Starting phenix.real_space_refine on Fri Mar 6 21:51:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjs_54952/03_2026/9sjs_54952_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjs_54952/03_2026/9sjs_54952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjs_54952/03_2026/9sjs_54952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjs_54952/03_2026/9sjs_54952.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjs_54952/03_2026/9sjs_54952_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjs_54952/03_2026/9sjs_54952_neut.cif" } resolution = 2.06 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= 0.003 sd= 0.283 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 Fe 24 7.16 5 Mg 24 5.21 5 S 168 5.16 5 C 21312 2.51 5 N 5952 2.21 5 O 7608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35088 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "B" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' FE': 4, ' MG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "V" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "X" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "Y" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Restraints were copied for chains: D, F, I, J, R, C, E, G, H, K, L, M, N, O, P, Q, S, T, V, W, X, Y Residues with excluded nonbonded symmetry interactions: 72 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb="FE FE A 203 " occ=0.25 residue: pdb="FE FE A 204 " occ=0.25 residue: pdb="FE FE A 205 " occ=0.25 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb="FE FE D 203 " occ=0.25 residue: pdb="FE FE D 204 " occ=0.25 residue: pdb="FE FE D 205 " occ=0.25 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb="FE FE F 203 " occ=0.25 residue: pdb="FE FE F 204 " occ=0.25 residue: pdb="FE FE F 205 " occ=0.25 ... (remaining 60 not shown) Time building chain proxies: 3.57, per 1000 atoms: 0.10 Number of scatterers: 35088 At special positions: 0 Unit cell: (136.752, 136.752, 136.752, 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) Fe 24 26.01 S 168 16.00 Mg 24 11.99 O 7608 8.00 N 5952 7.00 C 21312 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: 3.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 121 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'B' and resid 10 through 39 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 121 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'C' and resid 10 through 39 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 121 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'D' and resid 10 through 39 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'E' and resid 10 through 39 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 121 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'F' and resid 10 through 39 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 121 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'G' and resid 10 through 39 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 121 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'H' and resid 10 through 39 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 121 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'I' and resid 10 through 39 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 121 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'J' and resid 10 through 39 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 160 through 171 Processing helix chain 'K' and resid 10 through 39 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'L' and resid 10 through 39 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 121 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'M' and resid 10 through 39 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 160 through 171 Processing helix chain 'N' and resid 10 through 39 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 160 through 171 Processing helix chain 'O' and resid 10 through 39 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 121 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 160 through 171 Processing helix chain 'P' and resid 10 through 39 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 160 through 171 Processing helix chain 'Q' and resid 10 through 39 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 121 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 160 through 171 Processing helix chain 'R' and resid 10 through 39 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 121 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 160 through 171 Processing helix chain 'S' and resid 10 through 39 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 121 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 160 through 171 Processing helix chain 'T' and resid 10 through 39 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 121 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 160 through 171 Processing helix chain 'V' and resid 10 through 39 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 121 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 160 through 171 Processing helix chain 'W' and resid 10 through 39 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 160 through 171 Processing helix chain 'X' and resid 10 through 39 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 121 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 160 through 171 Processing helix chain 'Y' and resid 10 through 39 Processing helix chain 'Y' and resid 45 through 73 Processing helix chain 'Y' and resid 92 through 121 Processing helix chain 'Y' and resid 123 through 134 Processing helix chain 'Y' and resid 134 through 156 Processing helix chain 'Y' and resid 160 through 171 2688 hydrogen bonds defined for protein. 8064 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: 5.88 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11544 1.34 - 1.46: 5400 1.46 - 1.57: 17496 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34704 Sorted by residual: bond pdb=" CB GLU P 137 " pdb=" CG GLU P 137 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.14e-01 bond pdb=" CB GLU Q 137 " pdb=" CG GLU Q 137 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.14e-01 bond pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.14e-01 bond pdb=" CB GLU B 137 " pdb=" CG GLU B 137 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.14e-01 bond pdb=" CB GLU C 137 " pdb=" CG GLU C 137 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.14e-01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 45456 1.30 - 2.60: 984 2.60 - 3.89: 216 3.89 - 5.19: 24 5.19 - 6.49: 48 Bond angle restraints: 46728 Sorted by residual: angle pdb=" C TRP C 90 " pdb=" N GLU C 91 " pdb=" CA GLU C 91 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C TRP I 90 " pdb=" N GLU I 91 " pdb=" CA GLU I 91 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C TRP B 90 " pdb=" N GLU B 91 " pdb=" CA GLU B 91 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C TRP T 90 " pdb=" N GLU T 91 " pdb=" CA GLU T 91 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C TRP G 90 " pdb=" N GLU G 91 " pdb=" CA GLU G 91 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 ... (remaining 46723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 18408 17.32 - 34.64: 1800 34.64 - 51.97: 408 51.97 - 69.29: 192 69.29 - 86.61: 192 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA TRP I 90 " pdb=" C TRP I 90 " pdb=" N GLU I 91 " pdb=" CA GLU I 91 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP D 90 " pdb=" C TRP D 90 " pdb=" N GLU D 91 " pdb=" CA GLU D 91 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP K 90 " pdb=" C TRP K 90 " pdb=" N GLU K 91 " pdb=" CA GLU K 91 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3168 0.027 - 0.053: 1176 0.053 - 0.079: 264 0.079 - 0.106: 168 0.106 - 0.132: 144 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR G 36 " pdb=" N TYR G 36 " pdb=" C TYR G 36 " pdb=" CB TYR G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA TYR S 36 " pdb=" N TYR S 36 " pdb=" C TYR S 36 " pdb=" CB TYR S 36 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA TYR W 36 " pdb=" N TYR W 36 " pdb=" C TYR W 36 " pdb=" CB TYR W 36 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 4917 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 60 " -0.108 9.50e-02 1.11e+02 4.86e-02 1.70e+00 pdb=" NE ARG L 60 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG L 60 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 60 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 60 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 60 " 0.108 9.50e-02 1.11e+02 4.86e-02 1.70e+00 pdb=" NE ARG C 60 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 60 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 60 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 60 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 60 " -0.108 9.50e-02 1.11e+02 4.86e-02 1.70e+00 pdb=" NE ARG Y 60 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG Y 60 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 60 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 60 " -0.001 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 108 0.99 - 1.96: 0 1.96 - 2.94: 15240 2.94 - 3.92: 111192 3.92 - 4.90: 195408 Warning: very small nonbonded interaction distances. Nonbonded interactions: 321948 Sorted by model distance: nonbonded pdb="FE FE D 201 " pdb="FE FE D 203 " model vdw 0.006 1.480 nonbonded pdb=" O HOH M 341 " pdb=" O HOH N 341 " model vdw 0.006 3.040 nonbonded pdb=" O HOH I 341 " pdb=" O HOH K 341 " model vdw 0.006 3.040 nonbonded pdb="FE FE I 204 " pdb="FE FE I 205 " model vdw 0.006 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE D 204 " model vdw 0.006 1.480 ... (remaining 321943 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 25.780 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 0.027 34704 Z= 0.134 Angle : 0.522 6.489 46728 Z= 0.296 Chirality : 0.037 0.132 4920 Planarity : 0.004 0.049 6144 Dihedral : 17.954 86.610 13032 Min Nonbonded Distance : 0.006 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.65 % Allowed : 9.09 % Favored : 90.26 % 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 are not related in a simple way. whole: 5.09 (0.13), residues: 4104 helix: 3.97 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.74 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 60 TYR 0.017 0.002 TYR X 36 PHE 0.015 0.002 PHE N 38 TRP 0.011 0.003 TRP O 90 HIS 0.002 0.001 HIS T 125 Details of bonding type rmsd covalent geometry : bond 0.00251 (34704) covalent geometry : angle 0.52216 (46728) hydrogen bonds : bond 0.09491 ( 2688) hydrogen bonds : angle 3.82847 ( 8064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 840 time to evaluate : 1.432 Fit side-chains REVERT: A 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: B 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: C 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: D 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: E 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: F 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7982 (ttm-80) REVERT: G 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: H 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: I 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: J 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: K 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: L 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: M 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: N 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: O 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: P 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: R 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: S 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: T 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: V 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: W 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7982 (ttm-80) REVERT: X 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7985 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7983 (ttm-80) outliers start: 24 outliers final: 0 residues processed: 840 average time/residue: 0.9054 time to fit residues: 878.8018 Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 792 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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: 6.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 109 GLN B 11 GLN B 109 GLN C 11 GLN C 109 GLN D 11 GLN D 109 GLN E 11 GLN E 109 GLN F 11 GLN F 109 GLN G 11 GLN G 109 GLN H 11 GLN H 109 GLN I 11 GLN I 109 GLN J 11 GLN J 109 GLN K 11 GLN K 109 GLN L 11 GLN L 109 GLN M 11 GLN M 109 GLN N 11 GLN N 109 GLN O 11 GLN O 109 GLN P 11 GLN P 109 GLN Q 11 GLN Q 109 GLN R 11 GLN R 109 GLN S 11 GLN S 109 GLN T 11 GLN T 109 GLN V 11 GLN V 109 GLN W 11 GLN W 109 GLN X 11 GLN X 109 GLN Y 11 GLN Y 109 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137807 restraints weight = 27483.138| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 0.77 r_work: 0.3390 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 34704 Z= 0.225 Angle : 0.654 6.703 46728 Z= 0.367 Chirality : 0.044 0.180 4920 Planarity : 0.005 0.053 6144 Dihedral : 4.448 23.742 4512 Min Nonbonded Distance : 0.921 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 9.09 % 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 are not related in a simple way. whole: 4.61 (0.12), residues: 4104 helix: 3.65 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.50 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 60 TYR 0.025 0.003 TYR D 36 PHE 0.023 0.004 PHE P 38 TRP 0.013 0.004 TRP N 90 HIS 0.005 0.002 HIS R 54 Details of bonding type rmsd covalent geometry : bond 0.00461 (34704) covalent geometry : angle 0.65408 (46728) hydrogen bonds : bond 0.06787 ( 2688) hydrogen bonds : angle 3.94106 ( 8064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.375 Fit side-chains REVERT: A 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: B 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7938 (ttm-80) REVERT: C 60 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7939 (ttm-80) REVERT: D 60 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7947 (ttm-80) REVERT: E 60 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7946 (ttm-80) REVERT: F 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7942 (ttm-80) REVERT: G 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7939 (ttm-80) REVERT: H 60 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: I 60 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: J 60 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: K 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: L 60 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: M 60 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: N 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7940 (ttm-80) REVERT: O 60 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: P 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7940 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7938 (ttm-80) REVERT: R 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: S 60 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: T 60 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7940 (ttm-80) REVERT: V 60 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7942 (ttm-80) REVERT: W 60 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: X 60 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7939 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7946 (ttm-80) outliers start: 48 outliers final: 48 residues processed: 744 average time/residue: 0.8010 time to fit residues: 702.3559 Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 220 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 109 GLN B 22 ASN B 109 GLN C 22 ASN C 109 GLN D 22 ASN D 109 GLN E 22 ASN E 109 GLN F 22 ASN F 109 GLN G 109 GLN H 22 ASN H 109 GLN I 22 ASN I 109 GLN J 22 ASN J 109 GLN K 22 ASN K 109 GLN L 109 GLN M 22 ASN M 109 GLN N 22 ASN N 109 GLN O 22 ASN O 109 GLN P 22 ASN P 109 GLN Q 22 ASN Q 109 GLN R 22 ASN R 109 GLN S 22 ASN S 109 GLN T 22 ASN T 109 GLN V 22 ASN V 109 GLN W 22 ASN W 109 GLN X 22 ASN X 109 GLN Y 22 ASN Y 109 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140068 restraints weight = 27460.445| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.77 r_work: 0.3431 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34704 Z= 0.165 Angle : 0.560 6.226 46728 Z= 0.316 Chirality : 0.040 0.138 4920 Planarity : 0.004 0.034 6144 Dihedral : 4.350 24.409 4512 Min Nonbonded Distance : 0.995 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.60 % Allowed : 8.44 % Favored : 88.96 % 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 are not related in a simple way. whole: 4.94 (0.13), residues: 4104 helix: 3.89 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.57 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 60 TYR 0.021 0.003 TYR G 36 PHE 0.018 0.003 PHE O 38 TRP 0.012 0.003 TRP O 90 HIS 0.003 0.001 HIS O 54 Details of bonding type rmsd covalent geometry : bond 0.00323 (34704) covalent geometry : angle 0.55999 (46728) hydrogen bonds : bond 0.05911 ( 2688) hydrogen bonds : angle 3.77122 ( 8064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 788 time to evaluate : 1.353 Fit side-chains REVERT: A 60 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7927 (ttm-80) REVERT: B 60 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: C 60 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7927 (ttm-80) REVERT: D 60 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7933 (ttm-80) REVERT: E 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: F 60 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: G 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: H 60 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: I 60 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: J 60 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: K 60 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: L 60 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: M 60 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: N 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: O 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: P 60 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7926 (ttm-80) REVERT: R 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7933 (ttm-80) REVERT: S 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: T 60 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: V 60 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7933 (ttm-80) REVERT: W 60 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: X 60 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7933 (ttm-80) outliers start: 96 outliers final: 48 residues processed: 788 average time/residue: 0.8741 time to fit residues: 799.6775 Evaluate side-chains 821 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 773 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 21 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139240 restraints weight = 27465.842| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.77 r_work: 0.3420 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34704 Z= 0.184 Angle : 0.590 6.449 46728 Z= 0.331 Chirality : 0.041 0.141 4920 Planarity : 0.004 0.033 6144 Dihedral : 4.382 24.442 4512 Min Nonbonded Distance : 0.969 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.30 % Allowed : 9.09 % 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 are not related in a simple way. whole: 4.80 (0.12), residues: 4104 helix: 3.81 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.44 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.022 0.003 TYR D 36 PHE 0.020 0.003 PHE R 38 TRP 0.013 0.003 TRP M 90 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00370 (34704) covalent geometry : angle 0.58977 (46728) hydrogen bonds : bond 0.06187 ( 2688) hydrogen bonds : angle 3.81788 ( 8064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 749 time to evaluate : 1.348 Fit side-chains REVERT: K 60 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7980 (ttm-80) REVERT: N 60 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7977 (ttm-80) REVERT: O 60 ARG cc_start: 0.8340 (ttp80) cc_final: 0.7978 (ttm-80) REVERT: P 60 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7977 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7976 (ttm-80) REVERT: R 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7980 (ttm-80) REVERT: S 60 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7979 (ttm-80) REVERT: T 60 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7975 (ttm-80) REVERT: V 60 ARG cc_start: 0.8340 (ttp80) cc_final: 0.7977 (ttm-80) REVERT: W 60 ARG cc_start: 0.8340 (ttp80) cc_final: 0.7977 (ttm-80) REVERT: X 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7975 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7981 (ttm-80) outliers start: 48 outliers final: 48 residues processed: 749 average time/residue: 0.7805 time to fit residues: 688.3687 Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 272 optimal weight: 6.9990 chunk 396 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136847 restraints weight = 27383.851| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 0.76 r_work: 0.3396 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34704 Z= 0.194 Angle : 0.605 6.578 46728 Z= 0.339 Chirality : 0.041 0.145 4920 Planarity : 0.004 0.032 6144 Dihedral : 4.398 24.332 4512 Min Nonbonded Distance : 0.961 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 9.09 % Favored : 88.96 % 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 are not related in a simple way. whole: 4.73 (0.12), residues: 4104 helix: 3.75 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.45 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.023 0.003 TYR L 36 PHE 0.020 0.003 PHE B 38 TRP 0.013 0.004 TRP L 90 HIS 0.004 0.001 HIS V 54 Details of bonding type rmsd covalent geometry : bond 0.00394 (34704) covalent geometry : angle 0.60535 (46728) hydrogen bonds : bond 0.06327 ( 2688) hydrogen bonds : angle 3.84267 ( 8064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 768 time to evaluate : 1.337 Fit side-chains REVERT: K 60 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7990 (ttm-80) REVERT: N 60 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: O 60 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: P 60 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7987 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: R 60 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7985 (ttm-80) REVERT: S 60 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: T 60 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7985 (ttm-80) REVERT: V 60 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7982 (ttm-80) REVERT: W 60 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7988 (ttm-80) REVERT: X 60 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7981 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7996 (ttm-80) outliers start: 72 outliers final: 48 residues processed: 768 average time/residue: 0.8075 time to fit residues: 728.4857 Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 308 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 337 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 22 ASN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 22 ASN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141773 restraints weight = 27273.236| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 0.75 r_work: 0.3466 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 34704 Z= 0.131 Angle : 0.502 5.662 46728 Z= 0.283 Chirality : 0.037 0.134 4920 Planarity : 0.003 0.044 6144 Dihedral : 4.207 24.214 4512 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.95 % Allowed : 10.06 % Favored : 87.99 % 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 are not related in a simple way. whole: 5.24 (0.13), residues: 4104 helix: 4.12 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.59 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 60 TYR 0.018 0.002 TYR L 36 PHE 0.014 0.002 PHE N 38 TRP 0.011 0.003 TRP D 90 HIS 0.003 0.001 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00246 (34704) covalent geometry : angle 0.50169 (46728) hydrogen bonds : bond 0.05063 ( 2688) hydrogen bonds : angle 3.58066 ( 8064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 768 time to evaluate : 1.312 Fit side-chains REVERT: A 155 MET cc_start: 0.9105 (mtp) cc_final: 0.8885 (mtp) REVERT: B 155 MET cc_start: 0.9107 (mtp) cc_final: 0.8887 (mtp) REVERT: C 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8884 (mtp) REVERT: D 155 MET cc_start: 0.9107 (mtp) cc_final: 0.8888 (mtp) REVERT: E 155 MET cc_start: 0.9102 (mtp) cc_final: 0.8882 (mtp) REVERT: F 155 MET cc_start: 0.9104 (mtp) cc_final: 0.8884 (mtp) REVERT: G 155 MET cc_start: 0.9105 (mtp) cc_final: 0.8886 (mtp) REVERT: H 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8883 (mtp) REVERT: I 155 MET cc_start: 0.9106 (mtp) cc_final: 0.8886 (mtp) REVERT: J 155 MET cc_start: 0.9107 (mtp) cc_final: 0.8890 (mtp) REVERT: K 60 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7934 (ttm-80) REVERT: K 155 MET cc_start: 0.9104 (mtp) cc_final: 0.8883 (mtp) REVERT: L 155 MET cc_start: 0.9106 (mtp) cc_final: 0.8888 (mtp) REVERT: M 155 MET cc_start: 0.9104 (mtp) cc_final: 0.8886 (mtp) REVERT: N 60 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7934 (ttm-80) REVERT: N 155 MET cc_start: 0.9102 (mtp) cc_final: 0.8883 (mtp) REVERT: O 60 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: O 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8882 (mtp) REVERT: P 60 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: P 155 MET cc_start: 0.9105 (mtp) cc_final: 0.8886 (mtp) REVERT: Q 60 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: Q 155 MET cc_start: 0.9102 (mtp) cc_final: 0.8881 (mtp) REVERT: R 60 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: R 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8881 (mtp) REVERT: S 60 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7933 (ttm-80) REVERT: S 155 MET cc_start: 0.9105 (mtp) cc_final: 0.8887 (mtp) REVERT: T 60 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: T 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8881 (mtp) REVERT: V 60 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: V 155 MET cc_start: 0.9101 (mtp) cc_final: 0.8879 (mtp) REVERT: W 60 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: W 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8887 (mtp) REVERT: X 60 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: X 155 MET cc_start: 0.9104 (mtp) cc_final: 0.8885 (mtp) REVERT: Y 60 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: Y 155 MET cc_start: 0.9103 (mtp) cc_final: 0.8885 (mtp) outliers start: 72 outliers final: 24 residues processed: 768 average time/residue: 0.8038 time to fit residues: 724.2488 Evaluate side-chains 787 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 763 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 222 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 375 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137042 restraints weight = 27409.104| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 0.76 r_work: 0.3408 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34704 Z= 0.171 Angle : 0.571 6.299 46728 Z= 0.321 Chirality : 0.040 0.152 4920 Planarity : 0.004 0.047 6144 Dihedral : 4.315 24.252 4512 Min Nonbonded Distance : 1.002 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 11.36 % Favored : 86.69 % 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 are not related in a simple way. whole: 4.99 (0.13), residues: 4104 helix: 3.93 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.53 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 60 TYR 0.021 0.003 TYR D 36 PHE 0.019 0.003 PHE T 38 TRP 0.012 0.003 TRP L 90 HIS 0.005 0.001 HIS T 170 Details of bonding type rmsd covalent geometry : bond 0.00342 (34704) covalent geometry : angle 0.57147 (46728) hydrogen bonds : bond 0.05967 ( 2688) hydrogen bonds : angle 3.75248 ( 8064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 787 time to evaluate : 1.364 Fit side-chains REVERT: K 60 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7939 (ttm-80) REVERT: N 60 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: O 60 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7935 (ttm-80) REVERT: P 60 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7938 (ttm-80) REVERT: R 60 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7935 (ttm-80) REVERT: S 60 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7938 (ttm-80) REVERT: T 60 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7938 (ttm-80) REVERT: V 60 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7934 (ttm-80) REVERT: W 60 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: X 60 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7933 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7946 (ttm-80) outliers start: 72 outliers final: 24 residues processed: 811 average time/residue: 0.8550 time to fit residues: 808.4632 Evaluate side-chains 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 768 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 364 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135716 restraints weight = 27424.364| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 0.76 r_work: 0.3376 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34704 Z= 0.215 Angle : 0.645 6.658 46728 Z= 0.357 Chirality : 0.042 0.151 4920 Planarity : 0.004 0.044 6144 Dihedral : 4.419 24.212 4512 Min Nonbonded Distance : 1.001 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 10.25 % Favored : 87.80 % 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 are not related in a simple way. whole: 4.67 (0.12), residues: 4104 helix: 3.71 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.43 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.024 0.003 TYR K 36 PHE 0.021 0.004 PHE G 38 TRP 0.012 0.003 TRP L 90 HIS 0.006 0.002 HIS W 170 Details of bonding type rmsd covalent geometry : bond 0.00443 (34704) covalent geometry : angle 0.64530 (46728) hydrogen bonds : bond 0.06522 ( 2688) hydrogen bonds : angle 3.88275 ( 8064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 768 time to evaluate : 1.393 Fit side-chains REVERT: K 60 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7973 (ttm-80) REVERT: N 60 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7973 (ttm-80) REVERT: O 60 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7969 (ttm-80) REVERT: P 60 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7969 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7969 (ttm-80) REVERT: R 60 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7968 (ttm-80) REVERT: S 60 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7967 (ttm-80) REVERT: T 60 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7968 (ttm-80) REVERT: V 60 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7964 (ttm-80) REVERT: W 60 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7970 (ttm-80) REVERT: X 60 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7967 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7976 (ttm-80) outliers start: 72 outliers final: 48 residues processed: 768 average time/residue: 0.8353 time to fit residues: 751.3878 Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 768 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 325 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135420 restraints weight = 27467.224| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 0.75 r_work: 0.3361 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 34704 Z= 0.268 Angle : 0.717 7.069 46728 Z= 0.396 Chirality : 0.046 0.163 4920 Planarity : 0.005 0.065 6144 Dihedral : 4.549 23.629 4512 Min Nonbonded Distance : 0.982 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 11.04 % Favored : 87.66 % 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 are not related in a simple way. whole: 4.34 (0.12), residues: 4104 helix: 3.46 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.41 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 60 TYR 0.027 0.004 TYR B 36 PHE 0.023 0.004 PHE A 38 TRP 0.013 0.004 TRP L 90 HIS 0.006 0.002 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00564 (34704) covalent geometry : angle 0.71677 (46728) hydrogen bonds : bond 0.07034 ( 2688) hydrogen bonds : angle 4.00441 ( 8064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 768 time to evaluate : 1.408 Fit side-chains REVERT: A 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8879 (mtp) REVERT: B 155 MET cc_start: 0.9190 (mtp) cc_final: 0.8883 (mtp) REVERT: C 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8881 (mtp) REVERT: D 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8881 (mtp) REVERT: E 155 MET cc_start: 0.9182 (mtp) cc_final: 0.8870 (mtp) REVERT: F 155 MET cc_start: 0.9187 (mtp) cc_final: 0.8878 (mtp) REVERT: G 155 MET cc_start: 0.9189 (mtp) cc_final: 0.8884 (mtp) REVERT: H 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8880 (mtp) REVERT: I 155 MET cc_start: 0.9189 (mtp) cc_final: 0.8882 (mtp) REVERT: J 155 MET cc_start: 0.9192 (mtp) cc_final: 0.8887 (mtp) REVERT: K 60 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7977 (ttm-80) REVERT: K 155 MET cc_start: 0.9186 (mtp) cc_final: 0.8876 (mtp) REVERT: L 155 MET cc_start: 0.9187 (mtp) cc_final: 0.8879 (mtp) REVERT: M 155 MET cc_start: 0.9187 (mtp) cc_final: 0.8880 (mtp) REVERT: N 60 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7976 (ttm-80) REVERT: N 155 MET cc_start: 0.9185 (mtp) cc_final: 0.8877 (mtp) REVERT: O 60 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7975 (ttm-80) REVERT: O 155 MET cc_start: 0.9185 (mtp) cc_final: 0.8876 (mtp) REVERT: P 60 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7973 (ttm-80) REVERT: P 155 MET cc_start: 0.9190 (mtp) cc_final: 0.8885 (mtp) REVERT: Q 60 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7971 (ttm-80) REVERT: Q 155 MET cc_start: 0.9185 (mtp) cc_final: 0.8874 (mtp) REVERT: R 60 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7974 (ttm-80) REVERT: R 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8879 (mtp) REVERT: S 60 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7972 (ttm-80) REVERT: S 155 MET cc_start: 0.9190 (mtp) cc_final: 0.8883 (mtp) REVERT: T 60 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7976 (ttm-80) REVERT: T 155 MET cc_start: 0.9187 (mtp) cc_final: 0.8877 (mtp) REVERT: V 60 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7974 (ttm-80) REVERT: V 155 MET cc_start: 0.9184 (mtp) cc_final: 0.8876 (mtp) REVERT: W 60 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7975 (ttm-80) REVERT: W 155 MET cc_start: 0.9187 (mtp) cc_final: 0.8880 (mtp) REVERT: X 60 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7970 (ttm-80) REVERT: X 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8881 (mtp) REVERT: Y 60 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: Y 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8879 (mtp) outliers start: 48 outliers final: 48 residues processed: 768 average time/residue: 0.7961 time to fit residues: 716.8660 Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 768 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 267 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 349 optimal weight: 0.9990 chunk 323 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 381 optimal weight: 5.9990 chunk 404 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143539 restraints weight = 27561.824| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 0.73 r_work: 0.3438 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34704 Z= 0.164 Angle : 0.580 6.378 46728 Z= 0.322 Chirality : 0.040 0.169 4920 Planarity : 0.004 0.054 6144 Dihedral : 4.387 24.419 4512 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.30 % Allowed : 10.28 % Favored : 88.42 % 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 are not related in a simple way. whole: 4.86 (0.13), residues: 4104 helix: 3.86 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.41 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 60 TYR 0.020 0.003 TYR Y 36 PHE 0.018 0.003 PHE G 38 TRP 0.013 0.003 TRP J 90 HIS 0.004 0.001 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00324 (34704) covalent geometry : angle 0.58037 (46728) hydrogen bonds : bond 0.05781 ( 2688) hydrogen bonds : angle 3.75246 ( 8064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 768 time to evaluate : 1.289 Fit side-chains REVERT: A 155 MET cc_start: 0.9152 (mtp) cc_final: 0.8866 (mtp) REVERT: B 155 MET cc_start: 0.9154 (mtp) cc_final: 0.8869 (mtp) REVERT: C 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8864 (mtp) REVERT: D 155 MET cc_start: 0.9154 (mtp) cc_final: 0.8872 (mtp) REVERT: E 155 MET cc_start: 0.9149 (mtp) cc_final: 0.8864 (mtp) REVERT: F 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8864 (mtp) REVERT: G 155 MET cc_start: 0.9153 (mtp) cc_final: 0.8869 (mtp) REVERT: H 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8865 (mtp) REVERT: I 155 MET cc_start: 0.9155 (mtp) cc_final: 0.8872 (mtp) REVERT: J 155 MET cc_start: 0.9156 (mtp) cc_final: 0.8872 (mtp) REVERT: K 60 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7945 (ttm-80) REVERT: K 155 MET cc_start: 0.9152 (mtp) cc_final: 0.8868 (mtp) REVERT: L 155 MET cc_start: 0.9152 (mtp) cc_final: 0.8869 (mtp) REVERT: M 155 MET cc_start: 0.9149 (mtp) cc_final: 0.8865 (mtp) REVERT: N 60 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7947 (ttm-80) REVERT: N 155 MET cc_start: 0.9149 (mtp) cc_final: 0.8867 (mtp) REVERT: O 60 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7942 (ttm-80) REVERT: O 155 MET cc_start: 0.9150 (mtp) cc_final: 0.8862 (mtp) REVERT: P 60 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: P 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8869 (mtp) REVERT: Q 60 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: Q 155 MET cc_start: 0.9150 (mtp) cc_final: 0.8863 (mtp) REVERT: R 60 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: R 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8864 (mtp) REVERT: S 60 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7944 (ttm-80) REVERT: S 155 MET cc_start: 0.9154 (mtp) cc_final: 0.8873 (mtp) REVERT: T 60 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7944 (ttm-80) REVERT: T 155 MET cc_start: 0.9152 (mtp) cc_final: 0.8865 (mtp) REVERT: V 60 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: V 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8869 (mtp) REVERT: W 60 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7940 (ttm-80) REVERT: W 155 MET cc_start: 0.9151 (mtp) cc_final: 0.8867 (mtp) REVERT: X 60 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: X 155 MET cc_start: 0.9152 (mtp) cc_final: 0.8869 (mtp) REVERT: Y 60 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7950 (ttm-80) REVERT: Y 155 MET cc_start: 0.9152 (mtp) cc_final: 0.8868 (mtp) outliers start: 48 outliers final: 48 residues processed: 768 average time/residue: 0.8122 time to fit residues: 731.9069 Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 768 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain N residue 46 LYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 87 CYS Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 87 CYS Chi-restraints excluded: chain Q residue 46 LYS Chi-restraints excluded: chain Q residue 87 CYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 87 CYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 87 CYS Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 87 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 395 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 109 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN K 109 GLN L 109 GLN M 109 GLN N 109 GLN O 109 GLN P 109 GLN Q 109 GLN R 109 GLN S 109 GLN T 109 GLN V 109 GLN W 109 GLN X 109 GLN Y 109 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136676 restraints weight = 27324.845| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 0.75 r_work: 0.3395 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34704 Z= 0.206 Angle : 0.645 6.693 46728 Z= 0.357 Chirality : 0.043 0.159 4920 Planarity : 0.004 0.057 6144 Dihedral : 4.432 24.162 4512 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.30 % Allowed : 10.20 % 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 are not related in a simple way. whole: 4.61 (0.12), residues: 4104 helix: 3.68 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.35 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 60 TYR 0.023 0.003 TYR D 36 PHE 0.021 0.004 PHE N 38 TRP 0.013 0.004 TRP R 90 HIS 0.005 0.002 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00422 (34704) covalent geometry : angle 0.64523 (46728) hydrogen bonds : bond 0.06478 ( 2688) hydrogen bonds : angle 3.87972 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17795.64 seconds wall clock time: 303 minutes 4.29 seconds (18184.29 seconds total)