Starting phenix.real_space_refine on Tue Aug 26 19:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf1_13364/08_2025/7pf1_13364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf1_13364/08_2025/7pf1_13364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf1_13364/08_2025/7pf1_13364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf1_13364/08_2025/7pf1_13364.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf1_13364/08_2025/7pf1_13364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf1_13364/08_2025/7pf1_13364.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Mg 167 5.21 5 S 168 5.16 5 Cl 96 4.86 5 C 21408 2.51 5 N 6000 2.21 5 O 13807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41646 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' CL': 4, ' MG': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 3, ' MG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' CL': 5, ' MG': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 4, ' MG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "Q" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 3, ' MG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 3, ' MG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 5, ' MG': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "W" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 4, ' MG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "X" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "B" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "D" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "E" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 296 Classifications: {'water': 296} Link IDs: {None: 295} Chain: "F" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 292 Classifications: {'water': 292} Link IDs: {None: 291} Chain: "G" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 300 Classifications: {'water': 300} Link IDs: {None: 299} Chain: "H" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 297 Classifications: {'water': 297} Link IDs: {None: 296} Chain: "I" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "J" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 297 Classifications: {'water': 297} Link IDs: {None: 296} Chain: "L" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "M" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "N" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "O" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "Q" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 303 Classifications: {'water': 303} Link IDs: {None: 302} Chain: "R" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 295 Classifications: {'water': 295} Link IDs: {None: 294} Chain: "S" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 293 Classifications: {'water': 293} Link IDs: {None: 292} Chain: "T" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "U" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "V" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "W" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "X" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 833 SG CYS A 105 117.711 91.607 71.393 1.00 16.28 S Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 6.83, per 1000 atoms: 0.16 Number of scatterers: 41646 At special positions: 0 Unit cell: (133.168, 133.168, 133.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 96 17.00 S 168 16.00 Mg 167 11.99 O 13807 8.00 N 6000 7.00 C 21408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 45 Processing helix chain 'A' and resid 51 through 80 Processing helix chain 'A' and resid 98 through 127 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'B' and resid 16 through 45 Processing helix chain 'B' and resid 51 through 80 Processing helix chain 'B' and resid 98 through 127 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'C' and resid 16 through 45 Processing helix chain 'C' and resid 51 through 80 Processing helix chain 'C' and resid 98 through 127 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 140 through 162 Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'D' and resid 16 through 45 Processing helix chain 'D' and resid 51 through 80 Processing helix chain 'D' and resid 98 through 127 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 140 through 162 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'E' and resid 16 through 45 Processing helix chain 'E' and resid 51 through 80 Processing helix chain 'E' and resid 98 through 127 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 140 through 162 Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 16 through 45 Processing helix chain 'F' and resid 51 through 80 Processing helix chain 'F' and resid 98 through 127 Processing helix chain 'F' and resid 129 through 140 Processing helix chain 'F' and resid 140 through 162 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'G' and resid 16 through 45 Processing helix chain 'G' and resid 51 through 80 Processing helix chain 'G' and resid 98 through 127 Processing helix chain 'G' and resid 129 through 140 Processing helix chain 'G' and resid 140 through 162 Processing helix chain 'G' and resid 166 through 177 Processing helix chain 'H' and resid 16 through 45 Processing helix chain 'H' and resid 51 through 80 Processing helix chain 'H' and resid 98 through 127 Processing helix chain 'H' and resid 129 through 140 Processing helix chain 'H' and resid 140 through 162 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'I' and resid 16 through 45 Processing helix chain 'I' and resid 51 through 80 Processing helix chain 'I' and resid 98 through 127 Processing helix chain 'I' and resid 129 through 140 Processing helix chain 'I' and resid 140 through 162 Processing helix chain 'I' and resid 166 through 177 Processing helix chain 'J' and resid 16 through 45 Processing helix chain 'J' and resid 51 through 80 Processing helix chain 'J' and resid 98 through 127 Processing helix chain 'J' and resid 129 through 140 Processing helix chain 'J' and resid 140 through 162 Processing helix chain 'J' and resid 166 through 177 Processing helix chain 'K' and resid 16 through 45 Processing helix chain 'K' and resid 51 through 80 Processing helix chain 'K' and resid 98 through 127 Processing helix chain 'K' and resid 129 through 140 Processing helix chain 'K' and resid 140 through 162 Processing helix chain 'K' and resid 166 through 177 Processing helix chain 'L' and resid 16 through 45 Processing helix chain 'L' and resid 51 through 80 Processing helix chain 'L' and resid 98 through 127 Processing helix chain 'L' and resid 129 through 140 Processing helix chain 'L' and resid 140 through 162 Processing helix chain 'L' and resid 166 through 177 Processing helix chain 'M' and resid 16 through 45 Processing helix chain 'M' and resid 51 through 80 Processing helix chain 'M' and resid 98 through 127 Processing helix chain 'M' and resid 129 through 140 Processing helix chain 'M' and resid 140 through 162 Processing helix chain 'M' and resid 166 through 177 Processing helix chain 'N' and resid 16 through 45 Processing helix chain 'N' and resid 51 through 80 Processing helix chain 'N' and resid 98 through 127 Processing helix chain 'N' and resid 129 through 140 Processing helix chain 'N' and resid 140 through 162 Processing helix chain 'N' and resid 166 through 177 Processing helix chain 'O' and resid 16 through 45 Processing helix chain 'O' and resid 51 through 80 Processing helix chain 'O' and resid 98 through 127 Processing helix chain 'O' and resid 129 through 140 Processing helix chain 'O' and resid 140 through 162 Processing helix chain 'O' and resid 166 through 177 Processing helix chain 'P' and resid 16 through 45 Processing helix chain 'P' and resid 51 through 80 Processing helix chain 'P' and resid 98 through 127 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'P' and resid 140 through 162 Processing helix chain 'P' and resid 166 through 177 Processing helix chain 'Q' and resid 16 through 45 Processing helix chain 'Q' and resid 51 through 80 Processing helix chain 'Q' and resid 98 through 127 Processing helix chain 'Q' and resid 129 through 140 Processing helix chain 'Q' and resid 140 through 162 Processing helix chain 'Q' and resid 166 through 177 Processing helix chain 'R' and resid 16 through 45 Processing helix chain 'R' and resid 51 through 80 Processing helix chain 'R' and resid 98 through 127 Processing helix chain 'R' and resid 129 through 140 Processing helix chain 'R' and resid 140 through 162 Processing helix chain 'R' and resid 166 through 177 Processing helix chain 'S' and resid 16 through 45 Processing helix chain 'S' and resid 51 through 80 Processing helix chain 'S' and resid 98 through 127 Processing helix chain 'S' and resid 129 through 140 Processing helix chain 'S' and resid 140 through 162 Processing helix chain 'S' and resid 166 through 177 Processing helix chain 'T' and resid 16 through 45 Processing helix chain 'T' and resid 51 through 80 Processing helix chain 'T' and resid 98 through 127 Processing helix chain 'T' and resid 129 through 140 Processing helix chain 'T' and resid 140 through 162 Processing helix chain 'T' and resid 166 through 177 Processing helix chain 'U' and resid 16 through 45 Processing helix chain 'U' and resid 51 through 80 Processing helix chain 'U' and resid 98 through 127 Processing helix chain 'U' and resid 129 through 140 Processing helix chain 'U' and resid 140 through 162 Processing helix chain 'U' and resid 166 through 177 Processing helix chain 'V' and resid 16 through 45 Processing helix chain 'V' and resid 51 through 80 Processing helix chain 'V' and resid 98 through 127 Processing helix chain 'V' and resid 129 through 140 Processing helix chain 'V' and resid 140 through 162 Processing helix chain 'V' and resid 166 through 177 Processing helix chain 'W' and resid 16 through 45 Processing helix chain 'W' and resid 51 through 80 Processing helix chain 'W' and resid 98 through 127 Processing helix chain 'W' and resid 129 through 140 Processing helix chain 'W' and resid 140 through 162 Processing helix chain 'W' and resid 166 through 177 Processing helix chain 'X' and resid 16 through 45 Processing helix chain 'X' and resid 51 through 80 Processing helix chain 'X' and resid 98 through 127 Processing helix chain 'X' and resid 129 through 140 Processing helix chain 'X' and resid 140 through 162 Processing helix chain 'X' and resid 166 through 177 2712 hydrogen bonds defined for protein. 8136 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: 7.60 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8124 1.33 - 1.47: 9939 1.47 - 1.61: 16545 1.61 - 1.75: 0 1.75 - 1.89: 264 Bond restraints: 34872 Sorted by residual: bond pdb=" C SER D 166 " pdb=" O SER D 166 " ideal model delta sigma weight residual 1.233 1.341 -0.108 1.21e-02 6.83e+03 8.01e+01 bond pdb=" C SER I 166 " pdb=" O SER I 166 " ideal model delta sigma weight residual 1.233 1.341 -0.108 1.21e-02 6.83e+03 7.98e+01 bond pdb=" C SER J 166 " pdb=" O SER J 166 " ideal model delta sigma weight residual 1.233 1.340 -0.108 1.21e-02 6.83e+03 7.92e+01 bond pdb=" C SER V 166 " pdb=" O SER V 166 " ideal model delta sigma weight residual 1.233 1.340 -0.108 1.21e-02 6.83e+03 7.92e+01 bond pdb=" C SER H 166 " pdb=" O SER H 166 " ideal model delta sigma weight residual 1.233 1.340 -0.108 1.21e-02 6.83e+03 7.92e+01 ... (remaining 34867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 32223 1.52 - 3.04: 11681 3.04 - 4.55: 2266 4.55 - 6.07: 463 6.07 - 7.59: 335 Bond angle restraints: 46968 Sorted by residual: angle pdb=" CA SER K 166 " pdb=" C SER K 166 " pdb=" O SER K 166 " ideal model delta sigma weight residual 121.02 126.52 -5.50 1.15e+00 7.56e-01 2.29e+01 angle pdb=" CA SER L 166 " pdb=" C SER L 166 " pdb=" O SER L 166 " ideal model delta sigma weight residual 121.02 126.52 -5.50 1.15e+00 7.56e-01 2.29e+01 angle pdb=" CA SER T 166 " pdb=" C SER T 166 " pdb=" O SER T 166 " ideal model delta sigma weight residual 121.02 126.52 -5.50 1.15e+00 7.56e-01 2.28e+01 angle pdb=" CA SER D 166 " pdb=" C SER D 166 " pdb=" O SER D 166 " ideal model delta sigma weight residual 121.02 126.50 -5.48 1.15e+00 7.56e-01 2.27e+01 angle pdb=" CA SER W 166 " pdb=" C SER W 166 " pdb=" O SER W 166 " ideal model delta sigma weight residual 121.02 126.49 -5.47 1.15e+00 7.56e-01 2.26e+01 ... (remaining 46963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 19353 16.78 - 33.57: 1257 33.57 - 50.35: 294 50.35 - 67.13: 72 67.13 - 83.91: 120 Dihedral angle restraints: 21096 sinusoidal: 8712 harmonic: 12384 Sorted by residual: dihedral pdb=" C TYR U 42 " pdb=" N TYR U 42 " pdb=" CA TYR U 42 " pdb=" CB TYR U 42 " ideal model delta harmonic sigma weight residual -122.60 -132.43 9.83 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR D 42 " pdb=" N TYR D 42 " pdb=" CA TYR D 42 " pdb=" CB TYR D 42 " ideal model delta harmonic sigma weight residual -122.60 -132.43 9.83 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR S 42 " pdb=" N TYR S 42 " pdb=" CA TYR S 42 " pdb=" CB TYR S 42 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2215 0.076 - 0.152: 1524 0.152 - 0.228: 965 0.228 - 0.303: 192 0.303 - 0.379: 48 Chirality restraints: 4944 Sorted by residual: chirality pdb=" CA TYR S 42 " pdb=" N TYR S 42 " pdb=" C TYR S 42 " pdb=" CB TYR S 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA TYR V 42 " pdb=" N TYR V 42 " pdb=" C TYR V 42 " pdb=" CB TYR V 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA TYR U 42 " pdb=" N TYR U 42 " pdb=" C TYR U 42 " pdb=" CB TYR U 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4941 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 140 " 0.097 2.00e-02 2.50e+03 5.00e-02 5.00e+01 pdb=" CG TYR B 140 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 140 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR B 140 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 140 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 140 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 140 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 140 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 140 " 0.097 2.00e-02 2.50e+03 4.99e-02 4.99e+01 pdb=" CG TYR G 140 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR G 140 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR G 140 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR G 140 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G 140 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR G 140 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 140 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 140 " -0.097 2.00e-02 2.50e+03 4.99e-02 4.98e+01 pdb=" CG TYR L 140 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR L 140 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR L 140 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR L 140 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 140 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR L 140 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 140 " -0.056 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 765 2.39 - 3.02: 30960 3.02 - 3.65: 72760 3.65 - 4.27: 125428 4.27 - 4.90: 185366 Nonbonded interactions: 415279 Sorted by model distance: nonbonded pdb="MG MG R 207 " pdb=" O HOH R 341 " model vdw 1.766 2.170 nonbonded pdb="MG MG F 208 " pdb=" O HOH F 339 " model vdw 1.766 2.170 nonbonded pdb="MG MG P 206 " pdb=" O HOH P 341 " model vdw 1.766 2.170 nonbonded pdb="MG MG L 208 " pdb=" O HOH L 341 " model vdw 1.766 2.170 nonbonded pdb="MG MG E 208 " pdb=" O HOH E 341 " model vdw 1.766 2.170 ... (remaining 415274 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'B' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'C' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'D' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'E' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'F' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'G' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'H' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'I' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'J' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'K' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'L' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'M' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'N' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'O' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'P' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'Q' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'R' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'S' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'T' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'U' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'V' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'W' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'X' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.070 Process input model: 34.070 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.020 0.143 34872 Z= 1.256 Angle : 1.660 7.589 46968 Z= 1.058 Chirality : 0.122 0.379 4944 Planarity : 0.013 0.051 6192 Dihedral : 14.319 83.915 13080 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 1.95 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 1.14 (0.11), residues: 4128 helix: 1.02 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.16 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.005 ARG A 79 TYR 0.097 0.022 TYR B 140 PHE 0.053 0.017 PHE E 44 TRP 0.035 0.012 TRP C 96 HIS 0.028 0.009 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.01962 (34872) covalent geometry : angle 1.65981 (46968) hydrogen bonds : bond 0.13342 ( 2712) hydrogen bonds : angle 4.90353 ( 8136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1032 time to evaluate : 2.153 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 outliers start: 24 outliers final: 0 residues processed: 1032 average time/residue: 1.1604 time to fit residues: 1379.6643 Evaluate side-chains 508 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 115 GLN B 112 ASN B 115 GLN C 112 ASN C 115 GLN D 112 ASN D 115 GLN E 112 ASN E 115 GLN F 112 ASN F 115 GLN G 112 ASN G 115 GLN H 68 HIS H 112 ASN H 115 GLN I 112 ASN I 115 GLN J 112 ASN J 115 GLN K 112 ASN K 115 GLN L 112 ASN L 115 GLN M 112 ASN M 115 GLN N 112 ASN N 115 GLN O 112 ASN O 115 GLN P 112 ASN P 115 GLN Q 112 ASN Q 115 GLN R 112 ASN R 115 GLN S 112 ASN S 115 GLN T 112 ASN T 115 GLN U 112 ASN U 115 GLN V 112 ASN V 115 GLN W 112 ASN W 115 GLN X 112 ASN X 115 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.173825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155058 restraints weight = 30088.295| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 0.54 r_work: 0.3555 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34872 Z= 0.119 Angle : 0.512 5.383 46968 Z= 0.284 Chirality : 0.036 0.159 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.426 22.685 4536 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.95 % Allowed : 8.44 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.77 (0.13), residues: 4128 helix: 3.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.59 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 12 TYR 0.019 0.002 TYR P 42 PHE 0.011 0.002 PHE V 135 TRP 0.004 0.001 TRP P 96 HIS 0.006 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00227 (34872) covalent geometry : angle 0.51236 (46968) hydrogen bonds : bond 0.04455 ( 2712) hydrogen bonds : angle 3.54789 ( 8136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 630 time to evaluate : 1.725 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: A 119 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 159 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7843 (mtt180) REVERT: B 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: C 119 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: C 159 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7832 (mtt180) REVERT: D 119 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: D 159 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7834 (mtt180) REVERT: E 119 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: F 119 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: G 119 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: H 119 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: H 159 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7835 (mtt180) REVERT: I 119 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: I 159 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7837 (mtt180) REVERT: J 119 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: J 159 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7849 (mtt180) REVERT: K 119 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: K 159 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7824 (mtt180) REVERT: L 119 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: L 159 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7833 (mtt180) REVERT: M 119 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: N 119 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: O 119 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: O 159 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7849 (mtt180) REVERT: P 119 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: P 159 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7830 (mtt180) REVERT: Q 119 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: Q 159 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7839 (mtt180) REVERT: R 119 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: R 159 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7824 (mtt180) REVERT: S 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: T 119 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: U 119 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: V 119 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: V 159 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7842 (mtt180) REVERT: W 119 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: X 119 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: X 159 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7837 (mtt180) outliers start: 72 outliers final: 0 residues processed: 654 average time/residue: 1.1821 time to fit residues: 890.2468 Evaluate side-chains 545 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 521 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain H residue 119 GLU Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain U residue 119 GLU Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain W residue 119 GLU Chi-restraints excluded: chain X residue 119 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 115 GLN C 115 GLN D 115 GLN E 115 GLN F 115 GLN G 115 GLN H 115 GLN I 115 GLN J 115 GLN K 115 GLN L 115 GLN M 115 GLN N 115 GLN O 115 GLN P 115 GLN Q 115 GLN R 115 GLN S 115 GLN T 115 GLN U 115 GLN V 115 GLN W 115 GLN X 115 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146056 restraints weight = 29276.539| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 0.57 r_work: 0.3453 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34872 Z= 0.158 Angle : 0.558 5.502 46968 Z= 0.314 Chirality : 0.039 0.162 4944 Planarity : 0.003 0.022 6192 Dihedral : 4.488 19.906 4536 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.35 % Allowed : 9.20 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.89 (0.13), residues: 4128 helix: 3.83 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.51 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 159 TYR 0.026 0.003 TYR M 42 PHE 0.010 0.002 PHE W 84 TRP 0.006 0.002 TRP T 96 HIS 0.006 0.002 HIS I 139 Details of bonding type rmsd covalent geometry : bond 0.00314 (34872) covalent geometry : angle 0.55808 (46968) hydrogen bonds : bond 0.05893 ( 2712) hydrogen bonds : angle 3.69571 ( 8136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 598 time to evaluate : 1.790 Fit side-chains REVERT: A 48 ASP cc_start: 0.8546 (p0) cc_final: 0.8337 (p0) REVERT: B 48 ASP cc_start: 0.8560 (p0) cc_final: 0.8357 (p0) REVERT: C 48 ASP cc_start: 0.8559 (p0) cc_final: 0.8348 (p0) REVERT: F 48 ASP cc_start: 0.8566 (p0) cc_final: 0.8365 (p0) REVERT: G 48 ASP cc_start: 0.8556 (p0) cc_final: 0.8347 (p0) REVERT: H 48 ASP cc_start: 0.8553 (p0) cc_final: 0.8347 (p0) REVERT: I 48 ASP cc_start: 0.8561 (p0) cc_final: 0.8353 (p0) REVERT: L 48 ASP cc_start: 0.8558 (p0) cc_final: 0.8346 (p0) REVERT: N 48 ASP cc_start: 0.8561 (p0) cc_final: 0.8355 (p0) REVERT: O 48 ASP cc_start: 0.8554 (p0) cc_final: 0.8348 (p0) REVERT: Q 48 ASP cc_start: 0.8555 (p0) cc_final: 0.8349 (p0) REVERT: T 48 ASP cc_start: 0.8563 (p0) cc_final: 0.8357 (p0) REVERT: U 48 ASP cc_start: 0.8560 (p0) cc_final: 0.8357 (p0) REVERT: V 48 ASP cc_start: 0.8558 (p0) cc_final: 0.8351 (p0) REVERT: W 48 ASP cc_start: 0.8564 (p0) cc_final: 0.8357 (p0) REVERT: X 48 ASP cc_start: 0.8562 (p0) cc_final: 0.8346 (p0) outliers start: 50 outliers final: 0 residues processed: 600 average time/residue: 1.0708 time to fit residues: 750.2235 Evaluate side-chains 558 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 391 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 359 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.163591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.144799 restraints weight = 29472.639| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.56 r_work: 0.3438 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34872 Z= 0.181 Angle : 0.579 5.876 46968 Z= 0.328 Chirality : 0.040 0.160 4944 Planarity : 0.004 0.020 6192 Dihedral : 4.619 19.546 4536 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.06 % Allowed : 10.20 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.70 (0.13), residues: 4128 helix: 3.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 12 TYR 0.024 0.003 TYR G 42 PHE 0.010 0.002 PHE A 44 TRP 0.007 0.002 TRP F 96 HIS 0.006 0.002 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00373 (34872) covalent geometry : angle 0.57896 (46968) hydrogen bonds : bond 0.06279 ( 2712) hydrogen bonds : angle 3.71422 ( 8136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 617 time to evaluate : 1.793 Fit side-chains REVERT: A 48 ASP cc_start: 0.8507 (p0) cc_final: 0.8296 (p0) REVERT: B 48 ASP cc_start: 0.8523 (p0) cc_final: 0.8311 (p0) REVERT: C 48 ASP cc_start: 0.8518 (p0) cc_final: 0.8304 (p0) REVERT: F 48 ASP cc_start: 0.8519 (p0) cc_final: 0.8316 (p0) REVERT: G 48 ASP cc_start: 0.8520 (p0) cc_final: 0.8315 (p0) REVERT: H 48 ASP cc_start: 0.8513 (p0) cc_final: 0.8304 (p0) REVERT: I 48 ASP cc_start: 0.8517 (p0) cc_final: 0.8314 (p0) REVERT: L 48 ASP cc_start: 0.8511 (p0) cc_final: 0.8302 (p0) REVERT: O 48 ASP cc_start: 0.8524 (p0) cc_final: 0.8310 (p0) REVERT: Q 48 ASP cc_start: 0.8520 (p0) cc_final: 0.8320 (p0) REVERT: T 48 ASP cc_start: 0.8535 (p0) cc_final: 0.8325 (p0) REVERT: U 48 ASP cc_start: 0.8527 (p0) cc_final: 0.8315 (p0) REVERT: V 48 ASP cc_start: 0.8527 (p0) cc_final: 0.8315 (p0) REVERT: W 48 ASP cc_start: 0.8522 (p0) cc_final: 0.8317 (p0) REVERT: X 48 ASP cc_start: 0.8523 (p0) cc_final: 0.8313 (p0) outliers start: 39 outliers final: 0 residues processed: 642 average time/residue: 1.1203 time to fit residues: 834.4844 Evaluate side-chains 551 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 389 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 391 optimal weight: 0.5980 chunk 366 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 chunk 370 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN A 142 ASN B 108 HIS B 115 GLN C 108 HIS C 115 GLN C 142 ASN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN F 142 ASN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN K 142 ASN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 112 ASN N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.167718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.149057 restraints weight = 30137.506| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 0.57 r_work: 0.3490 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 34872 Z= 0.111 Angle : 0.459 4.928 46968 Z= 0.260 Chirality : 0.035 0.137 4944 Planarity : 0.002 0.016 6192 Dihedral : 4.299 19.169 4536 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.11 % Allowed : 11.39 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 5.17 (0.13), residues: 4128 helix: 4.09 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.34 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 159 TYR 0.017 0.002 TYR N 42 PHE 0.009 0.002 PHE A 44 TRP 0.007 0.001 TRP F 96 HIS 0.003 0.001 HIS S 154 Details of bonding type rmsd covalent geometry : bond 0.00202 (34872) covalent geometry : angle 0.45946 (46968) hydrogen bonds : bond 0.04682 ( 2712) hydrogen bonds : angle 3.37597 ( 8136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 548 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 548 average time/residue: 1.1711 time to fit residues: 743.7133 Evaluate side-chains 522 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 230 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 403 optimal weight: 9.9990 chunk 345 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN B 68 HIS B 108 HIS B 115 GLN C 108 HIS C 112 ASN C 115 GLN D 68 HIS D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 68 HIS F 108 HIS F 115 GLN G 68 HIS G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 68 HIS I 108 HIS I 115 GLN J 68 HIS J 108 HIS J 115 GLN K 108 HIS K 112 ASN K 115 GLN L 68 HIS L 108 HIS L 115 GLN M 68 HIS M 108 HIS M 115 GLN N 68 HIS N 108 HIS N 115 GLN O 68 HIS O 108 HIS O 115 GLN P 68 HIS P 108 HIS P 115 GLN Q 68 HIS Q 108 HIS Q 115 GLN R 68 HIS R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 68 HIS T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 68 HIS W 108 HIS W 115 GLN X 68 HIS X 108 HIS X 115 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145204 restraints weight = 30090.800| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.56 r_work: 0.3441 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34872 Z= 0.173 Angle : 0.568 5.818 46968 Z= 0.320 Chirality : 0.039 0.153 4944 Planarity : 0.003 0.016 6192 Dihedral : 4.594 19.353 4536 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 11.77 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.86 (0.13), residues: 4128 helix: 3.83 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 159 TYR 0.023 0.003 TYR N 42 PHE 0.010 0.002 PHE L 44 TRP 0.008 0.002 TRP F 96 HIS 0.006 0.002 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00355 (34872) covalent geometry : angle 0.56756 (46968) hydrogen bonds : bond 0.06146 ( 2712) hydrogen bonds : angle 3.64416 ( 8136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 568 time to evaluate : 2.073 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 568 average time/residue: 1.1146 time to fit residues: 735.4746 Evaluate side-chains 539 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 187 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 355 optimal weight: 0.4980 chunk 250 optimal weight: 0.6980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 68 HIS E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 68 HIS S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.149473 restraints weight = 30299.196| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 0.57 r_work: 0.3497 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34872 Z= 0.113 Angle : 0.466 4.971 46968 Z= 0.264 Chirality : 0.035 0.136 4944 Planarity : 0.002 0.016 6192 Dihedral : 4.310 19.025 4536 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.97 % Allowed : 10.74 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 5.28 (0.13), residues: 4128 helix: 4.15 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.44 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 159 TYR 0.017 0.002 TYR L 42 PHE 0.009 0.002 PHE J 44 TRP 0.008 0.002 TRP K 96 HIS 0.003 0.001 HIS S 131 Details of bonding type rmsd covalent geometry : bond 0.00204 (34872) covalent geometry : angle 0.46614 (46968) hydrogen bonds : bond 0.04709 ( 2712) hydrogen bonds : angle 3.36340 ( 8136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 509 time to evaluate : 1.776 Fit side-chains outliers start: 36 outliers final: 0 residues processed: 509 average time/residue: 1.1489 time to fit residues: 676.8001 Evaluate side-chains 509 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 208 optimal weight: 1.9990 chunk 153 optimal weight: 0.0470 chunk 131 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 112 ASN D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 112 ASN G 115 GLN H 108 HIS H 112 ASN H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 112 ASN J 115 GLN K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 112 ASN N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 112 ASN P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 68 HIS U 108 HIS U 115 GLN V 68 HIS V 108 HIS V 112 ASN V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 112 ASN X 115 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.168288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.149839 restraints weight = 30156.003| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 0.56 r_work: 0.3497 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34872 Z= 0.110 Angle : 0.463 4.748 46968 Z= 0.261 Chirality : 0.035 0.134 4944 Planarity : 0.002 0.018 6192 Dihedral : 4.247 18.882 4536 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.84 % Allowed : 10.58 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 5.42 (0.13), residues: 4128 helix: 4.25 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.45 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 159 TYR 0.017 0.002 TYR L 42 PHE 0.016 0.002 PHE A 84 TRP 0.008 0.002 TRP E 96 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00198 (34872) covalent geometry : angle 0.46295 (46968) hydrogen bonds : bond 0.04641 ( 2712) hydrogen bonds : angle 3.33174 ( 8136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 528 time to evaluate : 1.805 Fit side-chains outliers start: 31 outliers final: 0 residues processed: 528 average time/residue: 1.1142 time to fit residues: 683.3304 Evaluate side-chains 526 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 53 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 386 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 266 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 153 optimal weight: 0.0470 chunk 253 optimal weight: 9.9990 chunk 397 optimal weight: 4.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 108 HIS A 115 GLN B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 60 HIS E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 60 HIS L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 60 HIS N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 60 HIS U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 60 HIS W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.145980 restraints weight = 30004.233| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.56 r_work: 0.3455 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34872 Z= 0.159 Angle : 0.548 5.565 46968 Z= 0.310 Chirality : 0.038 0.146 4944 Planarity : 0.003 0.016 6192 Dihedral : 4.495 19.303 4536 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.27 % Allowed : 11.20 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 5.19 (0.13), residues: 4128 helix: 4.05 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.57 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 12 TYR 0.020 0.002 TYR K 42 PHE 0.011 0.002 PHE L 44 TRP 0.008 0.002 TRP E 96 HIS 0.005 0.001 HIS X 139 Details of bonding type rmsd covalent geometry : bond 0.00320 (34872) covalent geometry : angle 0.54779 (46968) hydrogen bonds : bond 0.05882 ( 2712) hydrogen bonds : angle 3.57428 ( 8136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 582 time to evaluate : 1.609 Fit side-chains outliers start: 47 outliers final: 0 residues processed: 582 average time/residue: 1.0948 time to fit residues: 741.5226 Evaluate side-chains 552 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 384 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 285 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 108 HIS A 115 GLN B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 60 HIS L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 60 HIS N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 60 HIS U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 60 HIS W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.146289 restraints weight = 29926.002| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 0.56 r_work: 0.3459 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34872 Z= 0.153 Angle : 0.552 5.566 46968 Z= 0.312 Chirality : 0.038 0.147 4944 Planarity : 0.003 0.017 6192 Dihedral : 4.483 18.536 4536 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.65 % Allowed : 11.50 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 5.12 (0.13), residues: 4128 helix: 4.00 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.57 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 159 TYR 0.021 0.002 TYR L 42 PHE 0.011 0.002 PHE B 44 TRP 0.007 0.002 TRP E 96 HIS 0.004 0.001 HIS P 154 Details of bonding type rmsd covalent geometry : bond 0.00305 (34872) covalent geometry : angle 0.55153 (46968) hydrogen bonds : bond 0.05749 ( 2712) hydrogen bonds : angle 3.56880 ( 8136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 551 time to evaluate : 1.798 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 551 average time/residue: 1.1373 time to fit residues: 725.4270 Evaluate side-chains 530 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 285 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 108 HIS A 115 GLN B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 60 HIS L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 60 HIS N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 60 HIS U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 60 HIS W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147715 restraints weight = 30114.296| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 0.56 r_work: 0.3473 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 34872 Z= 0.131 Angle : 0.515 5.321 46968 Z= 0.290 Chirality : 0.037 0.141 4944 Planarity : 0.003 0.018 6192 Dihedral : 4.366 18.259 4536 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.68 % Allowed : 11.44 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 5.29 (0.13), residues: 4128 helix: 4.14 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.51 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.019 0.002 TYR P 42 PHE 0.010 0.002 PHE F 44 TRP 0.007 0.002 TRP W 96 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00249 (34872) covalent geometry : angle 0.51491 (46968) hydrogen bonds : bond 0.05194 ( 2712) hydrogen bonds : angle 3.45879 ( 8136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19457.40 seconds wall clock time: 333 minutes 55.31 seconds (20035.31 seconds total)