Starting phenix.real_space_refine on Sat Jun 21 13:33:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0l_42860/06_2025/8v0l_42860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0l_42860/06_2025/8v0l_42860.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/8v0l_42860/06_2025/8v0l_42860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0l_42860/06_2025/8v0l_42860.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0l_42860/06_2025/8v0l_42860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0l_42860/06_2025/8v0l_42860.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 114 5.16 5 C 15834 2.51 5 N 4083 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24849 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8073 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 6 Chain: "C" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8073 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 6 Chain: "A" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8073 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} 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: "H" 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: "J" 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: "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: 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: "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 Time building chain proxies: 13.58, per 1000 atoms: 0.55 Number of scatterers: 24849 At special positions: 0 Unit cell: (135, 128.52, 174.96, 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 114 16.00 O 4818 8.00 N 4083 7.00 C 15834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.05 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 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=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=2.02 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 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 234 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN B1098 " " NAG F 1 " - " ASN B 801 " " NAG G 1 " - " ASN C 717 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 801 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A 801 " Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.9 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 25.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.841A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.210A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 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: 3.683A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.529A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.915A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.124A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.535A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.544A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.714A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (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: 4.115A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.733A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.522A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.611A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.072A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.083A 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 removed outlier: 3.565A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.503A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.698A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.174A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) 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: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.789A 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 removed outlier: 3.559A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.098A 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: 3.530A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.639A 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 1033 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.749A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.841A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.564A pdb=" N ARG A 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.186A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.940A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.013A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.547A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.637A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.217A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.559A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.877A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.972A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.464A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'C' and resid 23 through 30 removed outlier: 3.738A pdb=" N THR C 23 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 68 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.083A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.020A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.606A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.520A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.637A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AC8, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.836A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.501A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.075A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.644A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'A' and resid 24 through 30 removed outlier: 3.522A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.042A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.957A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.070A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.696A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.650A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.242A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.536A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.119A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.604A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1122 978 hydrogen bonds defined for protein. 2718 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: 10.03 Time building geometry restraints manager: 6.85 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: 7907 1.35 - 1.47: 6514 1.47 - 1.60: 10830 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25392 Sorted by residual: bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.337 1.377 -0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.33e+00 ... (remaining 25387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 33862 2.46 - 4.91: 592 4.91 - 7.37: 63 7.37 - 9.82: 18 9.82 - 12.28: 4 Bond angle restraints: 34539 Sorted by residual: angle pdb=" C SER A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.56 108.85 5.71 1.27e+00 6.20e-01 2.02e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.92e+01 angle pdb=" CB LYS A 558 " pdb=" CG LYS A 558 " pdb=" CD LYS A 558 " ideal model delta sigma weight residual 111.30 121.13 -9.83 2.30e+00 1.89e-01 1.83e+01 ... (remaining 34534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14083 17.57 - 35.13: 1368 35.13 - 52.70: 213 52.70 - 70.27: 65 70.27 - 87.83: 27 Dihedral angle restraints: 15756 sinusoidal: 6714 harmonic: 9042 Sorted by residual: dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 145.11 34.89 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA SER B 112 " pdb=" C SER B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3435 0.075 - 0.151: 585 0.151 - 0.226: 38 0.226 - 0.301: 12 0.301 - 0.376: 1 Chirality restraints: 4071 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE C 119 " pdb=" CA ILE C 119 " pdb=" CG1 ILE C 119 " pdb=" CG2 ILE C 119 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CG LEU A 390 " pdb=" CB LEU A 390 " pdb=" CD1 LEU A 390 " pdb=" CD2 LEU A 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4068 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 113 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LYS A 113 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS A 113 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 114 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 209 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.25e+00 pdb=" CG ASN C 343 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.024 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6891 2.82 - 3.34: 19890 3.34 - 3.86: 39877 3.86 - 4.38: 45501 4.38 - 4.90: 81665 Nonbonded interactions: 193824 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.299 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.301 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.305 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.313 3.040 ... (remaining 193819 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.200 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: 0.850 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 53.660 Find NCS groups from input model: 1.000 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 0.055 25476 Z= 0.219 Angle : 0.792 12.279 34752 Z= 0.413 Chirality : 0.054 0.376 4071 Planarity : 0.006 0.075 4404 Dihedral : 14.192 87.834 9819 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -1.01 (0.14), residues: 3063 helix: -0.16 (0.17), residues: 669 sheet: 0.61 (0.19), residues: 663 loop : -1.44 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS C 519 PHE 0.043 0.002 PHE C 106 TYR 0.020 0.001 TYR A1067 ARG 0.013 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 36) link_NAG-ASN : angle 2.25459 ( 108) link_BETA1-4 : bond 0.01348 ( 9) link_BETA1-4 : angle 3.75696 ( 27) hydrogen bonds : bond 0.12943 ( 978) hydrogen bonds : angle 6.52636 ( 2718) SS BOND : bond 0.00527 ( 39) SS BOND : angle 1.55809 ( 78) covalent geometry : bond 0.00440 (25392) covalent geometry : angle 0.77328 (34539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7908 (mt0) cc_final: 0.7669 (mt0) REVERT: B 780 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6987 (pt0) REVERT: B 998 THR cc_start: 0.8410 (m) cc_final: 0.8154 (p) REVERT: B 1050 MET cc_start: 0.8219 (mtp) cc_final: 0.7915 (ttm) REVERT: C 102 ARG cc_start: 0.6070 (mmp-170) cc_final: 0.5730 (mmp-170) REVERT: C 458 LYS cc_start: 0.8342 (mttt) cc_final: 0.7474 (mppt) REVERT: C 675 GLN cc_start: 0.7482 (mt0) cc_final: 0.7140 (pt0) REVERT: C 776 LYS cc_start: 0.8002 (tttm) cc_final: 0.7393 (ttmt) REVERT: C 902 MET cc_start: 0.8656 (mmm) cc_final: 0.8252 (mmt) REVERT: C 950 ASP cc_start: 0.7667 (m-30) cc_final: 0.7293 (m-30) REVERT: A 173 GLN cc_start: 0.5487 (tm-30) cc_final: 0.5146 (tm130) REVERT: A 239 GLN cc_start: 0.7563 (mm110) cc_final: 0.7354 (mm110) REVERT: A 574 ASP cc_start: 0.7507 (t70) cc_final: 0.7224 (t70) REVERT: A 584 ILE cc_start: 0.8482 (mt) cc_final: 0.8268 (mm) REVERT: A 675 GLN cc_start: 0.7112 (tp40) cc_final: 0.6208 (tt0) REVERT: A 1092 GLU cc_start: 0.7427 (pt0) cc_final: 0.7100 (pt0) outliers start: 0 outliers final: 1 residues processed: 265 average time/residue: 1.0322 time to fit residues: 331.7240 Evaluate side-chains 204 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 0.0070 chunk 242 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 474 GLN A 207 HIS A 314 GLN A 339 HIS A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113852 restraints weight = 27210.928| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.28 r_work: 0.3046 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25476 Z= 0.188 Angle : 0.607 10.008 34752 Z= 0.307 Chirality : 0.047 0.292 4071 Planarity : 0.004 0.049 4404 Dihedral : 6.676 59.511 4271 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.22 % Allowed : 6.44 % Favored : 92.33 % 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: -0.45 (0.14), residues: 3063 helix: 1.13 (0.19), residues: 696 sheet: 0.54 (0.19), residues: 678 loop : -1.32 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.007 0.001 HIS B1048 PHE 0.020 0.002 PHE B 377 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 36) link_NAG-ASN : angle 1.84839 ( 108) link_BETA1-4 : bond 0.00751 ( 9) link_BETA1-4 : angle 2.17628 ( 27) hydrogen bonds : bond 0.05646 ( 978) hydrogen bonds : angle 5.13125 ( 2718) SS BOND : bond 0.00681 ( 39) SS BOND : angle 1.46127 ( 78) covalent geometry : bond 0.00461 (25392) covalent geometry : angle 0.59239 (34539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7954 (mt0) cc_final: 0.7715 (mt0) REVERT: B 780 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7827 (mm-30) REVERT: B 787 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: B 935 GLN cc_start: 0.7385 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 981 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8071 (mm) REVERT: B 998 THR cc_start: 0.8868 (m) cc_final: 0.8544 (p) REVERT: C 102 ARG cc_start: 0.6379 (mmp-170) cc_final: 0.6040 (mmp-170) REVERT: C 190 ARG cc_start: 0.7633 (mtt180) cc_final: 0.7410 (mtp180) REVERT: C 375 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: C 458 LYS cc_start: 0.8611 (mttt) cc_final: 0.7660 (mppt) REVERT: C 776 LYS cc_start: 0.8238 (tttm) cc_final: 0.8012 (tttm) REVERT: C 804 GLN cc_start: 0.8749 (mt0) cc_final: 0.8486 (mm-40) REVERT: C 902 MET cc_start: 0.9059 (mmm) cc_final: 0.8657 (mmt) REVERT: C 950 ASP cc_start: 0.8392 (m-30) cc_final: 0.8048 (m-30) REVERT: A 173 GLN cc_start: 0.5846 (tm-30) cc_final: 0.5527 (tm130) REVERT: A 498 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7823 (mtt90) REVERT: A 574 ASP cc_start: 0.8003 (t70) cc_final: 0.7628 (t70) REVERT: A 603 ASN cc_start: 0.7734 (t0) cc_final: 0.7428 (t0) REVERT: A 675 GLN cc_start: 0.7389 (tp40) cc_final: 0.6235 (tt0) REVERT: A 1092 GLU cc_start: 0.8250 (pt0) cc_final: 0.7854 (pt0) outliers start: 33 outliers final: 21 residues processed: 240 average time/residue: 1.0363 time to fit residues: 300.0060 Evaluate side-chains 230 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 300 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 339 HIS B 519 HIS B 703 ASN C 239 GLN A 207 HIS A 314 GLN A 339 HIS A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114741 restraints weight = 27086.505| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.29 r_work: 0.3124 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25476 Z= 0.122 Angle : 0.531 9.561 34752 Z= 0.269 Chirality : 0.045 0.246 4071 Planarity : 0.004 0.047 4404 Dihedral : 6.153 58.397 4269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.26 % Allowed : 9.26 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: 3063 helix: 1.61 (0.20), residues: 696 sheet: 0.55 (0.19), residues: 681 loop : -1.21 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.006 0.001 HIS B 519 PHE 0.014 0.001 PHE B 238 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 36) link_NAG-ASN : angle 1.58780 ( 108) link_BETA1-4 : bond 0.00789 ( 9) link_BETA1-4 : angle 2.18942 ( 27) hydrogen bonds : bond 0.04747 ( 978) hydrogen bonds : angle 4.86230 ( 2718) SS BOND : bond 0.00385 ( 39) SS BOND : angle 1.23136 ( 78) covalent geometry : bond 0.00283 (25392) covalent geometry : angle 0.51825 (34539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 2.821 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8447 (m-30) cc_final: 0.8245 (m-30) REVERT: B 493 GLN cc_start: 0.7984 (mt0) cc_final: 0.7732 (mt0) REVERT: B 780 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7705 (mm-30) REVERT: B 787 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: B 935 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6963 (tm-30) REVERT: B 981 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (mm) REVERT: C 190 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7414 (mtp180) REVERT: C 375 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: C 458 LYS cc_start: 0.8589 (mttt) cc_final: 0.7616 (mppt) REVERT: C 776 LYS cc_start: 0.8133 (tttm) cc_final: 0.7912 (tttm) REVERT: C 804 GLN cc_start: 0.8498 (mt0) cc_final: 0.8216 (mm-40) REVERT: C 902 MET cc_start: 0.9069 (mmm) cc_final: 0.8658 (mmt) REVERT: C 950 ASP cc_start: 0.8357 (m-30) cc_final: 0.8012 (m-30) REVERT: A 574 ASP cc_start: 0.7828 (t70) cc_final: 0.7423 (t70) REVERT: A 603 ASN cc_start: 0.7729 (t0) cc_final: 0.7429 (t0) REVERT: A 619 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7200 (pt0) REVERT: A 675 GLN cc_start: 0.7469 (tp40) cc_final: 0.6275 (tt0) REVERT: A 1092 GLU cc_start: 0.8295 (pt0) cc_final: 0.7893 (pt0) outliers start: 34 outliers final: 21 residues processed: 232 average time/residue: 1.0470 time to fit residues: 294.6998 Evaluate side-chains 223 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 291 optimal weight: 0.5980 chunk 271 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 190 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 339 HIS B 901 GLN C 115 GLN C 955 ASN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111673 restraints weight = 27392.271| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.30 r_work: 0.3020 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25476 Z= 0.186 Angle : 0.588 9.691 34752 Z= 0.298 Chirality : 0.047 0.292 4071 Planarity : 0.004 0.060 4404 Dihedral : 6.166 59.036 4269 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.07 % Allowed : 10.56 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 3063 helix: 1.69 (0.20), residues: 699 sheet: 0.63 (0.19), residues: 657 loop : -1.26 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.021 0.002 PHE B 377 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 36) link_NAG-ASN : angle 1.70499 ( 108) link_BETA1-4 : bond 0.00757 ( 9) link_BETA1-4 : angle 2.16942 ( 27) hydrogen bonds : bond 0.05512 ( 978) hydrogen bonds : angle 4.92647 ( 2718) SS BOND : bond 0.00454 ( 39) SS BOND : angle 1.61990 ( 78) covalent geometry : bond 0.00461 (25392) covalent geometry : angle 0.57350 (34539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 2.695 Fit side-chains REVERT: B 269 TYR cc_start: 0.7422 (m-10) cc_final: 0.6596 (m-10) REVERT: B 780 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7835 (mm-30) REVERT: B 787 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 900 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8778 (mtm) REVERT: B 935 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7152 (tm-30) REVERT: B 981 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8161 (mm) REVERT: C 190 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7395 (mtp180) REVERT: C 375 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: C 458 LYS cc_start: 0.8628 (mttt) cc_final: 0.7644 (mppt) REVERT: C 776 LYS cc_start: 0.8227 (tttm) cc_final: 0.7994 (tttm) REVERT: C 804 GLN cc_start: 0.8496 (mt0) cc_final: 0.8191 (mm-40) REVERT: C 902 MET cc_start: 0.9105 (mmm) cc_final: 0.8903 (mmt) REVERT: C 950 ASP cc_start: 0.8466 (m-30) cc_final: 0.8163 (m-30) REVERT: A 52 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: A 239 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8024 (mm110) REVERT: A 574 ASP cc_start: 0.7835 (t70) cc_final: 0.7530 (t70) REVERT: A 603 ASN cc_start: 0.7874 (t0) cc_final: 0.7607 (t0) REVERT: A 675 GLN cc_start: 0.7463 (tp40) cc_final: 0.6312 (tt0) REVERT: A 1092 GLU cc_start: 0.8449 (pt0) cc_final: 0.8066 (pt0) outliers start: 56 outliers final: 31 residues processed: 239 average time/residue: 1.0157 time to fit residues: 294.5442 Evaluate side-chains 239 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 31 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 235 optimal weight: 0.0470 chunk 199 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 955 ASN A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.161742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112708 restraints weight = 27313.457| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.29 r_work: 0.3117 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25476 Z= 0.108 Angle : 0.523 9.587 34752 Z= 0.265 Chirality : 0.044 0.236 4071 Planarity : 0.003 0.054 4404 Dihedral : 5.844 56.639 4269 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 11.81 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.01 (0.15), residues: 3063 helix: 1.92 (0.20), residues: 696 sheet: 0.56 (0.19), residues: 681 loop : -1.14 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS B 66 PHE 0.015 0.001 PHE A 592 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 36) link_NAG-ASN : angle 1.58293 ( 108) link_BETA1-4 : bond 0.00781 ( 9) link_BETA1-4 : angle 2.11476 ( 27) hydrogen bonds : bond 0.04504 ( 978) hydrogen bonds : angle 4.74506 ( 2718) SS BOND : bond 0.00368 ( 39) SS BOND : angle 1.53635 ( 78) covalent geometry : bond 0.00245 (25392) covalent geometry : angle 0.50890 (34539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.7665 (m) cc_final: 0.7310 (t) REVERT: B 229 LEU cc_start: 0.2781 (OUTLIER) cc_final: 0.1605 (mp) REVERT: B 269 TYR cc_start: 0.7366 (m-10) cc_final: 0.6496 (m-10) REVERT: B 780 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7711 (mm-30) REVERT: B 787 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: B 900 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8635 (mtm) REVERT: B 935 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 981 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8142 (mm) REVERT: C 190 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7511 (mtp180) REVERT: C 375 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: C 458 LYS cc_start: 0.8619 (mttt) cc_final: 0.7643 (mppt) REVERT: C 804 GLN cc_start: 0.8202 (mt0) cc_final: 0.7926 (mm-40) REVERT: C 950 ASP cc_start: 0.8383 (m-30) cc_final: 0.8042 (m-30) REVERT: A 188 ASN cc_start: 0.8042 (m110) cc_final: 0.7655 (m-40) REVERT: A 239 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7985 (mm110) REVERT: A 574 ASP cc_start: 0.7810 (t70) cc_final: 0.7489 (t70) REVERT: A 603 ASN cc_start: 0.7795 (t0) cc_final: 0.7548 (t0) REVERT: A 675 GLN cc_start: 0.7431 (tp40) cc_final: 0.6270 (tt0) REVERT: A 1092 GLU cc_start: 0.8476 (pt0) cc_final: 0.8162 (pt0) outliers start: 42 outliers final: 29 residues processed: 234 average time/residue: 0.9609 time to fit residues: 275.3182 Evaluate side-chains 234 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 135 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 641 ASN B 703 ASN C 675 GLN C 955 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115990 restraints weight = 27275.479| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.05 r_work: 0.3009 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25476 Z= 0.252 Angle : 0.635 9.792 34752 Z= 0.322 Chirality : 0.049 0.241 4071 Planarity : 0.004 0.054 4404 Dihedral : 6.210 59.351 4269 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.44 % Allowed : 12.04 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.21 (0.15), residues: 3063 helix: 1.64 (0.20), residues: 699 sheet: 0.54 (0.19), residues: 666 loop : -1.24 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 64 HIS 0.006 0.002 HIS B1048 PHE 0.029 0.002 PHE B 377 TYR 0.022 0.002 TYR A1067 ARG 0.007 0.001 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 36) link_NAG-ASN : angle 1.78283 ( 108) link_BETA1-4 : bond 0.00759 ( 9) link_BETA1-4 : angle 2.21453 ( 27) hydrogen bonds : bond 0.06116 ( 978) hydrogen bonds : angle 4.99885 ( 2718) SS BOND : bond 0.00498 ( 39) SS BOND : angle 1.86952 ( 78) covalent geometry : bond 0.00639 (25392) covalent geometry : angle 0.62012 (34539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4620 (t80) REVERT: B 269 TYR cc_start: 0.7474 (m-10) cc_final: 0.6722 (m-10) REVERT: B 780 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7867 (mm-30) REVERT: B 787 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: B 935 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 977 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 375 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 458 LYS cc_start: 0.8665 (mttt) cc_final: 0.7697 (mppt) REVERT: C 804 GLN cc_start: 0.8355 (mt0) cc_final: 0.8096 (mm-40) REVERT: C 950 ASP cc_start: 0.8556 (m-30) cc_final: 0.8272 (m-30) REVERT: A 52 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7911 (tp40) REVERT: A 188 ASN cc_start: 0.8066 (m110) cc_final: 0.7655 (m-40) REVERT: A 239 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8113 (mm110) REVERT: A 357 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.8174 (mmm-85) REVERT: A 574 ASP cc_start: 0.7878 (t70) cc_final: 0.7533 (t70) REVERT: A 603 ASN cc_start: 0.8082 (t0) cc_final: 0.7824 (t0) REVERT: A 675 GLN cc_start: 0.7485 (tp40) cc_final: 0.6311 (tt0) REVERT: A 921 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7599 (mmpt) outliers start: 66 outliers final: 40 residues processed: 252 average time/residue: 0.9777 time to fit residues: 301.4702 Evaluate side-chains 247 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 99 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 283 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 703 ASN C 675 GLN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113485 restraints weight = 27320.881| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.29 r_work: 0.3064 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25476 Z= 0.123 Angle : 0.546 11.097 34752 Z= 0.275 Chirality : 0.045 0.238 4071 Planarity : 0.004 0.054 4404 Dihedral : 5.856 56.361 4269 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.15 % Allowed : 12.85 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.03 (0.15), residues: 3063 helix: 1.90 (0.20), residues: 699 sheet: 0.51 (0.19), residues: 687 loop : -1.14 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C 66 PHE 0.016 0.001 PHE B 377 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 36) link_NAG-ASN : angle 1.63389 ( 108) link_BETA1-4 : bond 0.00776 ( 9) link_BETA1-4 : angle 2.10702 ( 27) hydrogen bonds : bond 0.04734 ( 978) hydrogen bonds : angle 4.79554 ( 2718) SS BOND : bond 0.00404 ( 39) SS BOND : angle 1.79331 ( 78) covalent geometry : bond 0.00292 (25392) covalent geometry : angle 0.53004 (34539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2625 (OUTLIER) cc_final: 0.1379 (mp) REVERT: B 238 PHE cc_start: 0.5399 (OUTLIER) cc_final: 0.4604 (t80) REVERT: B 269 TYR cc_start: 0.7405 (m-10) cc_final: 0.6664 (m-10) REVERT: B 780 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7695 (mm-30) REVERT: B 787 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: B 935 GLN cc_start: 0.7442 (tm-30) cc_final: 0.7163 (tm-30) REVERT: C 305 SER cc_start: 0.9070 (t) cc_final: 0.8817 (p) REVERT: C 375 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: C 458 LYS cc_start: 0.8652 (mttt) cc_final: 0.7674 (mppt) REVERT: C 804 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: C 950 ASP cc_start: 0.8452 (m-30) cc_final: 0.8145 (m-30) REVERT: C 977 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (mp) REVERT: A 125 ASN cc_start: 0.5561 (OUTLIER) cc_final: 0.4874 (p0) REVERT: A 188 ASN cc_start: 0.8005 (m110) cc_final: 0.7640 (m-40) REVERT: A 239 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8020 (mm110) REVERT: A 357 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8134 (mmm-85) REVERT: A 574 ASP cc_start: 0.7780 (t70) cc_final: 0.7412 (t70) REVERT: A 603 ASN cc_start: 0.7895 (t0) cc_final: 0.7657 (t0) REVERT: A 675 GLN cc_start: 0.7416 (tp40) cc_final: 0.6238 (tt0) outliers start: 58 outliers final: 37 residues processed: 242 average time/residue: 0.9484 time to fit residues: 281.1728 Evaluate side-chains 238 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 265 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 152 optimal weight: 0.0270 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 955 ASN C1002 GLN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117969 restraints weight = 27286.386| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.05 r_work: 0.3044 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25476 Z= 0.153 Angle : 0.561 11.164 34752 Z= 0.284 Chirality : 0.046 0.239 4071 Planarity : 0.004 0.055 4404 Dihedral : 5.869 57.747 4269 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.26 % Allowed : 13.07 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.03 (0.15), residues: 3063 helix: 1.91 (0.20), residues: 699 sheet: 0.50 (0.19), residues: 687 loop : -1.14 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.020 0.001 PHE B 377 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 36) link_NAG-ASN : angle 1.65230 ( 108) link_BETA1-4 : bond 0.00757 ( 9) link_BETA1-4 : angle 2.10141 ( 27) hydrogen bonds : bond 0.05020 ( 978) hydrogen bonds : angle 4.81414 ( 2718) SS BOND : bond 0.00458 ( 39) SS BOND : angle 1.70666 ( 78) covalent geometry : bond 0.00375 (25392) covalent geometry : angle 0.54588 (34539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2787 (OUTLIER) cc_final: 0.1440 (mp) REVERT: B 238 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.4683 (t80) REVERT: B 269 TYR cc_start: 0.7477 (m-10) cc_final: 0.6764 (m-10) REVERT: B 780 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7800 (mm-30) REVERT: B 787 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: B 935 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7256 (tm-30) REVERT: C 305 SER cc_start: 0.9101 (t) cc_final: 0.8848 (p) REVERT: C 458 LYS cc_start: 0.8596 (mttt) cc_final: 0.7599 (mppt) REVERT: C 902 MET cc_start: 0.8924 (mmt) cc_final: 0.8554 (mmt) REVERT: C 950 ASP cc_start: 0.8536 (m-30) cc_final: 0.8234 (m-30) REVERT: C 977 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 125 ASN cc_start: 0.5583 (OUTLIER) cc_final: 0.4907 (p0) REVERT: A 188 ASN cc_start: 0.8019 (m110) cc_final: 0.7656 (m-40) REVERT: A 239 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8044 (mm110) REVERT: A 357 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8165 (mmm-85) REVERT: A 574 ASP cc_start: 0.7940 (t70) cc_final: 0.7593 (t70) REVERT: A 603 ASN cc_start: 0.7942 (t0) cc_final: 0.7713 (t0) REVERT: A 675 GLN cc_start: 0.7460 (tp40) cc_final: 0.6274 (tt0) REVERT: A 878 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8073 (mt) outliers start: 61 outliers final: 45 residues processed: 239 average time/residue: 0.9861 time to fit residues: 290.1217 Evaluate side-chains 243 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 14 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 955 ASN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110348 restraints weight = 27514.533| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.48 r_work: 0.3034 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25476 Z= 0.167 Angle : 0.572 11.086 34752 Z= 0.289 Chirality : 0.046 0.238 4071 Planarity : 0.004 0.056 4404 Dihedral : 5.904 57.678 4269 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.26 % Allowed : 13.15 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 3063 helix: 1.88 (0.20), residues: 699 sheet: 0.51 (0.19), residues: 687 loop : -1.15 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.020 0.001 PHE B 377 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 36) link_NAG-ASN : angle 1.66799 ( 108) link_BETA1-4 : bond 0.00763 ( 9) link_BETA1-4 : angle 2.09828 ( 27) hydrogen bonds : bond 0.05151 ( 978) hydrogen bonds : angle 4.83371 ( 2718) SS BOND : bond 0.00482 ( 39) SS BOND : angle 1.69151 ( 78) covalent geometry : bond 0.00411 (25392) covalent geometry : angle 0.55689 (34539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2730 (OUTLIER) cc_final: 0.1379 (mp) REVERT: B 238 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4669 (t80) REVERT: B 269 TYR cc_start: 0.7480 (m-10) cc_final: 0.6746 (m-10) REVERT: B 780 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 787 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: B 935 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 305 SER cc_start: 0.9067 (t) cc_final: 0.8804 (p) REVERT: C 458 LYS cc_start: 0.8584 (mttt) cc_final: 0.7583 (mppt) REVERT: C 902 MET cc_start: 0.8905 (mmt) cc_final: 0.8530 (mmt) REVERT: C 950 ASP cc_start: 0.8492 (m-30) cc_final: 0.8191 (m-30) REVERT: C 977 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 125 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.5314 (p0) REVERT: A 188 ASN cc_start: 0.7984 (m110) cc_final: 0.7596 (m-40) REVERT: A 239 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8006 (mm110) REVERT: A 357 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: A 574 ASP cc_start: 0.7818 (t70) cc_final: 0.7530 (t70) REVERT: A 603 ASN cc_start: 0.8016 (t0) cc_final: 0.7781 (t0) REVERT: A 675 GLN cc_start: 0.7417 (tp40) cc_final: 0.6229 (tt0) REVERT: A 878 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8061 (mt) outliers start: 61 outliers final: 48 residues processed: 234 average time/residue: 0.9909 time to fit residues: 282.6599 Evaluate side-chains 246 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 104 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 294 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 238 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 955 ASN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111535 restraints weight = 27457.256| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.29 r_work: 0.3062 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25476 Z= 0.116 Angle : 0.529 10.913 34752 Z= 0.267 Chirality : 0.044 0.235 4071 Planarity : 0.003 0.056 4404 Dihedral : 5.663 56.609 4269 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.81 % Allowed : 13.63 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.08 (0.15), residues: 3063 helix: 1.99 (0.20), residues: 696 sheet: 0.58 (0.19), residues: 693 loop : -1.07 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS B 66 PHE 0.016 0.001 PHE A 592 TYR 0.018 0.001 TYR A1067 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 36) link_NAG-ASN : angle 1.57932 ( 108) link_BETA1-4 : bond 0.00808 ( 9) link_BETA1-4 : angle 2.04532 ( 27) hydrogen bonds : bond 0.04451 ( 978) hydrogen bonds : angle 4.69298 ( 2718) SS BOND : bond 0.00416 ( 39) SS BOND : angle 1.41164 ( 78) covalent geometry : bond 0.00269 (25392) covalent geometry : angle 0.51592 (34539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2704 (OUTLIER) cc_final: 0.1384 (mp) REVERT: B 238 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4796 (t80) REVERT: B 269 TYR cc_start: 0.7428 (m-10) cc_final: 0.6763 (m-10) REVERT: B 780 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7694 (mm-30) REVERT: B 787 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: B 935 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 102 ARG cc_start: 0.6123 (mmp-170) cc_final: 0.5719 (mmp-170) REVERT: C 305 SER cc_start: 0.9061 (t) cc_final: 0.8829 (p) REVERT: C 458 LYS cc_start: 0.8569 (mttt) cc_final: 0.7569 (mppt) REVERT: C 950 ASP cc_start: 0.8401 (m-30) cc_final: 0.8064 (m-30) REVERT: A 125 ASN cc_start: 0.5329 (OUTLIER) cc_final: 0.5015 (p0) REVERT: A 188 ASN cc_start: 0.7948 (m110) cc_final: 0.7586 (m-40) REVERT: A 239 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7968 (mm110) REVERT: A 357 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8126 (mmm-85) REVERT: A 574 ASP cc_start: 0.7748 (t70) cc_final: 0.7432 (t70) REVERT: A 675 GLN cc_start: 0.7379 (tp40) cc_final: 0.6236 (tt0) outliers start: 49 outliers final: 42 residues processed: 234 average time/residue: 0.9895 time to fit residues: 282.0970 Evaluate side-chains 241 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 787 GLN A 314 GLN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118806 restraints weight = 27320.291| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.93 r_work: 0.3053 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25476 Z= 0.184 Angle : 0.589 11.289 34752 Z= 0.298 Chirality : 0.047 0.238 4071 Planarity : 0.004 0.053 4404 Dihedral : 5.882 58.329 4269 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.11 % Allowed : 13.63 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.00 (0.15), residues: 3063 helix: 1.87 (0.20), residues: 699 sheet: 0.65 (0.19), residues: 684 loop : -1.15 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.002 PHE B 377 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 36) link_NAG-ASN : angle 1.71593 ( 108) link_BETA1-4 : bond 0.00758 ( 9) link_BETA1-4 : angle 2.08587 ( 27) hydrogen bonds : bond 0.05405 ( 978) hydrogen bonds : angle 4.85652 ( 2718) SS BOND : bond 0.00480 ( 39) SS BOND : angle 1.77699 ( 78) covalent geometry : bond 0.00456 (25392) covalent geometry : angle 0.57354 (34539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16321.36 seconds wall clock time: 278 minutes 52.88 seconds (16732.88 seconds total)