Starting phenix.real_space_refine on Sat Jun 21 13:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uk1_42342/06_2025/8uk1_42342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uk1_42342/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uk1_42342/06_2025/8uk1_42342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uk1_42342/06_2025/8uk1_42342.map" model { file = "/net/cci-nas-00/data/ceres_data/8uk1_42342/06_2025/8uk1_42342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uk1_42342/06_2025/8uk1_42342.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.89, per 1000 atoms: 0.56 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: 5.48 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.34 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: 10.23 Time building geometry restraints manager: 6.61 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 1146 or resid 1301 through 1309)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 132 or resid 165 through 677 or resid 690 throu \ gh 1146 or resid 1301 through 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 54.100 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.120 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.002 TRP C 886 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.002 PHE B1121 TYR 0.025 0.001 TYR C 266 ARG 0.004 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 37) link_NAG-ASN : angle 2.50605 ( 111) link_BETA1-4 : bond 0.00832 ( 9) link_BETA1-4 : angle 1.68125 ( 27) hydrogen bonds : bond 0.13090 ( 980) hydrogen bonds : angle 6.33298 ( 2733) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.52206 ( 84) covalent geometry : bond 0.00422 (25350) covalent geometry : angle 0.74931 (34481) *********************** 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 : 2.669 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: 1.2406 time to fit residues: 358.3730 Evaluate side-chains 185 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 241 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 804 GLN A 901 GLN A 955 ASN A 957 GLN A 960 ASN B 394 ASN B 613 GLN B1005 GLN C 448 ASN C 493 GLN C1101 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123598 restraints weight = 26024.353| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.49 r_work: 0.3083 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 25438 Z= 0.272 Angle : 0.687 18.995 34703 Z= 0.348 Chirality : 0.050 0.233 4064 Planarity : 0.005 0.069 4395 Dihedral : 7.147 59.837 4282 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.45 % Allowed : 7.10 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3055 helix: 0.84 (0.19), residues: 691 sheet: 0.47 (0.19), residues: 690 loop : -1.28 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.008 0.002 HIS B1064 PHE 0.027 0.002 PHE C 377 TYR 0.025 0.002 TYR C1067 ARG 0.005 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 37) link_NAG-ASN : angle 2.31580 ( 111) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 1.35839 ( 27) hydrogen bonds : bond 0.07138 ( 980) hydrogen bonds : angle 5.42578 ( 2733) SS BOND : bond 0.00581 ( 42) SS BOND : angle 1.62774 ( 84) covalent geometry : bond 0.00686 (25350) covalent geometry : angle 0.67120 (34481) *********************** 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 241 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7259 (ttm170) REVERT: A 239 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: A 661 GLU cc_start: 0.8270 (mp0) cc_final: 0.8069 (mp0) REVERT: A 697 MET cc_start: 0.9381 (ptm) cc_final: 0.9114 (ptm) REVERT: A 994 ASP cc_start: 0.8717 (t70) cc_final: 0.8505 (t70) REVERT: B 375 PHE cc_start: 0.7655 (t80) cc_final: 0.7318 (m-80) REVERT: B 420 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8528 (p0) REVERT: B 556 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7561 (p0) REVERT: B 935 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 1101 HIS cc_start: 0.8177 (m90) cc_final: 0.7943 (m90) REVERT: C 467 ASP cc_start: 0.7861 (t0) cc_final: 0.7587 (m-30) REVERT: C 869 MET cc_start: 0.8935 (mtt) cc_final: 0.8667 (mtm) outliers start: 39 outliers final: 18 residues processed: 225 average time/residue: 1.2073 time to fit residues: 319.8487 Evaluate side-chains 203 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 723 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 420 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 875 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 107 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 235 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 304 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 564 GLN A 613 GLN A 935 GLN A 957 GLN A 965 GLN A1005 GLN B 52 GLN B 218 GLN B 394 ASN B 804 GLN B1005 GLN C 334 ASN C 448 ASN C 493 GLN C1101 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.174543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124816 restraints weight = 25824.562| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3023 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25438 Z= 0.125 Angle : 0.547 18.637 34703 Z= 0.276 Chirality : 0.044 0.256 4064 Planarity : 0.004 0.054 4395 Dihedral : 6.655 58.991 4282 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.34 % Allowed : 9.58 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3055 helix: 1.54 (0.20), residues: 696 sheet: 0.53 (0.19), residues: 686 loop : -1.16 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 PHE 0.024 0.001 PHE C 168 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 37) link_NAG-ASN : angle 1.94083 ( 111) link_BETA1-4 : bond 0.00443 ( 9) link_BETA1-4 : angle 1.19585 ( 27) hydrogen bonds : bond 0.05375 ( 980) hydrogen bonds : angle 5.11708 ( 2733) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.13538 ( 84) covalent geometry : bond 0.00290 (25350) covalent geometry : angle 0.53318 (34481) *********************** 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 235 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: A 467 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6145 (m-30) REVERT: A 697 MET cc_start: 0.9359 (ptm) cc_final: 0.9082 (ptm) REVERT: A 808 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: A 821 LEU cc_start: 0.8540 (mt) cc_final: 0.8316 (mp) REVERT: A 994 ASP cc_start: 0.8584 (t70) cc_final: 0.8376 (t70) REVERT: B 375 PHE cc_start: 0.7639 (t80) cc_final: 0.7273 (m-80) REVERT: B 493 GLN cc_start: 0.7926 (mt0) cc_final: 0.7612 (mt0) REVERT: B 556 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (p0) REVERT: B 878 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8188 (mt) REVERT: B 935 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 1101 HIS cc_start: 0.8166 (m90) cc_final: 0.7915 (m90) REVERT: C 319 ARG cc_start: 0.8259 (mmt180) cc_final: 0.7962 (ttt180) REVERT: C 467 ASP cc_start: 0.7781 (t0) cc_final: 0.7527 (m-30) REVERT: C 531 THR cc_start: 0.8176 (m) cc_final: 0.7771 (p) REVERT: C 1127 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7879 (m-30) outliers start: 36 outliers final: 16 residues processed: 223 average time/residue: 1.1113 time to fit residues: 297.0736 Evaluate side-chains 203 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 2.787 ------------------------------------------------------------------------------- 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 383 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 532 ASN 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 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU 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 Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 198 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 564 GLN A 613 GLN A 935 GLN A 960 ASN B 52 GLN B 394 ASN B1005 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123283 restraints weight = 26080.679| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.64 r_work: 0.3001 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25438 Z= 0.228 Angle : 0.647 18.318 34703 Z= 0.325 Chirality : 0.049 0.270 4064 Planarity : 0.004 0.043 4395 Dihedral : 6.823 59.307 4282 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.23 % Allowed : 11.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3055 helix: 1.46 (0.20), residues: 688 sheet: 0.38 (0.19), residues: 693 loop : -1.18 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS A1064 PHE 0.026 0.002 PHE C 168 TYR 0.023 0.002 TYR C1067 ARG 0.003 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 37) link_NAG-ASN : angle 2.28791 ( 111) link_BETA1-4 : bond 0.00390 ( 9) link_BETA1-4 : angle 1.37020 ( 27) hydrogen bonds : bond 0.06561 ( 980) hydrogen bonds : angle 5.28317 ( 2733) SS BOND : bond 0.00511 ( 42) SS BOND : angle 1.71106 ( 84) covalent geometry : bond 0.00573 (25350) covalent geometry : angle 0.62919 (34481) *********************** 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 246 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 239 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: A 467 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6202 (m-30) REVERT: A 661 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 697 MET cc_start: 0.9344 (ptm) cc_final: 0.9069 (ptm) REVERT: A 804 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8286 (mt0) REVERT: A 808 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: B 375 PHE cc_start: 0.7855 (t80) cc_final: 0.7442 (m-80) REVERT: B 493 GLN cc_start: 0.7837 (mt0) cc_final: 0.7504 (mt0) REVERT: B 556 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7497 (p0) REVERT: B 697 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8860 (ptp) REVERT: B 878 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8224 (mt) REVERT: B 1101 HIS cc_start: 0.8221 (m90) cc_final: 0.7998 (m90) REVERT: C 53 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7225 (t0) REVERT: C 319 ARG cc_start: 0.8389 (mmt180) cc_final: 0.8087 (ttt180) REVERT: C 326 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7504 (mp) REVERT: C 531 THR cc_start: 0.8192 (m) cc_final: 0.7885 (p) REVERT: C 571 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7515 (t70) REVERT: C 1113 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: C 1127 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7922 (m-30) outliers start: 60 outliers final: 34 residues processed: 219 average time/residue: 1.1367 time to fit residues: 297.1835 Evaluate side-chains 224 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 547 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 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 455 LEU 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 697 MET Chi-restraints excluded: chain B residue 719 THR 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 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 274 THR Chi-restraints excluded: chain C residue 326 ILE 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 1113 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 935 GLN B 52 GLN B 394 ASN B1005 GLN C 334 ASN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124053 restraints weight = 26073.000| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.67 r_work: 0.3051 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25438 Z= 0.154 Angle : 0.563 16.985 34703 Z= 0.285 Chirality : 0.046 0.255 4064 Planarity : 0.004 0.040 4395 Dihedral : 6.472 59.762 4282 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.97 % Allowed : 12.41 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3055 helix: 1.70 (0.20), residues: 692 sheet: 0.47 (0.19), residues: 695 loop : -1.10 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS C1064 PHE 0.019 0.001 PHE C 377 TYR 0.019 0.001 TYR C 28 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 37) link_NAG-ASN : angle 1.94894 ( 111) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.22741 ( 27) hydrogen bonds : bond 0.05489 ( 980) hydrogen bonds : angle 5.08539 ( 2733) SS BOND : bond 0.00427 ( 42) SS BOND : angle 1.23140 ( 84) covalent geometry : bond 0.00376 (25350) covalent geometry : angle 0.54926 (34481) *********************** 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 237 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 190 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7421 (mtp85) REVERT: A 239 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: A 355 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7536 (ttp-170) REVERT: A 467 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6231 (m-30) REVERT: A 661 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: A 697 MET cc_start: 0.9355 (ptm) cc_final: 0.9070 (ptm) REVERT: A 804 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8157 (mt0) REVERT: A 808 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: B 375 PHE cc_start: 0.7825 (t80) cc_final: 0.7406 (m-80) REVERT: B 493 GLN cc_start: 0.7815 (mt0) cc_final: 0.7467 (mt0) REVERT: B 556 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7485 (p0) REVERT: B 697 MET cc_start: 0.9045 (ptm) cc_final: 0.8806 (ptp) REVERT: B 935 GLN cc_start: 0.7925 (tt0) cc_final: 0.7585 (tt0) REVERT: C 53 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7110 (t0) REVERT: C 319 ARG cc_start: 0.8282 (mmt180) cc_final: 0.7998 (ttt180) REVERT: C 326 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7508 (mp) REVERT: C 531 THR cc_start: 0.8171 (m) cc_final: 0.7940 (p) REVERT: C 571 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7458 (t70) REVERT: C 1127 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7851 (m-30) outliers start: 53 outliers final: 29 residues processed: 218 average time/residue: 1.1459 time to fit residues: 297.4819 Evaluate side-chains 219 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 591 SER 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 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 556 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 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 274 THR 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 738 CYS Chi-restraints excluded: chain C residue 791 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 6 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 274 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 613 GLN B 52 GLN B 394 ASN B 437 ASN B 935 GLN B1005 GLN B1101 HIS C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.176833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125764 restraints weight = 25851.859| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.54 r_work: 0.3068 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25438 Z= 0.127 Angle : 0.534 16.004 34703 Z= 0.270 Chirality : 0.044 0.252 4064 Planarity : 0.003 0.040 4395 Dihedral : 6.191 59.650 4282 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.86 % Allowed : 12.74 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3055 helix: 1.89 (0.20), residues: 698 sheet: 0.50 (0.19), residues: 704 loop : -1.03 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 PHE 0.029 0.001 PHE C 168 TYR 0.018 0.001 TYR C 28 ARG 0.005 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 37) link_NAG-ASN : angle 1.83529 ( 111) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 1.18764 ( 27) hydrogen bonds : bond 0.05043 ( 980) hydrogen bonds : angle 4.95511 ( 2733) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.08960 ( 84) covalent geometry : bond 0.00302 (25350) covalent geometry : angle 0.52186 (34481) *********************** 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 236 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 190 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7249 (mtt180) REVERT: A 239 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: A 355 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7504 (ttp-170) REVERT: A 467 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: A 661 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: A 697 MET cc_start: 0.9345 (ptm) cc_final: 0.9118 (ptm) REVERT: A 804 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8111 (mt0) REVERT: A 808 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: A 1084 ASP cc_start: 0.7676 (t0) cc_final: 0.7316 (t0) REVERT: B 319 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7347 (ttt180) REVERT: B 375 PHE cc_start: 0.7796 (t80) cc_final: 0.7400 (m-80) REVERT: B 493 GLN cc_start: 0.7740 (mt0) cc_final: 0.7411 (mt0) REVERT: B 556 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7482 (p0) REVERT: B 900 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8843 (mtp) REVERT: C 53 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6999 (t0) REVERT: C 319 ARG cc_start: 0.8206 (mmt180) cc_final: 0.7939 (ttt180) REVERT: C 326 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7550 (mp) REVERT: C 690 GLN cc_start: 0.7035 (mt0) cc_final: 0.6769 (mt0) REVERT: C 1127 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7817 (m-30) outliers start: 50 outliers final: 24 residues processed: 216 average time/residue: 1.1847 time to fit residues: 305.5841 Evaluate side-chains 211 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 2.521 ------------------------------------------------------------------------------- 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 532 ASN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL 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 808 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER 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 556 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 988 GLU 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 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 Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 249 optimal weight: 0.0070 chunk 289 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- 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** B 52 GLN B 394 ASN B 935 GLN 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 = 0.3939 r_free = 0.3939 target = 0.176228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127368 restraints weight = 25893.689| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.52 r_work: 0.3129 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25438 Z= 0.108 Angle : 0.515 15.035 34703 Z= 0.260 Chirality : 0.044 0.256 4064 Planarity : 0.003 0.039 4395 Dihedral : 5.931 59.287 4282 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.93 % Allowed : 12.93 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3055 helix: 2.05 (0.20), residues: 706 sheet: 0.57 (0.19), residues: 704 loop : -0.97 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.000 HIS C 66 PHE 0.015 0.001 PHE A 592 TYR 0.017 0.001 TYR C 28 ARG 0.005 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 37) link_NAG-ASN : angle 1.70279 ( 111) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 1.13993 ( 27) hydrogen bonds : bond 0.04591 ( 980) hydrogen bonds : angle 4.82961 ( 2733) SS BOND : bond 0.00341 ( 42) SS BOND : angle 0.99877 ( 84) covalent geometry : bond 0.00247 (25350) covalent geometry : angle 0.50393 (34481) *********************** 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 234 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: A 190 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7313 (mtt180) REVERT: A 239 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: A 280 ASN cc_start: 0.7986 (p0) cc_final: 0.7778 (p0) REVERT: A 355 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7451 (ttp-170) REVERT: A 547 THR cc_start: 0.8089 (p) cc_final: 0.7854 (t) REVERT: A 661 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 675 GLN cc_start: 0.6732 (pp30) cc_final: 0.6445 (tp40) REVERT: A 697 MET cc_start: 0.9326 (ptm) cc_final: 0.9084 (ptm) REVERT: A 804 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8237 (mt0) REVERT: A 808 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: A 1084 ASP cc_start: 0.7732 (t0) cc_final: 0.7395 (t0) REVERT: B 335 LEU cc_start: 0.8510 (mm) cc_final: 0.8263 (mt) REVERT: B 375 PHE cc_start: 0.7798 (t80) cc_final: 0.7397 (m-80) REVERT: B 493 GLN cc_start: 0.7745 (mt0) cc_final: 0.7433 (mt0) REVERT: B 740 MET cc_start: 0.8739 (ttp) cc_final: 0.8537 (tpp) REVERT: B 900 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8663 (mtp) REVERT: B 935 GLN cc_start: 0.7803 (tt0) cc_final: 0.7132 (tm-30) REVERT: C 53 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6976 (t0) REVERT: C 319 ARG cc_start: 0.8154 (mmt180) cc_final: 0.7876 (ttt180) REVERT: C 392 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: C 690 GLN cc_start: 0.7044 (mt0) cc_final: 0.6771 (mt0) REVERT: C 1127 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7901 (t0) outliers start: 52 outliers final: 26 residues processed: 217 average time/residue: 1.0853 time to fit residues: 281.2308 Evaluate side-chains 210 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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 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 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 45 SER 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 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET 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 392 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 154 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 564 GLN A 804 GLN B 52 GLN B 394 ASN B 556 ASN B1005 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.176664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125610 restraints weight = 25911.984| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.55 r_work: 0.3048 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25438 Z= 0.173 Angle : 0.571 15.097 34703 Z= 0.289 Chirality : 0.046 0.243 4064 Planarity : 0.004 0.040 4395 Dihedral : 6.050 59.799 4282 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.78 % Allowed : 13.37 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3055 helix: 1.92 (0.20), residues: 696 sheet: 0.46 (0.19), residues: 707 loop : -1.03 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS A1064 PHE 0.028 0.001 PHE C 168 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 37) link_NAG-ASN : angle 1.87324 ( 111) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 1.26534 ( 27) hydrogen bonds : bond 0.05647 ( 980) hydrogen bonds : angle 4.97749 ( 2733) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.14420 ( 84) covalent geometry : bond 0.00433 (25350) covalent geometry : angle 0.55900 (34481) *********************** 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 228 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 190 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7344 (mtt180) REVERT: A 239 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: A 355 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7502 (ttp-170) REVERT: A 467 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6171 (m-30) REVERT: A 547 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7873 (t) REVERT: A 661 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: A 675 GLN cc_start: 0.6736 (pp30) cc_final: 0.6427 (tp40) REVERT: A 697 MET cc_start: 0.9325 (ptm) cc_final: 0.9109 (ptm) REVERT: A 763 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 804 GLN cc_start: 0.8792 (mm110) cc_final: 0.8251 (mt0) REVERT: A 808 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7221 (m-30) REVERT: A 1084 ASP cc_start: 0.7864 (t0) cc_final: 0.7561 (t0) REVERT: B 335 LEU cc_start: 0.8511 (mm) cc_final: 0.8296 (mt) REVERT: B 375 PHE cc_start: 0.7853 (t80) cc_final: 0.7400 (m-80) REVERT: B 493 GLN cc_start: 0.7768 (mt0) cc_final: 0.7419 (mt0) REVERT: B 697 MET cc_start: 0.9061 (ptm) cc_final: 0.8823 (ptp) REVERT: B 935 GLN cc_start: 0.7885 (tt0) cc_final: 0.7569 (tt0) REVERT: C 53 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7142 (t0) REVERT: C 319 ARG cc_start: 0.8231 (mmt180) cc_final: 0.7961 (ttt180) REVERT: C 571 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7408 (t70) REVERT: C 1127 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7824 (m-30) outliers start: 48 outliers final: 31 residues processed: 213 average time/residue: 1.1231 time to fit residues: 287.2680 Evaluate side-chains 217 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 2.895 ------------------------------------------------------------------------------- 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 591 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 763 LEU 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 875 SER 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 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 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 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 791 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 262 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 203 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 = 0.3964 r_free = 0.3964 target = 0.178363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118339 restraints weight = 25848.925| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.27 r_work: 0.3087 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1892 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= 0.114 Angle : 0.519 14.325 34703 Z= 0.263 Chirality : 0.044 0.254 4064 Planarity : 0.003 0.039 4395 Dihedral : 5.851 59.290 4282 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.71 % Allowed : 13.82 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3055 helix: 2.07 (0.20), residues: 699 sheet: 0.55 (0.19), residues: 705 loop : -0.96 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 66 PHE 0.014 0.001 PHE C 377 TYR 0.016 0.001 TYR C 28 ARG 0.011 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 37) link_NAG-ASN : angle 1.70605 ( 111) link_BETA1-4 : bond 0.00467 ( 9) link_BETA1-4 : angle 1.16951 ( 27) hydrogen bonds : bond 0.04748 ( 980) hydrogen bonds : angle 4.83757 ( 2733) SS BOND : bond 0.00332 ( 42) SS BOND : angle 0.99666 ( 84) covalent geometry : bond 0.00267 (25350) covalent geometry : angle 0.50792 (34481) *********************** 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 223 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 190 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7479 (mtp85) REVERT: A 239 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: A 280 ASN cc_start: 0.7890 (p0) cc_final: 0.7679 (p0) REVERT: A 355 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7433 (ttp-170) REVERT: A 467 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: A 499 PRO cc_start: 0.8339 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: A 547 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7850 (t) REVERT: A 661 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 675 GLN cc_start: 0.6870 (pp30) cc_final: 0.6401 (tp40) REVERT: A 697 MET cc_start: 0.9289 (ptm) cc_final: 0.9060 (ptm) REVERT: A 763 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7841 (mt) REVERT: A 804 GLN cc_start: 0.8797 (mm110) cc_final: 0.8100 (mt0) REVERT: A 808 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: A 1084 ASP cc_start: 0.7817 (t0) cc_final: 0.7486 (t0) REVERT: B 335 LEU cc_start: 0.8583 (mm) cc_final: 0.8350 (mt) REVERT: B 375 PHE cc_start: 0.7757 (t80) cc_final: 0.7284 (m-80) REVERT: B 493 GLN cc_start: 0.7667 (mt0) cc_final: 0.7336 (mt0) REVERT: B 697 MET cc_start: 0.8997 (ptm) cc_final: 0.8678 (ptp) REVERT: B 935 GLN cc_start: 0.7699 (tt0) cc_final: 0.7364 (tt0) REVERT: C 53 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6893 (t0) REVERT: C 319 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7926 (ttt180) REVERT: C 571 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7350 (t70) REVERT: C 1127 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7860 (t0) outliers start: 46 outliers final: 30 residues processed: 210 average time/residue: 1.0718 time to fit residues: 269.9673 Evaluate side-chains 218 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 2.811 ------------------------------------------------------------------------------- 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 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 763 LEU 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 875 SER 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 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 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 390 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 791 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 40 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 85 optimal weight: 0.0060 chunk 169 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 297 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 564 GLN B 52 GLN B 394 ASN B 556 ASN 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 = 0.3974 r_free = 0.3974 target = 0.179501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121526 restraints weight = 25797.109| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.55 r_work: 0.3017 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25438 Z= 0.106 Angle : 0.511 13.890 34703 Z= 0.259 Chirality : 0.044 0.250 4064 Planarity : 0.003 0.039 4395 Dihedral : 5.721 59.232 4282 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.60 % Allowed : 14.00 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3055 helix: 2.23 (0.20), residues: 700 sheet: 0.59 (0.19), residues: 707 loop : -0.92 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS A1064 PHE 0.030 0.001 PHE C 168 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 37) link_NAG-ASN : angle 1.64382 ( 111) link_BETA1-4 : bond 0.00460 ( 9) link_BETA1-4 : angle 1.14071 ( 27) hydrogen bonds : bond 0.04522 ( 980) hydrogen bonds : angle 4.75515 ( 2733) SS BOND : bond 0.00307 ( 42) SS BOND : angle 0.90129 ( 84) covalent geometry : bond 0.00244 (25350) covalent geometry : angle 0.50131 (34481) ********************** 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 225 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: A 190 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7454 (mtp85) REVERT: A 239 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: A 280 ASN cc_start: 0.7808 (p0) cc_final: 0.7600 (p0) REVERT: A 467 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: A 499 PRO cc_start: 0.8320 (Cg_endo) cc_final: 0.8084 (Cg_exo) REVERT: A 547 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 661 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: A 675 GLN cc_start: 0.6939 (pp30) cc_final: 0.6450 (tp40) REVERT: A 697 MET cc_start: 0.9264 (ptm) cc_final: 0.9030 (ptm) REVERT: A 804 GLN cc_start: 0.8677 (mm110) cc_final: 0.8125 (mt0) REVERT: A 1084 ASP cc_start: 0.7889 (t0) cc_final: 0.7603 (t0) REVERT: B 335 LEU cc_start: 0.8512 (mm) cc_final: 0.8288 (mt) REVERT: B 375 PHE cc_start: 0.7725 (t80) cc_final: 0.7230 (m-80) REVERT: B 493 GLN cc_start: 0.7625 (mt0) cc_final: 0.7284 (mt0) REVERT: B 697 MET cc_start: 0.8987 (ptm) cc_final: 0.8656 (ptp) REVERT: B 935 GLN cc_start: 0.7679 (tt0) cc_final: 0.7332 (tt0) REVERT: C 53 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6867 (t0) REVERT: C 319 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7886 (ttt180) REVERT: C 571 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7308 (t70) REVERT: C 1127 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7919 (t0) outliers start: 43 outliers final: 27 residues processed: 211 average time/residue: 1.0823 time to fit residues: 275.8015 Evaluate side-chains 215 residues out of total 2692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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 547 THR 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 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER 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 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 874 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 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 791 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 49 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 804 GLN B 52 GLN B 394 ASN 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 = 0.3964 r_free = 0.3964 target = 0.178488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120248 restraints weight = 25937.319| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.53 r_work: 0.2996 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25438 Z= 0.127 Angle : 0.528 13.718 34703 Z= 0.268 Chirality : 0.044 0.245 4064 Planarity : 0.003 0.039 4395 Dihedral : 5.745 59.430 4282 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.45 % Allowed : 14.34 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3055 helix: 2.14 (0.20), residues: 699 sheet: 0.54 (0.19), residues: 711 loop : -0.94 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 PHE 0.017 0.001 PHE C 377 TYR 0.017 0.001 TYR C1067 ARG 0.007 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 37) link_NAG-ASN : angle 1.67602 ( 111) link_BETA1-4 : bond 0.00462 ( 9) link_BETA1-4 : angle 1.17336 ( 27) hydrogen bonds : bond 0.04859 ( 980) hydrogen bonds : angle 4.79736 ( 2733) SS BOND : bond 0.00350 ( 42) SS BOND : angle 0.98099 ( 84) covalent geometry : bond 0.00305 (25350) covalent geometry : angle 0.51814 (34481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17004.28 seconds wall clock time: 290 minutes 9.49 seconds (17409.49 seconds total)