Starting phenix.real_space_refine on Fri Feb 6 04:29:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9han_51984/02_2026/9han_51984_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9han_51984/02_2026/9han_51984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9han_51984/02_2026/9han_51984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9han_51984/02_2026/9han_51984.map" model { file = "/net/cci-nas-00/data/ceres_data/9han_51984/02_2026/9han_51984_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9han_51984/02_2026/9han_51984_trim.cif" } resolution = 4.33 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= 0.002 sd= 0.082 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 6978 2.51 5 N 1948 2.21 5 O 2163 1.98 5 H 10831 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21974 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 3788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3788 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 232} Chain: "A" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3641 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3445 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 3788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3788 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 232} Chain: "D" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3641 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 224} Chain breaks: 1 Chain: "E" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3444 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.38, per 1000 atoms: 0.20 Number of scatterers: 21974 At special positions: 0 Unit cell: (135.956, 147.562, 89.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 2163 8.00 N 1948 7.00 C 6978 6.00 H 10831 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS C2206 " - pdb=" SG CYS C2420 " distance=2.03 Simple disulfide: pdb=" SG CYS C2216 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C2219 " - pdb=" SG CYS B 610 " distance=2.03 Simple disulfide: pdb=" SG CYS C2225 " - pdb=" SG CYS C2416 " distance=2.03 Simple disulfide: pdb=" SG CYS C2413 " - pdb=" SG CYS C2426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 819 " distance=2.04 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B1027 " distance=2.03 Simple disulfide: pdb=" SG CYS F2206 " - pdb=" SG CYS F2420 " distance=2.03 Simple disulfide: pdb=" SG CYS F2216 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F2219 " - pdb=" SG CYS E 610 " distance=2.03 Simple disulfide: pdb=" SG CYS F2225 " - pdb=" SG CYS F2416 " distance=2.03 Simple disulfide: pdb=" SG CYS F2413 " - pdb=" SG CYS F2426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 594 " - pdb=" SG CYS D 819 " distance=2.03 Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E1027 " 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 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 L 2 " - " BMA L 3 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " NAG-ASN " NAG C3101 " - " ASN C2387 " " NAG F3101 " - " ASN F2387 " " NAG G 1 " - " ASN A 895 " " NAG H 1 " - " ASN B 905 " " NAG I 1 " - " ASN B 962 " " NAG J 1 " - " ASN D 895 " " NAG K 1 " - " ASN E 962 " " NAG L 1 " - " ASN E 905 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 712.6 milliseconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 45.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'C' and resid 2205 through 2216 removed outlier: 3.860A pdb=" N VAL C2209 " --> pdb=" O GLN C2205 " (cutoff:3.500A) Processing helix chain 'C' and resid 2243 through 2261 Processing helix chain 'C' and resid 2294 through 2305 Processing helix chain 'C' and resid 2315 through 2326 removed outlier: 3.830A pdb=" N ALA C2319 " --> pdb=" O SER C2315 " (cutoff:3.500A) Processing helix chain 'C' and resid 2327 through 2330 removed outlier: 4.251A pdb=" N ARG C2330 " --> pdb=" O THR C2327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2327 through 2330' Processing helix chain 'C' and resid 2352 through 2365 removed outlier: 3.855A pdb=" N ARG C2356 " --> pdb=" O THR C2352 " (cutoff:3.500A) Processing helix chain 'C' and resid 2377 through 2385 Processing helix chain 'C' and resid 2403 through 2414 Processing helix chain 'A' and resid 592 through 604 removed outlier: 4.028A pdb=" N MET A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 861 Processing helix chain 'A' and resid 896 through 906 Processing helix chain 'A' and resid 915 through 930 Processing helix chain 'A' and resid 950 through 965 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 994 through 1001 Processing helix chain 'A' and resid 1007 through 1013 removed outlier: 3.990A pdb=" N LEU A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.519A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 871 Processing helix chain 'B' and resid 892 through 896 removed outlier: 4.332A pdb=" N GLN B 896 " --> pdb=" O PRO B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 924 through 943 Processing helix chain 'B' and resid 964 through 975 removed outlier: 3.543A pdb=" N ALA B 968 " --> pdb=" O SER B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 998 removed outlier: 3.559A pdb=" N LEU B 993 " --> pdb=" O ASP B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1014 Processing helix chain 'B' and resid 1015 through 1027 Processing helix chain 'F' and resid 2204 through 2214 removed outlier: 3.749A pdb=" N LEU F2208 " --> pdb=" O ASP F2204 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL F2209 " --> pdb=" O GLN F2205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F2210 " --> pdb=" O CYS F2206 " (cutoff:3.500A) Processing helix chain 'F' and resid 2243 through 2261 Processing helix chain 'F' and resid 2294 through 2305 Processing helix chain 'F' and resid 2315 through 2326 removed outlier: 3.995A pdb=" N ALA F2319 " --> pdb=" O SER F2315 " (cutoff:3.500A) Processing helix chain 'F' and resid 2327 through 2330 removed outlier: 4.205A pdb=" N ARG F2330 " --> pdb=" O THR F2327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2327 through 2330' Processing helix chain 'F' and resid 2352 through 2365 removed outlier: 3.718A pdb=" N ARG F2356 " --> pdb=" O THR F2352 " (cutoff:3.500A) Processing helix chain 'F' and resid 2377 through 2385 Processing helix chain 'F' and resid 2403 through 2414 removed outlier: 4.115A pdb=" N ASN F2409 " --> pdb=" O ASP F2405 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 604 removed outlier: 3.567A pdb=" N ILE D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET D 603 " --> pdb=" O ILE D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 861 Processing helix chain 'D' and resid 895 through 906 removed outlier: 4.428A pdb=" N LEU D 899 " --> pdb=" O ASN D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 930 Processing helix chain 'D' and resid 950 through 965 Processing helix chain 'D' and resid 978 through 988 Processing helix chain 'D' and resid 994 through 1001 Processing helix chain 'D' and resid 1007 through 1013 removed outlier: 4.099A pdb=" N LEU D1012 " --> pdb=" O TYR D1008 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D1013 " --> pdb=" O GLN D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1026 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 853 through 871 Processing helix chain 'E' and resid 892 through 896 removed outlier: 4.038A pdb=" N GLN E 896 " --> pdb=" O PRO E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 915 removed outlier: 3.646A pdb=" N ILE E 909 " --> pdb=" O ASN E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 943 Processing helix chain 'E' and resid 964 through 975 Processing helix chain 'E' and resid 989 through 998 removed outlier: 3.581A pdb=" N LEU E 993 " --> pdb=" O ASP E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1014 Processing helix chain 'E' and resid 1015 through 1027 Processing sheet with id=AA1, first strand: chain 'C' and resid 2283 through 2287 removed outlier: 4.973A pdb=" N THR C2285 " --> pdb=" O THR C2278 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR C2278 " --> pdb=" O THR C2285 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU C2231 " --> pdb=" O VAL C2340 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C2342 " --> pdb=" O GLU C2231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA C2233 " --> pdb=" O VAL C2342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 2331 through 2332 Processing sheet with id=AA3, first strand: chain 'C' and resid 2371 through 2373 removed outlier: 7.473A pdb=" N PHE C2371 " --> pdb=" O LEU C2395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.626A pdb=" N GLN A 876 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 829 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 875 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 831 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR A 877 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 833 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 939 " --> pdb=" O THR A 830 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 970 through 973 Processing sheet with id=AA6, first strand: chain 'B' and resid 842 through 846 removed outlier: 6.864A pdb=" N VAL B 843 " --> pdb=" O VAL B 953 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU B 955 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 845 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N PHE B1005 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 981 " --> pdb=" O PHE B1005 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU B1007 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA B 983 " --> pdb=" O GLU B1007 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 2283 through 2287 removed outlier: 4.931A pdb=" N THR F2285 " --> pdb=" O THR F2278 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR F2278 " --> pdb=" O THR F2285 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR F2230 " --> pdb=" O ARG F2273 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA F2275 " --> pdb=" O THR F2230 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU F2232 " --> pdb=" O ALA F2275 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL F2277 " --> pdb=" O LEU F2232 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE F2234 " --> pdb=" O VAL F2277 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TYR F2279 " --> pdb=" O PHE F2234 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU F2236 " --> pdb=" O TYR F2279 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU F2231 " --> pdb=" O VAL F2340 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F2342 " --> pdb=" O GLU F2231 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA F2233 " --> pdb=" O VAL F2342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2331 through 2332 Processing sheet with id=AA9, first strand: chain 'F' and resid 2371 through 2373 removed outlier: 7.232A pdb=" N PHE F2371 " --> pdb=" O LEU F2395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 830 through 833 removed outlier: 6.306A pdb=" N ILE D 831 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR D 877 " --> pdb=" O ILE D 831 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 833 " --> pdb=" O TYR D 877 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 876 " --> pdb=" O ARG D 884 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 970 through 973 Processing sheet with id=AB3, first strand: chain 'E' and resid 883 through 886 removed outlier: 3.663A pdb=" N ILE E 842 " --> pdb=" O ARG E 884 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP E 841 " --> pdb=" O SER E 951 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL E 953 " --> pdb=" O ASP E 841 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 843 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N PHE E1005 " --> pdb=" O PRO E 979 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 981 " --> pdb=" O PHE E1005 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLU E1007 " --> pdb=" O VAL E 981 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA E 983 " --> pdb=" O GLU E1007 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10821 1.04 - 1.23: 416 1.23 - 1.43: 4276 1.43 - 1.63: 6581 1.63 - 1.83: 74 Bond restraints: 22168 Sorted by residual: bond pdb=" N ILE C2419 " pdb=" CA ILE C2419 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.41e-02 5.03e+03 5.02e+00 bond pdb=" N CYS C2420 " pdb=" CA CYS C2420 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.28e-02 6.10e+03 4.95e+00 bond pdb=" N TYR D 817 " pdb=" H TYR D 817 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" N ASP C2418 " pdb=" H ASP C2418 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" N ARG C2199 " pdb=" H ARG C2199 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.48e+00 ... (remaining 22163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 38812 1.44 - 2.88: 982 2.88 - 4.32: 118 4.32 - 5.76: 18 5.76 - 7.20: 8 Bond angle restraints: 39938 Sorted by residual: angle pdb=" CA TYR D 817 " pdb=" C TYR D 817 " pdb=" O TYR D 817 " ideal model delta sigma weight residual 120.51 114.29 6.22 1.43e+00 4.89e-01 1.89e+01 angle pdb=" N TYR D 817 " pdb=" CA TYR D 817 " pdb=" CB TYR D 817 " ideal model delta sigma weight residual 110.49 103.29 7.20 1.69e+00 3.50e-01 1.81e+01 angle pdb=" CA ASP C2418 " pdb=" CB ASP C2418 " pdb=" CG ASP C2418 " ideal model delta sigma weight residual 112.60 116.10 -3.50 1.00e+00 1.00e+00 1.22e+01 angle pdb=" CA ASN C2421 " pdb=" C ASN C2421 " pdb=" O ASN C2421 " ideal model delta sigma weight residual 122.51 117.96 4.55 1.34e+00 5.57e-01 1.15e+01 angle pdb=" N CYS C2218 " pdb=" CA CYS C2218 " pdb=" CB CYS C2218 " ideal model delta sigma weight residual 114.17 110.45 3.72 1.14e+00 7.69e-01 1.06e+01 ... (remaining 39933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 9816 21.82 - 43.63: 673 43.63 - 65.45: 205 65.45 - 87.26: 26 87.26 - 109.08: 5 Dihedral angle restraints: 10725 sinusoidal: 6071 harmonic: 4654 Sorted by residual: dihedral pdb=" CB CYS F2206 " pdb=" SG CYS F2206 " pdb=" SG CYS F2420 " pdb=" CB CYS F2420 " ideal model delta sinusoidal sigma weight residual 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS D 594 " pdb=" SG CYS D 594 " pdb=" SG CYS D 819 " pdb=" CB CYS D 819 " ideal model delta sinusoidal sigma weight residual -86.00 -156.38 70.38 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CB CYS A 594 " pdb=" SG CYS A 594 " pdb=" SG CYS A 819 " pdb=" CB CYS A 819 " ideal model delta sinusoidal sigma weight residual -86.00 -143.47 57.47 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 10722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 1802 0.170 - 0.340: 5 0.340 - 0.511: 1 0.511 - 0.681: 0 0.681 - 0.851: 1 Chirality restraints: 1809 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.55 -0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 895 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1806 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C2199 " 0.903 9.50e-02 1.11e+02 3.02e-01 1.01e+02 pdb=" NE ARG C2199 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG C2199 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C2199 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C2199 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG C2199 " 0.017 2.00e-02 2.50e+03 pdb="HH12 ARG C2199 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG C2199 " 0.031 2.00e-02 2.50e+03 pdb="HH22 ARG C2199 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F2199 " 0.911 9.50e-02 1.11e+02 3.04e-01 9.78e+01 pdb=" NE ARG F2199 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG F2199 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG F2199 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F2199 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG F2199 " -0.020 2.00e-02 2.50e+03 pdb="HH12 ARG F2199 " 0.019 2.00e-02 2.50e+03 pdb="HH21 ARG F2199 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG F2199 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C2421 " -0.028 2.00e-02 2.50e+03 3.04e-02 1.39e+01 pdb=" CG ASN C2421 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C2421 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN C2421 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C2421 " -0.043 2.00e-02 2.50e+03 pdb="HD22 ASN C2421 " 0.045 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 968 2.15 - 2.76: 42240 2.76 - 3.37: 62014 3.37 - 3.99: 74248 3.99 - 4.60: 114598 Nonbonded interactions: 294068 Sorted by model distance: nonbonded pdb=" OE1 GLN A 976 " pdb=" H GLN A 976 " model vdw 1.534 2.450 nonbonded pdb=" H ASP A 592 " pdb=" OE2 GLU A 595 " model vdw 1.542 2.450 nonbonded pdb=" OE1 GLU B 854 " pdb=" H GLU B 854 " model vdw 1.558 2.450 nonbonded pdb=" OE1 GLU F2317 " pdb=" H GLU F2317 " model vdw 1.580 2.450 nonbonded pdb=" OE1 GLU C2317 " pdb=" H GLU C2317 " model vdw 1.592 2.450 ... (remaining 294063 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 'D' } ncs_group { reference = (chain 'B' and (resid 587 through 961 or (resid 962 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3)) or resid 963 through 1027)) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' } 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 group one per residue 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: 1.470 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.003 0.043 11368 Z= 0.169 Angle : 0.654 10.679 15444 Z= 0.328 Chirality : 0.047 0.851 1809 Planarity : 0.013 0.398 2004 Dihedral : 15.782 109.078 4461 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.23), residues: 1394 helix: 1.47 (0.22), residues: 560 sheet: -1.59 (0.35), residues: 238 loop : -1.66 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 894 TYR 0.013 0.001 TYR A1017 PHE 0.011 0.001 PHE B 922 TRP 0.003 0.001 TRP E1025 HIS 0.003 0.001 HIS C2414 Details of bonding type rmsd covalent geometry : bond 0.00346 (11337) covalent geometry : angle 0.61633 (15365) SS BOND : bond 0.00365 ( 14) SS BOND : angle 1.33564 ( 28) hydrogen bonds : bond 0.13683 ( 445) hydrogen bonds : angle 5.77776 ( 1305) link_BETA1-4 : bond 0.00516 ( 7) link_BETA1-4 : angle 3.91674 ( 21) link_BETA1-6 : bond 0.00662 ( 2) link_BETA1-6 : angle 1.78558 ( 6) link_NAG-ASN : bond 0.00820 ( 8) link_NAG-ASN : angle 3.99365 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2370 LEU cc_start: 0.8441 (mm) cc_final: 0.8204 (mm) REVERT: D 601 MET cc_start: 0.8183 (mmp) cc_final: 0.7681 (mmm) REVERT: E 847 ASP cc_start: 0.7380 (m-30) cc_final: 0.7056 (m-30) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.2135 time to fit residues: 54.8948 Evaluate side-chains 125 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0170 chunk 55 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN B 856 ASN B 970 HIS F2421 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.132605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.117341 restraints weight = 90430.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121397 restraints weight = 44551.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.123949 restraints weight = 26201.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125651 restraints weight = 17446.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126850 restraints weight = 12659.873| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11368 Z= 0.131 Angle : 0.597 9.389 15444 Z= 0.304 Chirality : 0.042 0.488 1809 Planarity : 0.005 0.057 2004 Dihedral : 9.388 70.801 1885 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1394 helix: 1.42 (0.22), residues: 568 sheet: -1.77 (0.34), residues: 230 loop : -1.69 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F2199 TYR 0.010 0.001 TYR D 817 PHE 0.010 0.001 PHE F2343 TRP 0.003 0.001 TRP E1025 HIS 0.002 0.001 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00285 (11337) covalent geometry : angle 0.57295 (15365) SS BOND : bond 0.00515 ( 14) SS BOND : angle 1.22380 ( 28) hydrogen bonds : bond 0.04274 ( 445) hydrogen bonds : angle 5.03139 ( 1305) link_BETA1-4 : bond 0.00400 ( 7) link_BETA1-4 : angle 2.84430 ( 21) link_BETA1-6 : bond 0.00345 ( 2) link_BETA1-6 : angle 1.40342 ( 6) link_NAG-ASN : bond 0.00736 ( 8) link_NAG-ASN : angle 3.16422 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2370 LEU cc_start: 0.8354 (mm) cc_final: 0.8143 (mm) REVERT: B 991 ASP cc_start: 0.8461 (p0) cc_final: 0.7891 (p0) REVERT: F 2357 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7177 (tm-30) REVERT: E 847 ASP cc_start: 0.7615 (m-30) cc_final: 0.7324 (m-30) REVERT: E 894 ARG cc_start: 0.7485 (tpm170) cc_final: 0.7279 (tpm170) REVERT: E 991 ASP cc_start: 0.8276 (p0) cc_final: 0.7883 (p0) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.2354 time to fit residues: 56.9706 Evaluate side-chains 124 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 136 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 970 HIS F2210 GLN D1018 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117511 restraints weight = 89800.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121523 restraints weight = 44225.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124090 restraints weight = 26182.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.125803 restraints weight = 17466.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.127017 restraints weight = 12712.518| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11368 Z= 0.125 Angle : 0.581 9.177 15444 Z= 0.292 Chirality : 0.041 0.471 1809 Planarity : 0.004 0.049 2004 Dihedral : 8.479 59.805 1885 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1394 helix: 1.48 (0.22), residues: 566 sheet: -1.81 (0.34), residues: 230 loop : -1.70 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F2330 TYR 0.007 0.001 TYR D 817 PHE 0.009 0.001 PHE B 922 TRP 0.015 0.002 TRP E1025 HIS 0.002 0.000 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00276 (11337) covalent geometry : angle 0.55525 (15365) SS BOND : bond 0.00289 ( 14) SS BOND : angle 1.34475 ( 28) hydrogen bonds : bond 0.03789 ( 445) hydrogen bonds : angle 4.84380 ( 1305) link_BETA1-4 : bond 0.00404 ( 7) link_BETA1-4 : angle 2.93541 ( 21) link_BETA1-6 : bond 0.00406 ( 2) link_BETA1-6 : angle 1.36542 ( 6) link_NAG-ASN : bond 0.00735 ( 8) link_NAG-ASN : angle 3.11772 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2370 LEU cc_start: 0.8433 (mm) cc_final: 0.8215 (mm) REVERT: A 843 ASN cc_start: 0.8359 (m-40) cc_final: 0.8079 (m-40) REVERT: B 991 ASP cc_start: 0.8514 (p0) cc_final: 0.7870 (p0) REVERT: F 2314 GLN cc_start: 0.8159 (tp40) cc_final: 0.7863 (tp40) REVERT: F 2357 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7200 (tm-30) REVERT: E 847 ASP cc_start: 0.7361 (m-30) cc_final: 0.6932 (m-30) REVERT: E 894 ARG cc_start: 0.7471 (tpm170) cc_final: 0.7265 (tpm170) REVERT: E 991 ASP cc_start: 0.8309 (p0) cc_final: 0.7847 (p0) outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.2336 time to fit residues: 57.8027 Evaluate side-chains 131 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 ASN B 970 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.132226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116821 restraints weight = 89797.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120893 restraints weight = 44238.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.123462 restraints weight = 25922.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125163 restraints weight = 17224.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126341 restraints weight = 12501.747| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11368 Z= 0.116 Angle : 0.566 8.872 15444 Z= 0.284 Chirality : 0.041 0.458 1809 Planarity : 0.004 0.044 2004 Dihedral : 7.863 57.368 1885 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.54 % Favored : 91.39 % Rotamer: Outliers : 0.08 % Allowed : 0.75 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.23), residues: 1394 helix: 1.44 (0.21), residues: 582 sheet: -1.81 (0.34), residues: 230 loop : -1.78 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1022 TYR 0.007 0.001 TYR D 896 PHE 0.017 0.001 PHE C2289 TRP 0.006 0.001 TRP E1025 HIS 0.003 0.000 HIS E 970 Details of bonding type rmsd covalent geometry : bond 0.00262 (11337) covalent geometry : angle 0.54101 (15365) SS BOND : bond 0.00476 ( 14) SS BOND : angle 1.25865 ( 28) hydrogen bonds : bond 0.03470 ( 445) hydrogen bonds : angle 4.69659 ( 1305) link_BETA1-4 : bond 0.00361 ( 7) link_BETA1-4 : angle 2.91378 ( 21) link_BETA1-6 : bond 0.00424 ( 2) link_BETA1-6 : angle 1.34681 ( 6) link_NAG-ASN : bond 0.00704 ( 8) link_NAG-ASN : angle 3.02220 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 MET cc_start: 0.8104 (tpt) cc_final: 0.7902 (tpp) REVERT: B 991 ASP cc_start: 0.8539 (p0) cc_final: 0.7922 (p0) REVERT: F 2357 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7183 (tm-30) REVERT: E 847 ASP cc_start: 0.7431 (m-30) cc_final: 0.7059 (m-30) REVERT: E 991 ASP cc_start: 0.8272 (p0) cc_final: 0.7878 (p0) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.2327 time to fit residues: 55.5088 Evaluate side-chains 129 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2249 GLN ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN B 970 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115355 restraints weight = 90343.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119385 restraints weight = 44713.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121940 restraints weight = 26336.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.123616 restraints weight = 17581.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124858 restraints weight = 12820.216| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11368 Z= 0.155 Angle : 0.587 9.377 15444 Z= 0.299 Chirality : 0.041 0.475 1809 Planarity : 0.004 0.037 2004 Dihedral : 7.716 58.544 1885 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.61 % Favored : 90.32 % Rotamer: Outliers : 0.08 % Allowed : 1.59 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.23), residues: 1394 helix: 1.32 (0.21), residues: 582 sheet: -1.90 (0.34), residues: 230 loop : -1.85 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 894 TYR 0.023 0.001 TYR A 926 PHE 0.014 0.001 PHE C2289 TRP 0.006 0.001 TRP E1025 HIS 0.003 0.001 HIS E 970 Details of bonding type rmsd covalent geometry : bond 0.00336 (11337) covalent geometry : angle 0.56112 (15365) SS BOND : bond 0.00197 ( 14) SS BOND : angle 1.36926 ( 28) hydrogen bonds : bond 0.03472 ( 445) hydrogen bonds : angle 4.74147 ( 1305) link_BETA1-4 : bond 0.00442 ( 7) link_BETA1-4 : angle 2.95459 ( 21) link_BETA1-6 : bond 0.00401 ( 2) link_BETA1-6 : angle 1.55955 ( 6) link_NAG-ASN : bond 0.00758 ( 8) link_NAG-ASN : angle 3.11494 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1017 TYR cc_start: 0.8250 (p90) cc_final: 0.7831 (p90) REVERT: B 989 ASP cc_start: 0.8818 (p0) cc_final: 0.8598 (p0) REVERT: B 991 ASP cc_start: 0.8595 (p0) cc_final: 0.7968 (p0) REVERT: F 2357 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 847 ASP cc_start: 0.7685 (m-30) cc_final: 0.7311 (m-30) REVERT: E 991 ASP cc_start: 0.8349 (p0) cc_final: 0.7998 (p0) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.2313 time to fit residues: 55.4712 Evaluate side-chains 127 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115553 restraints weight = 87648.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.119657 restraints weight = 42724.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122273 restraints weight = 24882.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124019 restraints weight = 16375.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.125238 restraints weight = 11721.564| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11368 Z= 0.130 Angle : 0.582 9.169 15444 Z= 0.292 Chirality : 0.041 0.466 1809 Planarity : 0.004 0.037 2004 Dihedral : 7.553 57.615 1885 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.08 % Allowed : 1.67 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1394 helix: 1.37 (0.21), residues: 584 sheet: -1.88 (0.34), residues: 230 loop : -1.79 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 853 TYR 0.010 0.001 TYR D1017 PHE 0.010 0.001 PHE C2289 TRP 0.006 0.001 TRP E1025 HIS 0.002 0.000 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00289 (11337) covalent geometry : angle 0.55415 (15365) SS BOND : bond 0.00199 ( 14) SS BOND : angle 1.84194 ( 28) hydrogen bonds : bond 0.03351 ( 445) hydrogen bonds : angle 4.62926 ( 1305) link_BETA1-4 : bond 0.00393 ( 7) link_BETA1-4 : angle 2.84776 ( 21) link_BETA1-6 : bond 0.00449 ( 2) link_BETA1-6 : angle 1.43822 ( 6) link_NAG-ASN : bond 0.00720 ( 8) link_NAG-ASN : angle 3.08245 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1017 TYR cc_start: 0.8029 (p90) cc_final: 0.7804 (p90) REVERT: B 603 MET cc_start: 0.8088 (tpt) cc_final: 0.7843 (tpp) REVERT: B 991 ASP cc_start: 0.8553 (p0) cc_final: 0.7943 (p0) REVERT: F 2314 GLN cc_start: 0.7577 (tp40) cc_final: 0.7204 (tp40) REVERT: F 2320 MET cc_start: 0.6049 (mmm) cc_final: 0.5793 (mmm) REVERT: F 2357 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7241 (tm-30) REVERT: E 847 ASP cc_start: 0.7717 (m-30) cc_final: 0.7359 (m-30) REVERT: E 991 ASP cc_start: 0.8330 (p0) cc_final: 0.7968 (p0) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.2240 time to fit residues: 54.5942 Evaluate side-chains 120 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 970 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.131819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116411 restraints weight = 86957.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120553 restraints weight = 42102.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123202 restraints weight = 24421.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124896 restraints weight = 15992.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.126098 restraints weight = 11517.694| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11368 Z= 0.110 Angle : 0.569 8.714 15444 Z= 0.285 Chirality : 0.041 0.446 1809 Planarity : 0.004 0.035 2004 Dihedral : 7.322 55.771 1885 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.32 % Favored : 91.54 % Rotamer: Outliers : 0.08 % Allowed : 0.83 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.23), residues: 1394 helix: 1.43 (0.21), residues: 584 sheet: -1.81 (0.34), residues: 230 loop : -1.73 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F2432 TYR 0.010 0.001 TYR D1017 PHE 0.010 0.001 PHE A 908 TRP 0.006 0.001 TRP E1025 HIS 0.002 0.000 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00251 (11337) covalent geometry : angle 0.54471 (15365) SS BOND : bond 0.00247 ( 14) SS BOND : angle 1.39984 ( 28) hydrogen bonds : bond 0.03259 ( 445) hydrogen bonds : angle 4.52596 ( 1305) link_BETA1-4 : bond 0.00358 ( 7) link_BETA1-4 : angle 2.70686 ( 21) link_BETA1-6 : bond 0.00459 ( 2) link_BETA1-6 : angle 1.33416 ( 6) link_NAG-ASN : bond 0.00687 ( 8) link_NAG-ASN : angle 3.00411 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 817 TYR cc_start: 0.7539 (m-10) cc_final: 0.7140 (m-10) REVERT: A 1017 TYR cc_start: 0.8197 (p90) cc_final: 0.7770 (p90) REVERT: B 603 MET cc_start: 0.8097 (tpt) cc_final: 0.7867 (tpp) REVERT: B 989 ASP cc_start: 0.8749 (p0) cc_final: 0.8544 (p0) REVERT: B 991 ASP cc_start: 0.8455 (p0) cc_final: 0.7796 (p0) REVERT: F 2357 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7238 (tm-30) REVERT: E 847 ASP cc_start: 0.7711 (m-30) cc_final: 0.7354 (m-30) REVERT: E 991 ASP cc_start: 0.8322 (p0) cc_final: 0.7967 (p0) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.2278 time to fit residues: 55.3796 Evaluate side-chains 126 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 97 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 970 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116472 restraints weight = 89810.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120541 restraints weight = 43969.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123144 restraints weight = 25838.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124858 restraints weight = 17164.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126086 restraints weight = 12477.140| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11368 Z= 0.119 Angle : 0.573 8.701 15444 Z= 0.288 Chirality : 0.041 0.439 1809 Planarity : 0.004 0.034 2004 Dihedral : 7.231 55.792 1885 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.75 % Favored : 91.10 % Rotamer: Outliers : 0.08 % Allowed : 0.92 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1394 helix: 1.46 (0.21), residues: 584 sheet: -1.91 (0.35), residues: 222 loop : -1.69 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1013 TYR 0.010 0.001 TYR D1017 PHE 0.011 0.001 PHE F2234 TRP 0.006 0.001 TRP E1025 HIS 0.002 0.000 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00268 (11337) covalent geometry : angle 0.55055 (15365) SS BOND : bond 0.00211 ( 14) SS BOND : angle 1.21158 ( 28) hydrogen bonds : bond 0.03196 ( 445) hydrogen bonds : angle 4.49885 ( 1305) link_BETA1-4 : bond 0.00349 ( 7) link_BETA1-4 : angle 2.62131 ( 21) link_BETA1-6 : bond 0.00432 ( 2) link_BETA1-6 : angle 1.37087 ( 6) link_NAG-ASN : bond 0.00685 ( 8) link_NAG-ASN : angle 2.95057 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ASN cc_start: 0.8326 (m-40) cc_final: 0.8111 (m-40) REVERT: A 1017 TYR cc_start: 0.8003 (p90) cc_final: 0.7753 (p90) REVERT: B 603 MET cc_start: 0.8102 (tpt) cc_final: 0.7867 (tpp) REVERT: B 989 ASP cc_start: 0.8937 (p0) cc_final: 0.8690 (p0) REVERT: B 991 ASP cc_start: 0.8361 (p0) cc_final: 0.7846 (p0) REVERT: F 2209 VAL cc_start: 0.7833 (t) cc_final: 0.7516 (p) REVERT: F 2357 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7270 (tm-30) REVERT: E 847 ASP cc_start: 0.7807 (m-30) cc_final: 0.7436 (m-30) REVERT: E 991 ASP cc_start: 0.8620 (p0) cc_final: 0.8002 (p0) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.2231 time to fit residues: 53.6684 Evaluate side-chains 131 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS F2244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.129967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114634 restraints weight = 87721.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.118674 restraints weight = 42975.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121222 restraints weight = 25150.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.122939 restraints weight = 16729.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.124157 restraints weight = 12031.382| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11368 Z= 0.170 Angle : 0.611 9.309 15444 Z= 0.312 Chirality : 0.041 0.461 1809 Planarity : 0.004 0.040 2004 Dihedral : 7.423 58.498 1885 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.11 % Favored : 89.74 % Rotamer: Outliers : 0.08 % Allowed : 0.42 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1394 helix: 1.35 (0.21), residues: 584 sheet: -1.96 (0.34), residues: 230 loop : -1.84 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 927 TYR 0.010 0.001 TYR D 817 PHE 0.013 0.001 PHE F2247 TRP 0.007 0.001 TRP E1025 HIS 0.003 0.001 HIS E 970 Details of bonding type rmsd covalent geometry : bond 0.00367 (11337) covalent geometry : angle 0.58631 (15365) SS BOND : bond 0.00270 ( 14) SS BOND : angle 1.76446 ( 28) hydrogen bonds : bond 0.03361 ( 445) hydrogen bonds : angle 4.63300 ( 1305) link_BETA1-4 : bond 0.00470 ( 7) link_BETA1-4 : angle 2.68363 ( 21) link_BETA1-6 : bond 0.00435 ( 2) link_BETA1-6 : angle 1.61768 ( 6) link_NAG-ASN : bond 0.00769 ( 8) link_NAG-ASN : angle 3.06655 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1017 TYR cc_start: 0.8154 (p90) cc_final: 0.7757 (p90) REVERT: B 603 MET cc_start: 0.8083 (tpt) cc_final: 0.7852 (tpp) REVERT: B 989 ASP cc_start: 0.8944 (p0) cc_final: 0.8709 (p0) REVERT: B 991 ASP cc_start: 0.8524 (p0) cc_final: 0.7911 (p0) REVERT: B 1007 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8075 (mm-30) REVERT: F 2209 VAL cc_start: 0.7824 (t) cc_final: 0.7513 (p) REVERT: F 2357 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7244 (tm-30) REVERT: E 847 ASP cc_start: 0.7926 (m-30) cc_final: 0.7550 (m-30) REVERT: E 991 ASP cc_start: 0.8621 (p0) cc_final: 0.8003 (p0) outliers start: 1 outliers final: 1 residues processed: 161 average time/residue: 0.2244 time to fit residues: 52.7476 Evaluate side-chains 127 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 129 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS F2244 GLN ** F2281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115818 restraints weight = 90447.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.119882 restraints weight = 44834.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122475 restraints weight = 26482.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124191 restraints weight = 17675.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.125432 restraints weight = 12819.568| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11368 Z= 0.127 Angle : 0.596 8.877 15444 Z= 0.302 Chirality : 0.041 0.441 1809 Planarity : 0.004 0.034 2004 Dihedral : 7.306 57.468 1885 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.90 % Favored : 90.96 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1394 helix: 1.40 (0.21), residues: 584 sheet: -1.95 (0.34), residues: 230 loop : -1.79 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1013 TYR 0.012 0.001 TYR D 926 PHE 0.023 0.001 PHE A1016 TRP 0.006 0.001 TRP E1025 HIS 0.004 0.000 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00289 (11337) covalent geometry : angle 0.57340 (15365) SS BOND : bond 0.00198 ( 14) SS BOND : angle 1.55295 ( 28) hydrogen bonds : bond 0.03278 ( 445) hydrogen bonds : angle 4.58756 ( 1305) link_BETA1-4 : bond 0.00368 ( 7) link_BETA1-4 : angle 2.59859 ( 21) link_BETA1-6 : bond 0.00449 ( 2) link_BETA1-6 : angle 1.39740 ( 6) link_NAG-ASN : bond 0.00687 ( 8) link_NAG-ASN : angle 2.99888 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2231 GLU cc_start: 0.5894 (tm-30) cc_final: 0.5398 (tm-30) REVERT: A 1017 TYR cc_start: 0.8046 (p90) cc_final: 0.7728 (p90) REVERT: B 603 MET cc_start: 0.8118 (tpt) cc_final: 0.7892 (tpp) REVERT: B 989 ASP cc_start: 0.8943 (p0) cc_final: 0.8697 (p0) REVERT: B 991 ASP cc_start: 0.8368 (p0) cc_final: 0.7816 (p0) REVERT: B 1007 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8101 (mm-30) REVERT: F 2209 VAL cc_start: 0.8002 (t) cc_final: 0.7700 (p) REVERT: F 2357 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7257 (tm-30) REVERT: E 847 ASP cc_start: 0.7874 (m-30) cc_final: 0.7491 (m-30) REVERT: E 991 ASP cc_start: 0.8415 (p0) cc_final: 0.7892 (p0) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.2241 time to fit residues: 51.4899 Evaluate side-chains 126 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS F2281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115300 restraints weight = 89674.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119344 restraints weight = 44502.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121936 restraints weight = 26282.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123636 restraints weight = 17526.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124721 restraints weight = 12764.575| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11368 Z= 0.142 Angle : 0.599 9.038 15444 Z= 0.306 Chirality : 0.041 0.446 1809 Planarity : 0.004 0.035 2004 Dihedral : 7.289 57.509 1885 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.68 % Favored : 90.17 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.23), residues: 1394 helix: 1.36 (0.21), residues: 584 sheet: -2.00 (0.34), residues: 230 loop : -1.83 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 838 TYR 0.023 0.001 TYR A 926 PHE 0.020 0.001 PHE A1016 TRP 0.007 0.001 TRP E1025 HIS 0.002 0.001 HIS E 970 Details of bonding type rmsd covalent geometry : bond 0.00314 (11337) covalent geometry : angle 0.57683 (15365) SS BOND : bond 0.00216 ( 14) SS BOND : angle 1.42580 ( 28) hydrogen bonds : bond 0.03339 ( 445) hydrogen bonds : angle 4.62476 ( 1305) link_BETA1-4 : bond 0.00422 ( 7) link_BETA1-4 : angle 2.57626 ( 21) link_BETA1-6 : bond 0.00457 ( 2) link_BETA1-6 : angle 1.49751 ( 6) link_NAG-ASN : bond 0.00718 ( 8) link_NAG-ASN : angle 3.00347 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3202.98 seconds wall clock time: 55 minutes 39.16 seconds (3339.16 seconds total)