Starting phenix.real_space_refine on Sun Oct 12 14:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0l_42860/10_2025/8v0l_42860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0l_42860/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v0l_42860/10_2025/8v0l_42860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0l_42860/10_2025/8v0l_42860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v0l_42860/10_2025/8v0l_42860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0l_42860/10_2025/8v0l_42860.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 6.63, per 1000 atoms: 0.27 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: 2.16 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.19 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: 6.16 Time building geometry restraints manager: 2.93 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: 0.04 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: 2.990 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.610 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.013 0.000 ARG A 319 TYR 0.020 0.001 TYR A1067 PHE 0.043 0.002 PHE C 106 TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00440 (25392) covalent geometry : angle 0.77328 (34539) SS BOND : bond 0.00527 ( 39) SS BOND : angle 1.55809 ( 78) hydrogen bonds : bond 0.12943 ( 978) hydrogen bonds : angle 6.52636 ( 2718) link_BETA1-4 : bond 0.01348 ( 9) link_BETA1-4 : angle 3.75696 ( 27) link_NAG-ASN : bond 0.00365 ( 36) link_NAG-ASN : angle 2.25459 ( 108) *********************** 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 : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7908 (mt0) cc_final: 0.7670 (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: 0.8155 (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: 0.7473 (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: 0.8260 (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: 0.7225 (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: 0.5224 time to fit residues: 166.4362 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 : 0.971 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 901 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110539 restraints weight = 27502.965| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.30 r_work: 0.2991 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 25476 Z= 0.265 Angle : 0.676 10.155 34752 Z= 0.343 Chirality : 0.050 0.281 4071 Planarity : 0.005 0.054 4404 Dihedral : 6.935 59.660 4271 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.37 % Allowed : 7.07 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3063 helix: 0.88 (0.19), residues: 696 sheet: 0.64 (0.19), residues: 663 loop : -1.42 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.024 0.002 TYR A1067 PHE 0.025 0.002 PHE C 377 TRP 0.014 0.002 TRP C 436 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00664 (25392) covalent geometry : angle 0.66035 (34539) SS BOND : bond 0.00599 ( 39) SS BOND : angle 1.78996 ( 78) hydrogen bonds : bond 0.06662 ( 978) hydrogen bonds : angle 5.32554 ( 2718) link_BETA1-4 : bond 0.00850 ( 9) link_BETA1-4 : angle 2.33968 ( 27) link_NAG-ASN : bond 0.00403 ( 36) link_NAG-ASN : angle 1.99597 ( 108) *********************** 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 264 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7912 (mt0) cc_final: 0.7637 (mt0) REVERT: B 787 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: B 935 GLN cc_start: 0.7377 (tm-30) cc_final: 0.7115 (tm-30) REVERT: B 981 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 1050 MET cc_start: 0.8931 (mtp) cc_final: 0.8711 (mtp) REVERT: C 102 ARG cc_start: 0.6412 (mmp-170) cc_final: 0.6119 (mmp-170) REVERT: C 190 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7397 (mtp180) REVERT: C 375 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: C 458 LYS cc_start: 0.8653 (mttt) cc_final: 0.7701 (mppt) REVERT: C 804 GLN cc_start: 0.8801 (mt0) cc_final: 0.8499 (mm-40) REVERT: C 902 MET cc_start: 0.9078 (mmm) cc_final: 0.8680 (mmt) REVERT: C 950 ASP cc_start: 0.8461 (m-30) cc_final: 0.8157 (m-30) REVERT: A 52 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: A 173 GLN cc_start: 0.5892 (tm-30) cc_final: 0.5563 (tm130) REVERT: A 498 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7619 (mtt90) REVERT: A 574 ASP cc_start: 0.8016 (t70) cc_final: 0.7649 (t70) REVERT: A 603 ASN cc_start: 0.8003 (t0) cc_final: 0.7659 (t0) REVERT: A 675 GLN cc_start: 0.7368 (tp40) cc_final: 0.6186 (tt0) REVERT: A 804 GLN cc_start: 0.8656 (mt0) cc_final: 0.8331 (mt0) REVERT: A 921 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7520 (mmpt) REVERT: A 935 GLN cc_start: 0.6888 (tt0) cc_final: 0.6584 (tt0) REVERT: A 1092 GLU cc_start: 0.8243 (pt0) cc_final: 0.7841 (pt0) outliers start: 37 outliers final: 22 residues processed: 242 average time/residue: 0.5374 time to fit residues: 155.4650 Evaluate side-chains 224 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 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 52 GLN 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 271 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 273 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 115 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120616 restraints weight = 27316.078| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.62 r_work: 0.3088 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25476 Z= 0.114 Angle : 0.540 9.599 34752 Z= 0.274 Chirality : 0.044 0.240 4071 Planarity : 0.004 0.060 4404 Dihedral : 6.349 59.194 4269 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.15 % Allowed : 9.78 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 3063 helix: 1.56 (0.20), residues: 699 sheet: 0.48 (0.19), residues: 681 loop : -1.29 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE B 377 TRP 0.009 0.001 TRP C 436 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00257 (25392) covalent geometry : angle 0.52656 (34539) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.27879 ( 78) hydrogen bonds : bond 0.04882 ( 978) hydrogen bonds : angle 4.94316 ( 2718) link_BETA1-4 : bond 0.00832 ( 9) link_BETA1-4 : angle 2.20088 ( 27) link_NAG-ASN : bond 0.00237 ( 36) link_NAG-ASN : angle 1.66241 ( 108) *********************** 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 254 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.992 Fit side-chains REVERT: B 269 TYR cc_start: 0.7431 (m-10) cc_final: 0.6564 (m-10) REVERT: B 493 GLN cc_start: 0.8041 (mt0) cc_final: 0.7809 (mt0) REVERT: B 780 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7863 (pt0) REVERT: B 787 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: B 935 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 981 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8171 (mm) REVERT: C 190 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7531 (mtp180) REVERT: C 375 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: C 458 LYS cc_start: 0.8629 (mttt) cc_final: 0.7703 (mppt) REVERT: C 804 GLN cc_start: 0.8735 (mt0) cc_final: 0.8382 (mm-40) REVERT: C 902 MET cc_start: 0.9083 (mmm) cc_final: 0.8707 (mmt) REVERT: C 950 ASP cc_start: 0.8466 (m-30) cc_final: 0.8150 (m-30) REVERT: A 498 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7845 (mtt90) REVERT: A 574 ASP cc_start: 0.7922 (t70) cc_final: 0.7537 (t70) REVERT: A 603 ASN cc_start: 0.7879 (t0) cc_final: 0.7593 (t0) REVERT: A 619 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: A 675 GLN cc_start: 0.7514 (tp40) cc_final: 0.6370 (tt0) REVERT: A 1092 GLU cc_start: 0.8340 (pt0) cc_final: 0.7965 (pt0) outliers start: 31 outliers final: 16 residues processed: 237 average time/residue: 0.4905 time to fit residues: 140.1185 Evaluate side-chains 217 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 375 PHE 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 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 619 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 209 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 804 GLN C 955 ASN A 207 HIS 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 = 0.3794 r_free = 0.3794 target = 0.159256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114751 restraints weight = 27430.537| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.02 r_work: 0.2997 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 25476 Z= 0.299 Angle : 0.694 10.692 34752 Z= 0.352 Chirality : 0.051 0.332 4071 Planarity : 0.005 0.059 4404 Dihedral : 6.726 59.988 4269 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.56 % Allowed : 11.11 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.14), residues: 3063 helix: 1.26 (0.20), residues: 699 sheet: 0.38 (0.19), residues: 681 loop : -1.39 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1039 TYR 0.024 0.002 TYR A1067 PHE 0.031 0.002 PHE B 377 TRP 0.014 0.002 TRP B 64 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00755 (25392) covalent geometry : angle 0.67847 (34539) SS BOND : bond 0.00577 ( 39) SS BOND : angle 2.02083 ( 78) hydrogen bonds : bond 0.06788 ( 978) hydrogen bonds : angle 5.22203 ( 2718) link_BETA1-4 : bond 0.00584 ( 9) link_BETA1-4 : angle 2.25131 ( 27) link_NAG-ASN : bond 0.00222 ( 36) link_NAG-ASN : angle 1.92856 ( 108) *********************** 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 281 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.4766 (t80) REVERT: B 269 TYR cc_start: 0.7582 (m-10) cc_final: 0.6847 (m-10) REVERT: B 787 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: B 935 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 977 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8097 (mp) REVERT: C 375 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: C 458 LYS cc_start: 0.8659 (mttt) cc_final: 0.7713 (mppt) REVERT: C 902 MET cc_start: 0.9116 (mmm) cc_final: 0.8901 (mmt) REVERT: C 950 ASP cc_start: 0.8566 (m-30) cc_final: 0.8284 (m-30) REVERT: A 52 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7922 (tp40) REVERT: A 498 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7790 (mtt90) REVERT: A 574 ASP cc_start: 0.7949 (t70) cc_final: 0.7619 (t70) REVERT: A 603 ASN cc_start: 0.8274 (t0) cc_final: 0.7976 (t0) REVERT: A 675 GLN cc_start: 0.7475 (tp40) cc_final: 0.6297 (tt0) REVERT: A 921 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7632 (mmpt) outliers start: 69 outliers final: 40 residues processed: 249 average time/residue: 0.4778 time to fit residues: 143.5299 Evaluate side-chains 249 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 503 VAL 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 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 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 615 VAL 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 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 52 GLN 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 415 THR Chi-restraints excluded: chain A residue 492 LEU 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 931 ILE 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 148 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 675 GLN C 804 GLN C 955 ASN C1002 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113279 restraints weight = 27221.532| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.29 r_work: 0.3059 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25476 Z= 0.120 Angle : 0.547 10.850 34752 Z= 0.276 Chirality : 0.045 0.230 4071 Planarity : 0.004 0.052 4404 Dihedral : 6.127 58.204 4269 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.59 % Allowed : 12.85 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 3063 helix: 1.73 (0.20), residues: 699 sheet: 0.44 (0.19), residues: 693 loop : -1.24 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.016 0.001 TYR A1067 PHE 0.016 0.001 PHE B 377 TRP 0.009 0.001 TRP C 436 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00276 (25392) covalent geometry : angle 0.53196 (34539) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.56788 ( 78) hydrogen bonds : bond 0.04761 ( 978) hydrogen bonds : angle 4.86264 ( 2718) link_BETA1-4 : bond 0.00895 ( 9) link_BETA1-4 : angle 2.15684 ( 27) link_NAG-ASN : bond 0.00260 ( 36) link_NAG-ASN : angle 1.66653 ( 108) *********************** 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 258 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2733 (OUTLIER) cc_final: 0.1655 (mp) REVERT: B 238 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.4566 (t80) REVERT: B 269 TYR cc_start: 0.7419 (m-10) cc_final: 0.6774 (m-10) REVERT: B 493 GLN cc_start: 0.7950 (mt0) cc_final: 0.7629 (mt0) REVERT: B 780 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7832 (pt0) REVERT: B 787 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: B 935 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7088 (tm-30) REVERT: C 375 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: C 458 LYS cc_start: 0.8647 (mttt) cc_final: 0.7672 (mppt) REVERT: C 804 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: C 950 ASP cc_start: 0.8448 (m-30) cc_final: 0.8148 (m-30) REVERT: C 977 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 188 ASN cc_start: 0.8033 (m110) cc_final: 0.7646 (m-40) REVERT: A 239 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8002 (mm110) REVERT: A 498 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7713 (mtt90) REVERT: A 574 ASP cc_start: 0.7785 (t70) cc_final: 0.7424 (t70) REVERT: A 603 ASN cc_start: 0.7961 (t0) cc_final: 0.7713 (t0) REVERT: A 675 GLN cc_start: 0.7427 (tp40) cc_final: 0.6259 (tt0) REVERT: A 835 LYS cc_start: 0.5743 (mmpt) cc_final: 0.4549 (tttt) outliers start: 43 outliers final: 22 residues processed: 239 average time/residue: 0.4772 time to fit residues: 139.2521 Evaluate side-chains 227 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL 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 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 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 207 HIS 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 571 ASP Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 3 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 519 HIS C 955 ASN C1002 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 = 0.3775 r_free = 0.3775 target = 0.157740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108379 restraints weight = 27462.992| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.29 r_work: 0.2994 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 25476 Z= 0.232 Angle : 0.645 17.149 34752 Z= 0.325 Chirality : 0.049 0.315 4071 Planarity : 0.004 0.053 4404 Dihedral : 6.356 58.998 4269 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.52 % Allowed : 13.04 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 3063 helix: 1.58 (0.20), residues: 699 sheet: 0.48 (0.19), residues: 666 loop : -1.32 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.021 0.002 TYR A1067 PHE 0.027 0.002 PHE B 377 TRP 0.010 0.002 TRP C 436 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00581 (25392) covalent geometry : angle 0.62519 (34539) SS BOND : bond 0.00528 ( 39) SS BOND : angle 2.46456 ( 78) hydrogen bonds : bond 0.05938 ( 978) hydrogen bonds : angle 5.01504 ( 2718) link_BETA1-4 : bond 0.00757 ( 9) link_BETA1-4 : angle 2.20850 ( 27) link_NAG-ASN : bond 0.00192 ( 36) link_NAG-ASN : angle 1.78422 ( 108) *********************** 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: 68 poor density : 212 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 238 PHE cc_start: 0.5526 (OUTLIER) cc_final: 0.4766 (t80) REVERT: B 269 TYR cc_start: 0.7579 (m-10) cc_final: 0.6886 (m-10) REVERT: B 493 GLN cc_start: 0.7997 (mt0) cc_final: 0.7687 (mt0) REVERT: B 787 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: B 935 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7247 (tm-30) REVERT: C 375 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: C 458 LYS cc_start: 0.8663 (mttt) cc_final: 0.7691 (mppt) REVERT: C 571 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7701 (t0) REVERT: C 950 ASP cc_start: 0.8494 (m-30) cc_final: 0.8204 (m-30) REVERT: C 977 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 239 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8048 (mm110) REVERT: A 357 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: A 498 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7763 (mtt90) REVERT: A 574 ASP cc_start: 0.7858 (t70) cc_final: 0.7543 (t70) REVERT: A 603 ASN cc_start: 0.8123 (t0) cc_final: 0.7880 (t0) REVERT: A 675 GLN cc_start: 0.7444 (tp40) cc_final: 0.6269 (tt0) REVERT: A 878 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 921 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7497 (mmpt) outliers start: 68 outliers final: 43 residues processed: 257 average time/residue: 0.4707 time to fit residues: 147.5803 Evaluate side-chains 251 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL 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 390 LEU 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 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 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 375 PHE Chi-restraints excluded: chain C residue 391 CYS 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 724 THR 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 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 GLN 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 581 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 878 LEU 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 208 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 519 HIS 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 = 0.3834 r_free = 0.3834 target = 0.163199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119273 restraints weight = 27222.583| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.92 r_work: 0.3074 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25476 Z= 0.135 Angle : 0.576 12.543 34752 Z= 0.290 Chirality : 0.046 0.237 4071 Planarity : 0.004 0.050 4404 Dihedral : 6.069 56.811 4269 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.26 % Allowed : 13.89 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 3063 helix: 1.80 (0.20), residues: 699 sheet: 0.44 (0.19), residues: 687 loop : -1.23 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.017 0.001 TYR A1067 PHE 0.017 0.001 PHE B 377 TRP 0.009 0.001 TRP C 436 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00322 (25392) covalent geometry : angle 0.55623 (34539) SS BOND : bond 0.00388 ( 39) SS BOND : angle 2.26953 ( 78) hydrogen bonds : bond 0.04921 ( 978) hydrogen bonds : angle 4.85268 ( 2718) link_BETA1-4 : bond 0.00779 ( 9) link_BETA1-4 : angle 2.13179 ( 27) link_NAG-ASN : bond 0.00206 ( 36) link_NAG-ASN : angle 1.70603 ( 108) *********************** 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 270 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2900 (OUTLIER) cc_final: 0.1526 (mp) REVERT: B 238 PHE cc_start: 0.5485 (OUTLIER) cc_final: 0.4753 (t80) REVERT: B 269 TYR cc_start: 0.7546 (m-10) cc_final: 0.6873 (m-10) REVERT: B 493 GLN cc_start: 0.8033 (mt0) cc_final: 0.7740 (mt0) REVERT: B 780 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7800 (pt0) REVERT: B 787 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 935 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 458 LYS cc_start: 0.8662 (mttt) cc_final: 0.7691 (mppt) REVERT: C 804 GLN cc_start: 0.8642 (mt0) cc_final: 0.8301 (mm-40) REVERT: C 950 ASP cc_start: 0.8514 (m-30) cc_final: 0.8221 (m-30) REVERT: A 125 ASN cc_start: 0.5573 (OUTLIER) cc_final: 0.4886 (p0) REVERT: A 188 ASN cc_start: 0.8018 (m110) cc_final: 0.7545 (m-40) REVERT: A 239 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8092 (mm110) REVERT: A 498 ARG cc_start: 0.8026 (mtt90) cc_final: 0.7722 (mtt90) REVERT: A 574 ASP cc_start: 0.7877 (t70) cc_final: 0.7622 (t70) REVERT: A 603 ASN cc_start: 0.8036 (t0) cc_final: 0.7827 (t0) REVERT: A 675 GLN cc_start: 0.7451 (tp40) cc_final: 0.6265 (tt0) REVERT: A 835 LYS cc_start: 0.5676 (mmpt) cc_final: 0.4424 (tttt) REVERT: A 878 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8076 (mt) outliers start: 61 outliers final: 37 residues processed: 248 average time/residue: 0.4781 time to fit residues: 144.1529 Evaluate side-chains 243 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL 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 615 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 207 HIS Chi-restraints excluded: chain C residue 391 CYS 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 549 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 763 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 239 GLN 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 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 859 THR Chi-restraints excluded: chain A residue 878 LEU 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 171 optimal weight: 0.6980 chunk 297 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 247 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B1101 HIS C 207 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110080 restraints weight = 27330.155| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.28 r_work: 0.3028 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1841 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= 0.132 Angle : 0.563 11.699 34752 Z= 0.283 Chirality : 0.045 0.236 4071 Planarity : 0.004 0.050 4404 Dihedral : 5.924 57.428 4269 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.30 % Allowed : 13.93 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 3063 helix: 1.89 (0.20), residues: 699 sheet: 0.54 (0.19), residues: 678 loop : -1.20 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE B 377 TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00316 (25392) covalent geometry : angle 0.54579 (34539) SS BOND : bond 0.00430 ( 39) SS BOND : angle 2.05946 ( 78) hydrogen bonds : bond 0.04782 ( 978) hydrogen bonds : angle 4.78599 ( 2718) link_BETA1-4 : bond 0.00766 ( 9) link_BETA1-4 : angle 2.10211 ( 27) link_NAG-ASN : bond 0.00194 ( 36) link_NAG-ASN : angle 1.65392 ( 108) *********************** 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 268 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.1467 (mp) REVERT: B 238 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.4830 (t80) REVERT: B 269 TYR cc_start: 0.7491 (m-10) cc_final: 0.6810 (m-10) REVERT: B 420 ASP cc_start: 0.8340 (m-30) cc_final: 0.8139 (m-30) REVERT: B 493 GLN cc_start: 0.8003 (mt0) cc_final: 0.7714 (mt0) REVERT: B 780 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7802 (pt0) REVERT: B 787 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: B 935 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7313 (tm-30) REVERT: C 305 SER cc_start: 0.9053 (t) cc_final: 0.8805 (p) REVERT: C 458 LYS cc_start: 0.8563 (mttt) cc_final: 0.7555 (mppt) REVERT: C 804 GLN cc_start: 0.8682 (mt0) cc_final: 0.8247 (mm-40) REVERT: C 950 ASP cc_start: 0.8447 (m-30) cc_final: 0.8134 (m-30) REVERT: A 188 ASN cc_start: 0.7847 (m110) cc_final: 0.7482 (m-40) REVERT: A 239 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8051 (mm110) REVERT: A 357 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8266 (mmm-85) REVERT: A 574 ASP cc_start: 0.7721 (t70) cc_final: 0.7468 (t70) REVERT: A 675 GLN cc_start: 0.7415 (tp40) cc_final: 0.6239 (tt0) outliers start: 62 outliers final: 47 residues processed: 247 average time/residue: 0.4980 time to fit residues: 148.5339 Evaluate side-chains 250 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL 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 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 878 LEU 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 323 THR Chi-restraints excluded: chain C residue 391 CYS 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 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 724 THR 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 197 ILE Chi-restraints excluded: chain A residue 239 GLN 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 581 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 859 THR 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 277 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 207 HIS C 955 ASN 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 = 0.3800 r_free = 0.3800 target = 0.160181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109157 restraints weight = 27404.781| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.45 r_work: 0.3008 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25476 Z= 0.180 Angle : 0.603 12.207 34752 Z= 0.303 Chirality : 0.047 0.238 4071 Planarity : 0.004 0.050 4404 Dihedral : 6.046 58.143 4269 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.22 % Allowed : 14.15 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3063 helix: 1.78 (0.20), residues: 699 sheet: 0.53 (0.19), residues: 672 loop : -1.25 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.019 0.001 TYR A1067 PHE 0.021 0.002 PHE B 377 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00446 (25392) covalent geometry : angle 0.58433 (34539) SS BOND : bond 0.00471 ( 39) SS BOND : angle 2.21087 ( 78) hydrogen bonds : bond 0.05417 ( 978) hydrogen bonds : angle 4.89489 ( 2718) link_BETA1-4 : bond 0.00776 ( 9) link_BETA1-4 : angle 2.14413 ( 27) link_NAG-ASN : bond 0.00164 ( 36) link_NAG-ASN : angle 1.73758 ( 108) *********************** 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 275 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2804 (OUTLIER) cc_final: 0.1510 (mp) REVERT: B 238 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.4765 (t80) REVERT: B 269 TYR cc_start: 0.7568 (m-10) cc_final: 0.6852 (m-10) REVERT: B 780 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7746 (pt0) REVERT: B 787 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 935 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 102 ARG cc_start: 0.6129 (mmp-170) cc_final: 0.5689 (mmp-170) REVERT: C 458 LYS cc_start: 0.8567 (mttt) cc_final: 0.7564 (mppt) REVERT: C 804 GLN cc_start: 0.8700 (mt0) cc_final: 0.8354 (mm-40) REVERT: C 902 MET cc_start: 0.8936 (mmt) cc_final: 0.8531 (mmt) REVERT: C 950 ASP cc_start: 0.8450 (m-30) cc_final: 0.8148 (m-30) REVERT: A 125 ASN cc_start: 0.5450 (OUTLIER) cc_final: 0.4741 (p0) REVERT: A 188 ASN cc_start: 0.7845 (m110) cc_final: 0.7459 (m-40) REVERT: A 239 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8024 (mm110) REVERT: A 357 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8226 (mmm-85) REVERT: A 574 ASP cc_start: 0.7735 (t70) cc_final: 0.7510 (t70) REVERT: A 675 GLN cc_start: 0.7401 (tp40) cc_final: 0.6208 (tt0) outliers start: 60 outliers final: 48 residues processed: 254 average time/residue: 0.4928 time to fit residues: 151.6946 Evaluate side-chains 259 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL 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 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 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 503 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 724 THR 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 25 THR 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 239 GLN 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 573 THR Chi-restraints excluded: chain A residue 581 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 859 THR 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 72 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 chunk 113 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS C 207 HIS C 804 GLN C 955 ASN C1002 GLN A 49 HIS A 339 HIS A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117600 restraints weight = 27421.712| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.99 r_work: 0.3074 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25476 Z= 0.126 Angle : 0.557 11.750 34752 Z= 0.280 Chirality : 0.045 0.236 4071 Planarity : 0.004 0.051 4404 Dihedral : 5.841 56.845 4269 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.04 % Allowed : 14.59 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.15), residues: 3063 helix: 1.93 (0.20), residues: 699 sheet: 0.59 (0.19), residues: 684 loop : -1.15 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.018 0.001 TYR A1067 PHE 0.015 0.001 PHE A 592 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00297 (25392) covalent geometry : angle 0.54014 (34539) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.94212 ( 78) hydrogen bonds : bond 0.04707 ( 978) hydrogen bonds : angle 4.76335 ( 2718) link_BETA1-4 : bond 0.00789 ( 9) link_BETA1-4 : angle 2.08610 ( 27) link_NAG-ASN : bond 0.00252 ( 36) link_NAG-ASN : angle 1.66647 ( 108) ********************** 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 264 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.2713 (OUTLIER) cc_final: 0.1516 (mp) REVERT: B 238 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.4859 (t80) REVERT: B 269 TYR cc_start: 0.7576 (m-10) cc_final: 0.6892 (m-10) REVERT: B 375 PHE cc_start: 0.8441 (t80) cc_final: 0.8223 (t80) REVERT: B 493 GLN cc_start: 0.8018 (mt0) cc_final: 0.7743 (mt0) REVERT: B 780 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7813 (pt0) REVERT: B 787 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 935 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 102 ARG cc_start: 0.6156 (mmp-170) cc_final: 0.5715 (mmp-170) REVERT: C 305 SER cc_start: 0.9079 (t) cc_final: 0.8844 (p) REVERT: C 458 LYS cc_start: 0.8579 (mttt) cc_final: 0.7594 (mppt) REVERT: C 804 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8289 (mm-40) REVERT: C 950 ASP cc_start: 0.8492 (m-30) cc_final: 0.8192 (m-30) REVERT: A 188 ASN cc_start: 0.7885 (m110) cc_final: 0.7523 (m-40) REVERT: A 239 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8073 (mm110) REVERT: A 357 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8296 (mmm-85) REVERT: A 574 ASP cc_start: 0.7766 (t70) cc_final: 0.7519 (t70) REVERT: A 675 GLN cc_start: 0.7421 (tp40) cc_final: 0.6265 (tt0) outliers start: 55 outliers final: 44 residues processed: 246 average time/residue: 0.4829 time to fit residues: 144.2665 Evaluate side-chains 249 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL 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 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 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 503 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 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN 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 25 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 GLN 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 581 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 859 THR 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 176 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.159997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108952 restraints weight = 27423.140| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.45 r_work: 0.3039 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2012 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= 0.181 Angle : 0.601 11.665 34752 Z= 0.302 Chirality : 0.047 0.237 4071 Planarity : 0.004 0.049 4404 Dihedral : 5.965 58.271 4269 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.07 % Allowed : 14.67 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 3063 helix: 1.83 (0.20), residues: 699 sheet: 0.59 (0.19), residues: 678 loop : -1.20 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.020 0.001 TYR A1067 PHE 0.021 0.002 PHE B 377 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00450 (25392) covalent geometry : angle 0.58299 (34539) SS BOND : bond 0.00449 ( 39) SS BOND : angle 2.17530 ( 78) hydrogen bonds : bond 0.05328 ( 978) hydrogen bonds : angle 4.85797 ( 2718) link_BETA1-4 : bond 0.00770 ( 9) link_BETA1-4 : angle 2.12307 ( 27) link_NAG-ASN : bond 0.00214 ( 36) link_NAG-ASN : angle 1.71383 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8149.30 seconds wall clock time: 139 minutes 43.89 seconds (8383.89 seconds total)