Starting phenix.real_space_refine on Sun Jan 26 13:27:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0l_42860/01_2025/8v0l_42860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0l_42860/01_2025/8v0l_42860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0l_42860/01_2025/8v0l_42860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0l_42860/01_2025/8v0l_42860.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0l_42860/01_2025/8v0l_42860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0l_42860/01_2025/8v0l_42860.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15834 2.51 5 N 4083 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24849 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8073 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 6 Chain: "C" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8073 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 6 Chain: "A" Number of atoms: 8073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8073 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.82, per 1000 atoms: 0.56 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: 6.57 Conformation dependent library (CDL) restraints added in 3.0 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5820 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 25.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.841A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.210A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.683A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.529A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.915A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.124A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.535A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.544A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.714A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.115A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.733A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.546A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.522A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.611A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.072A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.565A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.503A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.698A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.174A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.789A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.559A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.098A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.530A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.749A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.841A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.564A pdb=" N ARG A 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.186A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.940A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.013A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.547A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.637A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.217A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.559A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.877A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.972A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.464A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'C' and resid 23 through 30 removed outlier: 3.738A pdb=" N THR C 23 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 68 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.083A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.020A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.606A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.520A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.637A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AC8, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.836A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.501A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.075A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.644A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'A' and resid 24 through 30 removed outlier: 3.522A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.042A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.957A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.070A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.696A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.650A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.242A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.536A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.119A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.604A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1120 through 1122 978 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.89 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7907 1.35 - 1.47: 6514 1.47 - 1.60: 10830 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25392 Sorted by residual: bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.337 1.377 -0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.33e+00 ... (remaining 25387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 33862 2.46 - 4.91: 592 4.91 - 7.37: 63 7.37 - 9.82: 18 9.82 - 12.28: 4 Bond angle restraints: 34539 Sorted by residual: angle pdb=" C SER A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.56 108.85 5.71 1.27e+00 6.20e-01 2.02e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.92e+01 angle pdb=" CB LYS A 558 " pdb=" CG LYS A 558 " pdb=" CD LYS A 558 " ideal model delta sigma weight residual 111.30 121.13 -9.83 2.30e+00 1.89e-01 1.83e+01 ... (remaining 34534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14083 17.57 - 35.13: 1368 35.13 - 52.70: 213 52.70 - 70.27: 65 70.27 - 87.83: 27 Dihedral angle restraints: 15756 sinusoidal: 6714 harmonic: 9042 Sorted by residual: dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 145.11 34.89 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA SER B 112 " pdb=" C SER B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3435 0.075 - 0.151: 585 0.151 - 0.226: 38 0.226 - 0.301: 12 0.301 - 0.376: 1 Chirality restraints: 4071 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE C 119 " pdb=" CA ILE C 119 " pdb=" CG1 ILE C 119 " pdb=" CG2 ILE C 119 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CG LEU A 390 " pdb=" CB LEU A 390 " pdb=" CD1 LEU A 390 " pdb=" CD2 LEU A 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4068 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 113 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LYS A 113 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS A 113 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 114 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 209 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.25e+00 pdb=" CG ASN C 343 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.024 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6891 2.82 - 3.34: 19890 3.34 - 3.86: 39877 3.86 - 4.38: 45501 4.38 - 4.90: 81665 Nonbonded interactions: 193824 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.299 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.301 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.305 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.313 3.040 ... (remaining 193819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 54.800 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.370 ------------------------------------------------------------------------------- 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 25392 Z= 0.291 Angle : 0.773 12.279 34539 Z= 0.409 Chirality : 0.054 0.376 4071 Planarity : 0.006 0.075 4404 Dihedral : 14.192 87.834 9819 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3063 helix: -0.16 (0.17), residues: 669 sheet: 0.61 (0.19), residues: 663 loop : -1.44 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS C 519 PHE 0.043 0.002 PHE C 106 TYR 0.020 0.001 TYR A1067 ARG 0.013 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7908 (mt0) cc_final: 0.7669 (mt0) REVERT: B 780 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6987 (pt0) REVERT: B 998 THR cc_start: 0.8410 (m) cc_final: 0.8154 (p) REVERT: B 1050 MET cc_start: 0.8219 (mtp) cc_final: 0.7915 (ttm) REVERT: C 102 ARG cc_start: 0.6070 (mmp-170) cc_final: 0.5730 (mmp-170) REVERT: C 458 LYS cc_start: 0.8342 (mttt) cc_final: 0.7474 (mppt) REVERT: C 675 GLN cc_start: 0.7482 (mt0) cc_final: 0.7140 (pt0) REVERT: C 776 LYS cc_start: 0.8002 (tttm) cc_final: 0.7393 (ttmt) REVERT: C 902 MET cc_start: 0.8656 (mmm) cc_final: 0.8252 (mmt) REVERT: C 950 ASP cc_start: 0.7667 (m-30) cc_final: 0.7293 (m-30) REVERT: A 173 GLN cc_start: 0.5487 (tm-30) cc_final: 0.5146 (tm130) REVERT: A 239 GLN cc_start: 0.7563 (mm110) cc_final: 0.7354 (mm110) REVERT: A 574 ASP cc_start: 0.7507 (t70) cc_final: 0.7224 (t70) REVERT: A 584 ILE cc_start: 0.8482 (mt) cc_final: 0.8268 (mm) REVERT: A 675 GLN cc_start: 0.7112 (tp40) cc_final: 0.6208 (tt0) REVERT: A 1092 GLU cc_start: 0.7427 (pt0) cc_final: 0.7100 (pt0) outliers start: 0 outliers final: 1 residues processed: 265 average time/residue: 1.0227 time to fit residues: 328.9450 Evaluate side-chains 204 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 0.0070 chunk 242 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 474 GLN A 207 HIS A 314 GLN A 339 HIS A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116270 restraints weight = 27134.188| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.25 r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25392 Z= 0.258 Angle : 0.570 10.101 34539 Z= 0.292 Chirality : 0.046 0.298 4071 Planarity : 0.004 0.049 4404 Dihedral : 6.640 59.629 4271 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.19 % Allowed : 6.11 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3063 helix: 1.18 (0.19), residues: 696 sheet: 0.55 (0.19), residues: 678 loop : -1.30 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.006 0.001 HIS B1048 PHE 0.018 0.001 PHE B 377 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7949 (mt0) cc_final: 0.7668 (mt0) REVERT: B 780 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7862 (mm-30) REVERT: B 787 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: B 935 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7080 (tm-30) REVERT: B 981 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8119 (mm) REVERT: B 998 THR cc_start: 0.8868 (m) cc_final: 0.8559 (p) REVERT: B 1050 MET cc_start: 0.8844 (mtp) cc_final: 0.8633 (ttm) REVERT: B 1092 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: C 102 ARG cc_start: 0.6336 (mmp-170) cc_final: 0.5994 (mmp-170) REVERT: C 190 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7381 (mtp180) REVERT: C 375 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: C 458 LYS cc_start: 0.8598 (mttt) cc_final: 0.7648 (mppt) REVERT: C 776 LYS cc_start: 0.8238 (tttm) cc_final: 0.8024 (tttm) REVERT: C 804 GLN cc_start: 0.8711 (mt0) cc_final: 0.8439 (mm-40) REVERT: C 902 MET cc_start: 0.9028 (mmm) cc_final: 0.8624 (mmt) REVERT: C 950 ASP cc_start: 0.8380 (m-30) cc_final: 0.8045 (m-30) REVERT: A 173 GLN cc_start: 0.5779 (tm-30) cc_final: 0.5440 (tm130) REVERT: A 498 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7826 (mtt90) REVERT: A 574 ASP cc_start: 0.8013 (t70) cc_final: 0.7637 (t70) REVERT: A 603 ASN cc_start: 0.7694 (t0) cc_final: 0.7391 (t0) REVERT: A 675 GLN cc_start: 0.7399 (tp40) cc_final: 0.6255 (tt0) REVERT: A 1092 GLU cc_start: 0.8257 (pt0) cc_final: 0.7867 (pt0) outliers start: 32 outliers final: 19 residues processed: 241 average time/residue: 1.0879 time to fit residues: 315.5489 Evaluate side-chains 227 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 PHE 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 335 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 300 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 703 ASN C 239 GLN A 207 HIS A 314 GLN A 339 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.163443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114327 restraints weight = 27087.543| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.30 r_work: 0.3065 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25392 Z= 0.209 Angle : 0.526 9.575 34539 Z= 0.270 Chirality : 0.045 0.250 4071 Planarity : 0.004 0.048 4404 Dihedral : 6.116 58.146 4269 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.52 % Allowed : 9.11 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3063 helix: 1.63 (0.20), residues: 699 sheet: 0.57 (0.19), residues: 681 loop : -1.23 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE B 377 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG A 319 *********************** 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 259 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 2.699 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7988 (mt0) cc_final: 0.7756 (mt0) REVERT: B 780 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7740 (mm-30) REVERT: B 787 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: B 900 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8690 (mtm) REVERT: B 935 GLN cc_start: 0.7336 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 981 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8024 (mm) REVERT: C 190 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7434 (mtp180) REVERT: C 375 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: C 458 LYS cc_start: 0.8593 (mttt) cc_final: 0.7624 (mppt) REVERT: C 776 LYS cc_start: 0.8171 (tttm) cc_final: 0.7954 (tttm) REVERT: C 804 GLN cc_start: 0.8514 (mt0) cc_final: 0.8229 (mm-40) REVERT: C 902 MET cc_start: 0.9080 (mmm) cc_final: 0.8674 (mmt) REVERT: C 950 ASP cc_start: 0.8384 (m-30) cc_final: 0.8037 (m-30) REVERT: A 239 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7998 (mm110) REVERT: A 574 ASP cc_start: 0.7831 (t70) cc_final: 0.7439 (t70) REVERT: A 603 ASN cc_start: 0.7784 (t0) cc_final: 0.7484 (t0) REVERT: A 619 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: A 675 GLN cc_start: 0.7478 (tp40) cc_final: 0.6281 (tt0) REVERT: A 1092 GLU cc_start: 0.8288 (pt0) cc_final: 0.7889 (pt0) outliers start: 41 outliers final: 26 residues processed: 236 average time/residue: 1.0873 time to fit residues: 312.4011 Evaluate side-chains 230 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 394 ASN 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 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 291 optimal weight: 0.0270 chunk 271 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: