_2025/8uk1_42342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uk1_42342/08_2025/8uk1_42342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uk1_42342/08_2025/8uk1_42342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uk1_42342/08_2025/8uk1_42342.map" } resolution = 3.0 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= -0.000 sd= 0.065 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 115 5.16 5 C 15810 2.51 5 N 4073 2.21 5 O 4808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24806 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8084 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "B" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7988 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 6 Chain: "C" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8090 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.11, per 1000 atoms: 0.21 Number of scatterers: 24806 At special positions: 0 Unit cell: (135, 129.6, 172.8, 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 115 16.00 O 4808 8.00 N 4073 7.00 C 15810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 991.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5804 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 44 sheets defined 25.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 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 367 through 372 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.693A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.096A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.748A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (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 1032 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.615A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 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: 3.744A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.724A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.736A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.777A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.082A 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 945 through 965 removed outlier: 3.612A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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 1032 removed outlier: 4.156A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.867A 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: 4.224A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.516A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.160A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.642A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.080A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.098A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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: 3.576A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.933A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.748A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.843A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.903A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.626A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.303A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.726A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.682A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.389A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, 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: 8.856A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.797A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.866A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.078A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.563A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 29 removed outlier: 3.665A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.402A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.394A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.330A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.593A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.078A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.963A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.131A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.540A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.020A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.713A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.681A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.797A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 645 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.247A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (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 removed outlier: 3.577A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.073A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.707A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.457A 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: 6.103A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A 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: 4.602A 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 1122 984 hydrogen bonds defined for protein. 2733 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7891 1.35 - 1.47: 6441 1.47 - 1.60: 10876 1.60 - 1.72: 0 1.72 - 1.85: 142 Bond restraints: 25350 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 25345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 33992 2.68 - 5.36: 432 5.36 - 8.03: 49 8.03 - 10.71: 5 10.71 - 13.39: 3 Bond angle restraints: 34481 Sorted by residual: angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 120.33 124.82 -4.49 8.00e-01 1.56e+00 3.15e+01 angle pdb=" C LEU A 212 " pdb=" N GLU A 213 " pdb=" CA GLU A 213 " ideal model delta sigma weight residual 120.82 128.83 -8.01 1.50e+00 4.44e-01 2.85e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 122.07 129.51 -7.44 1.43e+00 4.89e-01 2.70e+01 angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.87 6.36 1.36e+00 5.41e-01 2.19e+01 angle pdb=" C VAL A1040 " pdb=" N ASP A1041 " pdb=" CA ASP A1041 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 ... (remaining 34476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14207 17.56 - 35.12: 1236 35.12 - 52.68: 214 52.68 - 70.25: 56 70.25 - 87.81: 35 Dihedral angle restraints: 15748 sinusoidal: 6730 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 177.12 -84.12 1 1.00e+01 1.00e-02 8.62e+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 -7.61 -78.39 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 51.42 41.58 1 1.00e+01 1.00e-02 2.42e+01 ... (remaining 15745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3405 0.073 - 0.146: 620 0.146 - 0.218: 32 0.218 - 0.291: 6 0.291 - 0.364: 1 Chirality restraints: 4064 Sorted by residual: chirality pdb=" C2 NAG C1310 " pdb=" C1 NAG C1310 " pdb=" C3 NAG C1310 " pdb=" N2 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE A 22 " pdb=" CA ILE A 22 " pdb=" CG1 ILE A 22 " pdb=" CG2 ILE A 22 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU C 390 " pdb=" CB LEU C 390 " pdb=" CD1 LEU C 390 " pdb=" CD2 LEU C 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4061 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " -0.054 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 209 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.025 2.00e-02 2.50e+03 2.31e-02 6.68e+00 pdb=" CG ASN A 343 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 745 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" CG ASP B 745 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP B 745 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 745 " -0.015 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6915 2.82 - 3.34: 19691 3.34 - 3.86: 39901 3.86 - 4.38: 45258 4.38 - 4.90: 81552 Nonbonded interactions: 193317 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.297 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.305 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.314 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.314 3.040 ... (remaining 193312 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 24 through 132 or resid 165 through 677 or resid 690 throu \ gh 1309)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 132 or resid 165 through 677 or resid 690 throu \ gh 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.080 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.600 Find NCS groups from input model: 0.520 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.004 0.047 25438 Z= 0.212 Angle : 0.765 13.392 34703 Z= 0.400 Chirality : 0.053 0.364 4064 Planarity : 0.006 0.084 4395 Dihedral : 13.801 87.806 9818 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3055 helix: -0.23 (0.17), residues: 690 sheet: 0.53 (0.19), residues: 695 loop : -1.34 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.025 0.001 TYR C 266 PHE 0.018 0.002 PHE B1121 TRP 0.034 0.002 TRP C 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00422 (25350) covalent geometry : angle 0.74931 (34481) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.52206 ( 84) hydrogen bonds : bond 0.13090 ( 980) hydrogen bonds : angle 6.33298 ( 2733) link_BETA1-4 : bond 0.00832 ( 9) link_BETA1-4 : angle 1.68125 ( 27) link_NAG-ASN : bond 0.00322 ( 37) link_NAG-ASN : angle 2.50605 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.9057 (ptm) cc_final: 0.8812 (ptm) REVERT: A 821 LEU cc_start: 0.8236 (mt) cc_final: 0.8014 (mp) REVERT: B 935 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 1101 HIS cc_start: 0.7435 (m90) cc_final: 0.7229 (m90) REVERT: C 420 ASP cc_start: 0.7270 (m-30) cc_final: 0.6806 (m-30) REVERT: C 869 MET cc_start: 0.8521 (mtt) cc_final: 0.8279 (mtt) REVERT: C 995 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7321 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.4632 time to fit residues: 133.8622 Evaluate side-chains 184 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN A 957 GLN A 960 ASN B 394 ASN B 613 GLN B 804 GLN B1005 GLN C 448 ASN C 493 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.176726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126756 restraints weight = 26038.364| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.40 r_work: 0.3125 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25438 Z= 0.168 Angle : 0.584 17.814 34703 Z= 0.295 Chirality : 0.046 0.232 4064 Planarity : 0.004 0.067 4395 Dihedral : 6.922 59.478 4282 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.19 % Allowed : 6.61 % Favored : 92.20 % 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 aren not related in a simple way. whole: -0.30 (0.15), residues: 3055 helix: 1.16 (0.19), residues: 695 sheet: 0.56 (0.19), residues: 688 loop : -1.16 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 466 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.001 PHE C 168 TRP 0.015 0.002 TRP C 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00410 (25350) covalent geometry : angle 0.57035 (34481) SS BOND : bond 0.00394 ( 42) SS BOND : angle 1.27687 ( 84) hydrogen bonds : bond 0.05743 ( 980) hydrogen bonds : angle 5.22941 ( 2733) link_BETA1-4 : bond 0.00344 ( 9) link_BETA1-4 : angle 1.22838 ( 27) link_NAG-ASN : bond 0.00268 ( 37) link_NAG-ASN : angle 2.02670 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7185 (ttm170) REVERT: A 239 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: A 697 MET cc_start: 0.9373 (ptm) cc_final: 0.9138 (ptm) REVERT: A 821 LEU cc_start: 0.8486 (mt) cc_final: 0.8245 (mp) REVERT: A 994 ASP cc_start: 0.8597 (t70) cc_final: 0.8334 (t70) REVERT: B 375 PHE cc_start: 0.7401 (t80) cc_final: 0.6978 (m-80) REVERT: B 493 GLN cc_start: 0.7881 (mt0) cc_final: 0.7420 (mt0) REVERT: B 556 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7542 (p0) REVERT: B 780 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: B 935 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 1101 HIS cc_start: 0.8133 (m90) cc_final: 0.7885 (m90) REVERT: C 531 THR cc_start: 0.8192 (m) cc_final: 0.7722 (p) REVERT: C 1127 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7921 (m-30) outliers start: 32 outliers final: 14 residues processed: 223 average time/residue: 0.4811 time to fit residues: 126.1628 Evaluate side-chains 205 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 280 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.0040 chunk 70 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN A 955 ASN A 957 GLN A 960 ASN A 965 GLN B 218 GLN B 394 ASN B1005 GLN C 334 ASN C 493 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.177590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128115 restraints weight = 26095.386| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.44 r_work: 0.3136 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25438 Z= 0.117 Angle : 0.524 18.615 34703 Z= 0.264 Chirality : 0.044 0.261 4064 Planarity : 0.004 0.049 4395 Dihedral : 6.436 59.976 4282 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.26 % Allowed : 8.80 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3055 helix: 1.76 (0.20), residues: 696 sheet: 0.63 (0.19), residues: 693 loop : -1.05 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.017 0.001 TYR C1067 PHE 0.025 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (25350) covalent geometry : angle 0.51231 (34481) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.04642 ( 84) hydrogen bonds : bond 0.04946 ( 980) hydrogen bonds : angle 4.99335 ( 2733) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.17708 ( 27) link_NAG-ASN : bond 0.00254 ( 37) link_NAG-ASN : angle 1.79794 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: A 466 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7093 (ttp-110) REVERT: A 467 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.5959 (m-30) REVERT: A 661 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: A 697 MET cc_start: 0.9371 (ptm) cc_final: 0.9035 (ptm) REVERT: A 821 LEU cc_start: 0.8483 (mt) cc_final: 0.8249 (mp) REVERT: B 92 PHE cc_start: 0.6455 (t80) cc_final: 0.6115 (t80) REVERT: B 375 PHE cc_start: 0.7492 (t80) cc_final: 0.7045 (m-80) REVERT: B 556 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 935 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 1101 HIS cc_start: 0.8132 (m90) cc_final: 0.7858 (m90) REVERT: C 326 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7488 (mp) REVERT: C 531 THR cc_start: 0.8192 (m) cc_final: 0.7826 (p) REVERT: C 571 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7466 (t70) REVERT: C 869 MET cc_start: 0.8779 (mtt) cc_final: 0.8549 (mtm) outliers start: 34 outliers final: 13 residues processed: 212 average time/residue: 0.4608 time to fit residues: 116.2614 Evaluate side-chains 200 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 213 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 258 optimal weight: 0.0570 chunk 278 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 264 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 519 HIS A 613 GLN A 957 GLN B 52 GLN B 394 ASN B 540 ASN B1005 GLN C 448 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.173942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121881 restraints weight = 26096.032| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.70 r_work: 0.3025 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25438 Z= 0.253 Angle : 0.663 20.070 34703 Z= 0.333 Chirality : 0.050 0.298 4064 Planarity : 0.004 0.043 4395 Dihedral : 6.775 59.950 4282 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 10.48 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -0.24 (0.15), residues: 3055 helix: 1.47 (0.20), residues: 691 sheet: 0.41 (0.19), residues: 691 loop : -1.15 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.023 0.002 TYR C1067 PHE 0.025 0.002 PHE C 168 TRP 0.012 0.002 TRP C 436 HIS 0.009 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00639 (25350) covalent geometry : angle 0.64592 (34481) SS BOND : bond 0.00545 ( 42) SS BOND : angle 1.63110 ( 84) hydrogen bonds : bond 0.06767 ( 980) hydrogen bonds : angle 5.28261 ( 2733) link_BETA1-4 : bond 0.00474 ( 9) link_BETA1-4 : angle 1.38418 ( 27) link_NAG-ASN : bond 0.00332 ( 37) link_NAG-ASN : angle 2.28299 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 239 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: A 355 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7404 (ttp-170) REVERT: A 467 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6256 (m-30) REVERT: A 547 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 661 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: A 697 MET cc_start: 0.9349 (ptm) cc_final: 0.9061 (ptm) REVERT: A 808 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: B 375 PHE cc_start: 0.7840 (t80) cc_final: 0.7424 (m-80) REVERT: B 556 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 878 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8197 (mt) REVERT: B 1101 HIS cc_start: 0.8250 (m90) cc_final: 0.8031 (m90) REVERT: C 53 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7260 (t0) REVERT: C 531 THR cc_start: 0.8190 (m) cc_final: 0.7850 (p) REVERT: C 571 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7509 (t70) REVERT: C 869 MET cc_start: 0.8821 (mtt) cc_final: 0.8591 (mtm) outliers start: 57 outliers final: 29 residues processed: 216 average time/residue: 0.4680 time to fit residues: 119.9308 Evaluate side-chains 213 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 244 optimal weight: 0.2980 chunk 196 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 262 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 204 optimal weight: 0.1980 chunk 174 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1005 GLN B 52 GLN B 394 ASN B1005 GLN C 334 ASN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.177132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128360 restraints weight = 25812.073| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.28 r_work: 0.3136 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25438 Z= 0.099 Angle : 0.510 16.545 34703 Z= 0.259 Chirality : 0.043 0.263 4064 Planarity : 0.003 0.040 4395 Dihedral : 6.258 58.654 4282 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.56 % Allowed : 11.92 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.09 (0.15), residues: 3055 helix: 1.91 (0.20), residues: 706 sheet: 0.56 (0.19), residues: 693 loop : -1.02 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.017 0.001 TYR C 28 PHE 0.014 0.001 PHE C 377 TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00214 (25350) covalent geometry : angle 0.49852 (34481) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.08252 ( 84) hydrogen bonds : bond 0.04592 ( 980) hydrogen bonds : angle 4.93542 ( 2733) link_BETA1-4 : bond 0.00474 ( 9) link_BETA1-4 : angle 1.12635 ( 27) link_NAG-ASN : bond 0.00338 ( 37) link_NAG-ASN : angle 1.75224 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: A 190 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7357 (mtp85) REVERT: A 239 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: A 355 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7245 (ttp-170) REVERT: A 547 THR cc_start: 0.8072 (p) cc_final: 0.7833 (t) REVERT: A 661 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: A 697 MET cc_start: 0.9362 (ptm) cc_final: 0.9049 (ptm) REVERT: A 821 LEU cc_start: 0.8485 (mt) cc_final: 0.8266 (mp) REVERT: B 335 LEU cc_start: 0.8520 (mm) cc_final: 0.8299 (mt) REVERT: B 375 PHE cc_start: 0.7769 (t80) cc_final: 0.7370 (m-80) REVERT: B 493 GLN cc_start: 0.7922 (mt0) cc_final: 0.7578 (mt0) REVERT: B 556 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7500 (p0) REVERT: C 53 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7003 (t0) REVERT: C 212 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5142 (pp) REVERT: C 326 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7552 (mp) REVERT: C 498 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7969 (mtp85) REVERT: C 531 THR cc_start: 0.8196 (m) cc_final: 0.7958 (p) REVERT: C 690 GLN cc_start: 0.7108 (mt0) cc_final: 0.6791 (mt0) outliers start: 42 outliers final: 15 residues processed: 207 average time/residue: 0.4595 time to fit residues: 112.8277 Evaluate side-chains 195 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 179 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 301 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 52 GLN B 394 ASN B 437 ASN B1005 GLN B1101 HIS C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.173878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124367 restraints weight = 26021.244| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.33 r_work: 0.3090 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25438 Z= 0.168 Angle : 0.570 17.043 34703 Z= 0.288 Chirality : 0.046 0.244 4064 Planarity : 0.004 0.041 4395 Dihedral : 6.263 59.873 4282 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.86 % Allowed : 12.18 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -0.01 (0.15), residues: 3055 helix: 1.75 (0.20), residues: 710 sheet: 0.51 (0.19), residues: 702 loop : -1.07 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE C 168 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (25350) covalent geometry : angle 0.55787 (34481) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.16429 ( 84) hydrogen bonds : bond 0.05640 ( 980) hydrogen bonds : angle 5.02213 ( 2733) link_BETA1-4 : bond 0.00431 ( 9) link_BETA1-4 : angle 1.23775 ( 27) link_NAG-ASN : bond 0.00282 ( 37) link_NAG-ASN : angle 1.89079 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: A 190 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7203 (mtt180) REVERT: A 239 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: A 355 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7265 (ttp-170) REVERT: A 467 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6219 (m-30) REVERT: A 547 THR cc_start: 0.8089 (p) cc_final: 0.7844 (t) REVERT: A 661 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: A 697 MET cc_start: 0.9343 (ptm) cc_final: 0.9118 (ptm) REVERT: A 804 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8217 (mt0) REVERT: A 808 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: A 1084 ASP cc_start: 0.7606 (t0) cc_final: 0.7230 (t0) REVERT: B 375 PHE cc_start: 0.7809 (t80) cc_final: 0.7413 (m-80) REVERT: B 493 GLN cc_start: 0.7914 (mt0) cc_final: 0.7586 (mt0) REVERT: B 556 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7479 (p0) REVERT: B 697 MET cc_start: 0.9059 (ptm) cc_final: 0.8784 (ptp) REVERT: B 900 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8711 (mtp) REVERT: C 53 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7129 (t0) REVERT: C 212 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5174 (pp) REVERT: C 498 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7944 (mtp85) REVERT: C 531 THR cc_start: 0.8206 (m) cc_final: 0.7989 (p) REVERT: C 571 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7453 (t70) REVERT: C 869 MET cc_start: 0.8857 (mtt) cc_final: 0.8623 (mtt) outliers start: 50 outliers final: 28 residues processed: 208 average time/residue: 0.4538 time to fit residues: 112.6060 Evaluate side-chains 213 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 275 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B1005 GLN B1101 HIS C 334 ASN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.177314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126216 restraints weight = 25998.544| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.54 r_work: 0.3106 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25438 Z= 0.124 Angle : 0.529 15.918 34703 Z= 0.267 Chirality : 0.044 0.252 4064 Planarity : 0.003 0.040 4395 Dihedral : 6.060 59.423 4282 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.67 % Allowed : 12.56 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.10 (0.15), residues: 3055 helix: 1.90 (0.20), residues: 710 sheet: 0.54 (0.19), residues: 703 loop : -1.01 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.017 0.001 TYR C 28 PHE 0.016 0.001 PHE C 377 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00294 (25350) covalent geometry : angle 0.51707 (34481) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.05579 ( 84) hydrogen bonds : bond 0.04972 ( 980) hydrogen bonds : angle 4.91148 ( 2733) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 1.15973 ( 27) link_NAG-ASN : bond 0.00268 ( 37) link_NAG-ASN : angle 1.76266 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 190 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7220 (mtt180) REVERT: A 239 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: A 355 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7258 (ttp-170) REVERT: A 467 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6211 (m-30) REVERT: A 547 THR cc_start: 0.8086 (p) cc_final: 0.7856 (t) REVERT: A 661 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: A 675 GLN cc_start: 0.6740 (pp30) cc_final: 0.6350 (tp40) REVERT: A 697 MET cc_start: 0.9345 (ptm) cc_final: 0.9112 (ptm) REVERT: A 804 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8088 (mt0) REVERT: A 808 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: A 1084 ASP cc_start: 0.7701 (t0) cc_final: 0.7333 (t0) REVERT: B 375 PHE cc_start: 0.7779 (t80) cc_final: 0.7363 (m-80) REVERT: B 493 GLN cc_start: 0.7915 (mt0) cc_final: 0.7528 (mt0) REVERT: B 697 MET cc_start: 0.9055 (ptm) cc_final: 0.8776 (ptp) REVERT: B 900 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8693 (mtm) REVERT: C 53 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7062 (t0) REVERT: C 498 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: C 571 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7444 (t70) REVERT: C 690 GLN cc_start: 0.7166 (mt0) cc_final: 0.6882 (mt0) REVERT: C 869 MET cc_start: 0.8834 (mtt) cc_final: 0.8364 (mtt) REVERT: C 1127 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7832 (m-30) outliers start: 45 outliers final: 24 residues processed: 205 average time/residue: 0.4694 time to fit residues: 113.4575 Evaluate side-chains 205 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU 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 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 212 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 175 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN B 52 GLN B 394 ASN B 556 ASN B1005 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.175337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124118 restraints weight = 25929.611| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.62 r_work: 0.3023 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25438 Z= 0.170 Angle : 0.570 15.762 34703 Z= 0.288 Chirality : 0.046 0.245 4064 Planarity : 0.004 0.043 4395 Dihedral : 6.099 59.847 4282 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.86 % Allowed : 12.59 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -0.00 (0.15), residues: 3055 helix: 1.77 (0.20), residues: 710 sheet: 0.50 (0.19), residues: 697 loop : -1.06 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 190 TYR 0.019 0.001 TYR C1067 PHE 0.029 0.001 PHE C 168 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00420 (25350) covalent geometry : angle 0.55799 (34481) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.16573 ( 84) hydrogen bonds : bond 0.05645 ( 980) hydrogen bonds : angle 4.99317 ( 2733) link_BETA1-4 : bond 0.00409 ( 9) link_BETA1-4 : angle 1.25623 ( 27) link_NAG-ASN : bond 0.00270 ( 37) link_NAG-ASN : angle 1.86722 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: A 190 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7289 (mtt180) REVERT: A 239 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: A 355 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7285 (ttp-170) REVERT: A 467 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6162 (m-30) REVERT: A 547 THR cc_start: 0.8044 (p) cc_final: 0.7814 (t) REVERT: A 661 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: A 675 GLN cc_start: 0.6747 (pp30) cc_final: 0.6438 (tp40) REVERT: A 697 MET cc_start: 0.9335 (ptm) cc_final: 0.9120 (ptm) REVERT: A 808 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: B 375 PHE cc_start: 0.7840 (t80) cc_final: 0.7400 (m-80) REVERT: B 493 GLN cc_start: 0.7962 (mt0) cc_final: 0.7599 (mt0) REVERT: B 697 MET cc_start: 0.9071 (ptm) cc_final: 0.8798 (ptp) REVERT: B 900 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8724 (mtp) REVERT: C 53 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7136 (t0) REVERT: C 326 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 571 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7474 (t70) REVERT: C 869 MET cc_start: 0.8849 (mtt) cc_final: 0.8630 (mtt) outliers start: 50 outliers final: 29 residues processed: 203 average time/residue: 0.4424 time to fit residues: 107.1318 Evaluate side-chains 210 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 290 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 556 ASN B 935 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.177763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126622 restraints weight = 25999.073| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.60 r_work: 0.3086 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25438 Z= 0.109 Angle : 0.513 14.634 34703 Z= 0.260 Chirality : 0.044 0.255 4064 Planarity : 0.003 0.039 4395 Dihedral : 5.847 59.276 4282 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.52 % Allowed : 13.00 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.18 (0.15), residues: 3055 helix: 1.97 (0.20), residues: 713 sheet: 0.59 (0.19), residues: 694 loop : -0.96 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 190 TYR 0.016 0.001 TYR A1067 PHE 0.014 0.001 PHE C 377 TRP 0.011 0.001 TRP C 436 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00253 (25350) covalent geometry : angle 0.50279 (34481) SS BOND : bond 0.00324 ( 42) SS BOND : angle 0.95614 ( 84) hydrogen bonds : bond 0.04678 ( 980) hydrogen bonds : angle 4.82530 ( 2733) link_BETA1-4 : bond 0.00451 ( 9) link_BETA1-4 : angle 1.15502 ( 27) link_NAG-ASN : bond 0.00252 ( 37) link_NAG-ASN : angle 1.69330 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 190 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7311 (mtt180) REVERT: A 239 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: A 280 ASN cc_start: 0.7992 (p0) cc_final: 0.7775 (p0) REVERT: A 467 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6181 (m-30) REVERT: A 547 THR cc_start: 0.8034 (p) cc_final: 0.7812 (t) REVERT: A 661 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: A 675 GLN cc_start: 0.6972 (pp30) cc_final: 0.6504 (tp40) REVERT: A 697 MET cc_start: 0.9340 (ptm) cc_final: 0.9107 (ptm) REVERT: A 1084 ASP cc_start: 0.7669 (t0) cc_final: 0.7378 (t0) REVERT: B 32 PHE cc_start: 0.6488 (m-80) cc_final: 0.6236 (m-10) REVERT: B 375 PHE cc_start: 0.7793 (t80) cc_final: 0.7339 (m-80) REVERT: B 493 GLN cc_start: 0.7898 (mt0) cc_final: 0.7569 (mt0) REVERT: B 697 MET cc_start: 0.9042 (ptm) cc_final: 0.8763 (ptp) REVERT: C 53 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7010 (t0) REVERT: C 326 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7554 (mp) REVERT: C 869 MET cc_start: 0.8825 (mtt) cc_final: 0.8331 (mtt) outliers start: 41 outliers final: 24 residues processed: 201 average time/residue: 0.5269 time to fit residues: 126.5749 Evaluate side-chains 200 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 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 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 23 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 56 optimal weight: 0.0010 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 394 ASN B 556 ASN B 935 GLN B1005 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.178418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127210 restraints weight = 25942.035| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.55 r_work: 0.3098 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25438 Z= 0.106 Angle : 0.508 14.412 34703 Z= 0.257 Chirality : 0.044 0.250 4064 Planarity : 0.003 0.039 4395 Dihedral : 5.764 59.145 4282 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.30 % Allowed : 13.30 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.15), residues: 3055 helix: 2.11 (0.20), residues: 706 sheet: 0.61 (0.19), residues: 695 loop : -0.95 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.016 0.001 TYR A1067 PHE 0.029 0.001 PHE C 168 TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00243 (25350) covalent geometry : angle 0.49840 (34481) SS BOND : bond 0.00339 ( 42) SS BOND : angle 0.88648 ( 84) hydrogen bonds : bond 0.04530 ( 980) hydrogen bonds : angle 4.76877 ( 2733) link_BETA1-4 : bond 0.00488 ( 9) link_BETA1-4 : angle 1.13943 ( 27) link_NAG-ASN : bond 0.00244 ( 37) link_NAG-ASN : angle 1.63320 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 190 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7537 (mtp85) REVERT: A 239 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: A 280 ASN cc_start: 0.7992 (p0) cc_final: 0.7783 (p0) REVERT: A 467 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: A 499 PRO cc_start: 0.8374 (Cg_endo) cc_final: 0.8119 (Cg_exo) REVERT: A 547 THR cc_start: 0.8037 (p) cc_final: 0.7811 (t) REVERT: A 661 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: A 675 GLN cc_start: 0.6972 (pp30) cc_final: 0.6528 (tp40) REVERT: A 697 MET cc_start: 0.9318 (ptm) cc_final: 0.9076 (ptm) REVERT: A 808 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: A 935 GLN cc_start: 0.6760 (tt0) cc_final: 0.6547 (mt0) REVERT: A 1084 ASP cc_start: 0.7801 (t0) cc_final: 0.7566 (t0) REVERT: B 375 PHE cc_start: 0.7759 (t80) cc_final: 0.7323 (m-80) REVERT: B 493 GLN cc_start: 0.7901 (mt0) cc_final: 0.7553 (mt0) REVERT: B 935 GLN cc_start: 0.7857 (tt0) cc_final: 0.7160 (tm-30) REVERT: C 53 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6943 (t0) REVERT: C 326 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7579 (mp) REVERT: C 420 ASP cc_start: 0.7403 (m-30) cc_final: 0.6921 (m-30) REVERT: C 690 GLN cc_start: 0.7154 (mt0) cc_final: 0.6854 (mt0) REVERT: C 869 MET cc_start: 0.8841 (mtt) cc_final: 0.8614 (mtt) REVERT: C 1127 ASP cc_start: 0.8129 (m-30) cc_final: 0.7918 (t0) outliers start: 35 outliers final: 23 residues processed: 203 average time/residue: 0.5087 time to fit residues: 123.7621 Evaluate side-chains 203 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 270 optimal weight: 0.4980 chunk 299 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 613 GLN B 52 GLN B 394 ASN B 556 ASN B1005 GLN C 935 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122738 restraints weight = 26013.533| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.73 r_work: 0.2979 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25438 Z= 0.216 Angle : 0.605 14.770 34703 Z= 0.307 Chirality : 0.048 0.235 4064 Planarity : 0.004 0.041 4395 Dihedral : 6.092 59.764 4282 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.49 % Allowed : 13.26 % 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 aren not related in a simple way. whole: 0.00 (0.15), residues: 3055 helix: 1.78 (0.20), residues: 700 sheet: 0.45 (0.19), residues: 687 loop : -1.00 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.021 0.002 TYR C1067 PHE 0.025 0.002 PHE C 377 TRP 0.012 0.002 TRP A 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00542 (25350) covalent geometry : angle 0.59290 (34481) SS BOND : bond 0.00532 ( 42) SS BOND : angle 1.20939 ( 84) hydrogen bonds : bond 0.06142 ( 980) hydrogen bonds : angle 5.04537 ( 2733) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.33371 ( 27) link_NAG-ASN : bond 0.00270 ( 37) link_NAG-ASN : angle 1.94708 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7188.94 seconds wall clock time: 123 minutes 15.09 seconds (7395.09 seconds total)