Starting phenix.real_space_refine on Mon Jul 6 10:43:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjs_54952/07_2026/9sjs_54952_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjs_54952/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9sjs_54952/07_2026/9sjs_54952_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjs_54952/07_2026/9sjs_54952_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sjs_54952/07_2026/9sjs_54952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjs_54952/07_2026/9sjs_54952.map" } 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-6108/lib/python3.11/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, 1 Ad-hoc single atom residues: {' FE': 4} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 4.00, per 1000 atoms: 0.11 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 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: 0.44 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: 5.76 Time building geometry restraints manager: 4.17 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 2.960 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 2.960 nonbonded pdb="FE FE D 201 " pdb="FE FE D 204 " model vdw 0.006 2.960 ... (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: 0.11 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.740 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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/Z covalent geometry : bond 0.00251 / 0.13 (34704) covalent geometry : angle 0.52216 / 0.30 (46728) hydrogen bonds : bond 0.09491 / 6.39 ( 2688) hydrogen bonds : angle 3.82847 / 2.77 ( 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 : 1.460 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: 0.7750 time to fit residues: 759.0485 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 : 1.253 ------------------------------------------------------------------------------- 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... 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 = 0.3731 r_free = 0.3731 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140542 restraints weight = 27519.613| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 0.79 r_work: 0.3394 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.0927 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= 0.226 Angle : 0.658 6.819 46728 Z= 0.370 Chirality : 0.045 0.225 4920 Planarity : 0.005 0.057 6144 Dihedral : 4.511 23.884 4512 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.87 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: 4.53 (0.12), residues: 4104 helix: 3.59 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.46 (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 E 36 PHE 0.023 0.004 PHE B 38 TRP 0.013 0.004 TRP H 90 HIS 0.005 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 (34704) covalent geometry : angle 0.65772 / 0.37 (46728) hydrogen bonds : bond 0.06808 / 4.61 ( 2688) hydrogen bonds : angle 3.97791 / 2.87 ( 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 814 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 766 time to evaluate : 1.348 Fit side-chains REVERT: A 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7914 (ttm-80) REVERT: B 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7913 (ttm-80) REVERT: C 60 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7913 (ttm-80) REVERT: D 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7918 (ttm-80) REVERT: E 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7918 (ttm-80) REVERT: F 60 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7917 (ttm-80) REVERT: G 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7917 (ttm-80) REVERT: H 60 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7915 (ttm-80) REVERT: I 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7914 (ttm-80) REVERT: J 60 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7915 (ttm-80) REVERT: K 60 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7914 (ttm-80) REVERT: L 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7915 (ttm-80) REVERT: M 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7917 (ttm-80) REVERT: N 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7916 (ttm-80) REVERT: O 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7914 (ttm-80) REVERT: P 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7915 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7912 (ttm-80) REVERT: R 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7918 (ttm-80) REVERT: S 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7919 (ttm-80) REVERT: T 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7917 (ttm-80) REVERT: V 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7917 (ttm-80) REVERT: W 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7918 (ttm-80) REVERT: X 60 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7913 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7919 (ttm-80) outliers start: 48 outliers final: 24 residues processed: 766 average time/residue: 0.7747 time to fit residues: 697.3539 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 : 1.189 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 220 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 109 GLN G 109 GLN H 22 ASN H 109 GLN I 22 ASN I 109 GLN 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 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138181 restraints weight = 27550.741| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 0.76 r_work: 0.3469 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34704 Z= 0.172 Angle : 0.572 6.294 46728 Z= 0.322 Chirality : 0.040 0.138 4920 Planarity : 0.004 0.034 6144 Dihedral : 4.355 24.298 4512 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.95 % Allowed : 9.25 % Favored : 88.80 % 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: 4.83 (0.12), residues: 4104 helix: 3.81 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.54 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 60 TYR 0.021 0.003 TYR G 36 PHE 0.019 0.003 PHE L 38 TRP 0.012 0.003 TRP P 90 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (34704) covalent geometry : angle 0.57195 / 0.32 (46728) hydrogen bonds : bond 0.06056 / 4.11 ( 2688) hydrogen bonds : angle 3.81357 / 2.74 ( 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 846 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 774 time to evaluate : 1.264 Fit side-chains REVERT: K 60 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8000 (ttm-80) REVERT: N 60 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8000 (ttm-80) REVERT: O 60 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7999 (ttm-80) REVERT: P 60 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7998 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7998 (ttm-80) REVERT: R 60 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8000 (ttm-80) REVERT: S 60 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7999 (ttm-80) REVERT: T 60 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7999 (ttm-80) REVERT: V 60 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8000 (ttm-80) REVERT: W 60 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8002 (ttm-80) REVERT: X 60 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7996 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8003 (ttm-80) outliers start: 72 outliers final: 24 residues processed: 774 average time/residue: 0.7592 time to fit residues: 691.6347 Evaluate side-chains 806 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 782 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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=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: 20.0000 chunk 288 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3676 r_free = 0.3676 target = 0.149820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137138 restraints weight = 27428.644| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.77 r_work: 0.3412 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 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 = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34704 Z= 0.200 Angle : 0.617 6.618 46728 Z= 0.345 Chirality : 0.041 0.146 4920 Planarity : 0.004 0.036 6144 Dihedral : 4.422 24.288 4512 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.24 % Allowed : 9.79 % 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: 4.64 (0.12), residues: 4104 helix: 3.67 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.51 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 60 TYR 0.023 0.003 TYR A 36 PHE 0.021 0.003 PHE P 38 TRP 0.014 0.004 TRP C 90 HIS 0.005 0.001 HIS T 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (34704) covalent geometry : angle 0.61749 / 0.35 (46728) hydrogen bonds : bond 0.06415 / 4.35 ( 2688) hydrogen bonds : angle 3.88349 / 2.79 ( 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 814 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 768 time to evaluate : 1.141 Fit side-chains REVERT: K 60 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7990 (ttm-80) REVERT: N 60 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7993 (ttm-80) REVERT: O 60 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7992 (ttm-80) REVERT: P 60 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7992 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7992 (ttm-80) REVERT: R 60 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7986 (ttm-80) REVERT: S 60 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7992 (ttm-80) REVERT: T 60 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: V 60 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7988 (ttm-80) REVERT: W 60 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7988 (ttm-80) REVERT: X 60 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7981 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7996 (ttm-80) outliers start: 46 outliers final: 46 residues processed: 768 average time/residue: 0.7062 time to fit residues: 642.0713 Evaluate side-chains 790 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 744 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 396 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 187 optimal weight: 0.0060 chunk 406 optimal weight: 8.9990 chunk 359 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 109 GLN C 109 GLN D 109 GLN E 109 GLN F 22 ASN F 109 GLN G 22 ASN G 109 GLN H 109 GLN I 109 GLN J 22 ASN 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 22 ASN 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138178 restraints weight = 27352.557| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 0.75 r_work: 0.3450 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 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 = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34704 Z= 0.160 Angle : 0.554 6.193 46728 Z= 0.311 Chirality : 0.039 0.138 4920 Planarity : 0.003 0.025 6144 Dihedral : 4.323 24.422 4512 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.35 % Allowed : 10.17 % Favored : 88.47 % 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: 4.95 (0.13), residues: 4104 helix: 3.90 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.56 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 60 TYR 0.020 0.002 TYR G 36 PHE 0.017 0.003 PHE L 38 TRP 0.012 0.003 TRP W 90 HIS 0.003 0.001 HIS L 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (34704) covalent geometry : angle 0.55389 / 0.31 (46728) hydrogen bonds : bond 0.05778 / 3.92 ( 2688) hydrogen bonds : angle 3.74486 / 2.69 ( 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 842 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 792 time to evaluate : 1.407 Fit side-chains REVERT: K 60 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7929 (ttm-80) REVERT: N 60 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7934 (ttm-80) REVERT: O 60 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: P 60 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7926 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: R 60 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: S 60 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: T 60 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7927 (ttm-80) REVERT: V 60 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7926 (ttm-80) REVERT: W 60 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7925 (ttm-80) REVERT: X 60 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7919 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7935 (ttm-80) outliers start: 50 outliers final: 26 residues processed: 792 average time/residue: 0.7177 time to fit residues: 670.4881 Evaluate side-chains 770 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 744 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 46 LYS 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 46 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 308 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 182 optimal weight: 0.5980 chunk 340 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3681 r_free = 0.3681 target = 0.150743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138202 restraints weight = 27278.659| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.75 r_work: 0.3423 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0953 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= 0.166 Angle : 0.561 6.227 46728 Z= 0.315 Chirality : 0.039 0.139 4920 Planarity : 0.004 0.045 6144 Dihedral : 4.338 24.394 4512 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.95 % Allowed : 9.58 % Favored : 88.47 % 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: 4.93 (0.13), residues: 4104 helix: 3.88 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.55 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 60 TYR 0.020 0.003 TYR M 36 PHE 0.018 0.003 PHE C 38 TRP 0.012 0.003 TRP N 90 HIS 0.004 0.001 HIS I 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (34704) covalent geometry : angle 0.56106 / 0.32 (46728) hydrogen bonds : bond 0.05906 / 4.01 ( 2688) hydrogen bonds : angle 3.76785 / 2.71 ( 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 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 744 time to evaluate : 1.361 Fit side-chains REVERT: K 60 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: N 60 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7934 (ttm-80) REVERT: O 60 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: P 60 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: R 60 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: S 60 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7932 (ttm-80) REVERT: T 60 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7927 (ttm-80) REVERT: V 60 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7924 (ttm-80) REVERT: W 60 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7928 (ttm-80) REVERT: X 60 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7925 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7939 (ttm-80) outliers start: 72 outliers final: 48 residues processed: 768 average time/residue: 0.7462 time to fit residues: 676.4679 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 : 1.255 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 222 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 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... 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 = 0.3671 r_free = 0.3671 target = 0.150222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137654 restraints weight = 27384.352| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 0.75 r_work: 0.3410 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 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 = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34704 Z= 0.172 Angle : 0.580 6.270 46728 Z= 0.324 Chirality : 0.040 0.139 4920 Planarity : 0.004 0.039 6144 Dihedral : 4.345 24.427 4512 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.30 % Allowed : 10.93 % Favored : 87.77 % 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: 4.87 (0.13), residues: 4104 helix: 3.85 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.51 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 60 TYR 0.021 0.003 TYR G 36 PHE 0.018 0.003 PHE H 38 TRP 0.012 0.003 TRP Y 90 HIS 0.004 0.001 HIS L 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (34704) covalent geometry : angle 0.58017 / 0.32 (46728) hydrogen bonds : bond 0.05975 / 4.05 ( 2688) hydrogen bonds : angle 3.78247 / 2.72 ( 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 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.329 Fit side-chains REVERT: K 60 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7992 (ttm-80) REVERT: N 60 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7993 (ttm-80) REVERT: O 60 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7991 (ttm-80) REVERT: P 60 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7992 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7990 (ttm-80) REVERT: R 60 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7994 (ttm-80) REVERT: S 60 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7994 (ttm-80) REVERT: T 60 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: V 60 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7986 (ttm-80) REVERT: W 60 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7993 (ttm-80) REVERT: X 60 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7985 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8271 (ttp80) cc_final: 0.8000 (ttm-80) outliers start: 48 outliers final: 48 residues processed: 744 average time/residue: 0.6895 time to fit residues: 609.2196 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 : 1.328 ------------------------------------------------------------------------------- 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=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: 0.0980 chunk 138 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3678 r_free = 0.3678 target = 0.150559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138117 restraints weight = 27256.053| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.75 r_work: 0.3406 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 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 = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1038 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= 0.167 Angle : 0.572 6.193 46728 Z= 0.320 Chirality : 0.039 0.138 4920 Planarity : 0.003 0.035 6144 Dihedral : 4.342 24.395 4512 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.65 % Allowed : 9.50 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.87 (0.13), residues: 4104 helix: 3.84 (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 0.005 0.001 ARG J 60 TYR 0.021 0.003 TYR D 36 PHE 0.018 0.003 PHE L 38 TRP 0.012 0.003 TRP K 90 HIS 0.004 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (34704) covalent geometry : angle 0.57241 / 0.32 (46728) hydrogen bonds : bond 0.05916 / 4.01 ( 2688) hydrogen bonds : angle 3.76687 / 2.71 ( 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 811 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 750 time to evaluate : 1.072 Fit side-chains REVERT: K 60 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7990 (ttm-80) REVERT: N 60 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7985 (ttm-80) REVERT: O 60 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7984 (ttm-80) REVERT: P 60 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7986 (ttm-80) REVERT: R 60 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: S 60 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: T 60 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7982 (ttm-80) REVERT: V 60 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: W 60 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7981 (ttm-80) REVERT: X 60 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7981 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7995 (ttm-80) outliers start: 61 outliers final: 48 residues processed: 750 average time/residue: 0.7107 time to fit residues: 631.8173 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 : 1.182 ------------------------------------------------------------------------------- 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: 5.9990 chunk 251 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.148348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136040 restraints weight = 27543.837| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 0.74 r_work: 0.3372 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1180 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= 0.263 Angle : 0.710 7.090 46728 Z= 0.394 Chirality : 0.046 0.161 4920 Planarity : 0.005 0.058 6144 Dihedral : 4.562 23.620 4512 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 10.25 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.12), residues: 4104 helix: 3.43 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.31 (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 C 36 PHE 0.025 0.004 PHE S 38 TRP 0.013 0.004 TRP K 90 HIS 0.006 0.002 HIS J 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 (34704) covalent geometry : angle 0.70981 / 0.39 (46728) hydrogen bonds : bond 0.06957 / 4.71 ( 2688) hydrogen bonds : angle 3.98270 / 2.86 ( 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 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.261 Fit side-chains REVERT: A 155 MET cc_start: 0.9184 (mtp) cc_final: 0.8888 (mtp) REVERT: B 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8889 (mtp) REVERT: D 155 MET cc_start: 0.9189 (mtp) cc_final: 0.8893 (mtp) REVERT: E 155 MET cc_start: 0.9182 (mtp) cc_final: 0.8885 (mtp) REVERT: H 155 MET cc_start: 0.9190 (mtp) cc_final: 0.8892 (mtp) REVERT: I 155 MET cc_start: 0.9187 (mtp) cc_final: 0.8891 (mtp) REVERT: K 60 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7990 (ttm-80) REVERT: K 155 MET cc_start: 0.9185 (mtp) cc_final: 0.8889 (mtp) REVERT: L 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8890 (mtp) REVERT: M 155 MET cc_start: 0.9185 (mtp) cc_final: 0.8888 (mtp) REVERT: N 60 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7987 (ttm-80) REVERT: N 155 MET cc_start: 0.9185 (mtp) cc_final: 0.8888 (mtp) REVERT: O 60 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: O 155 MET cc_start: 0.9182 (mtp) cc_final: 0.8882 (mtp) REVERT: P 60 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7986 (ttm-80) REVERT: P 155 MET cc_start: 0.9184 (mtp) cc_final: 0.8887 (mtp) REVERT: Q 60 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: Q 155 MET cc_start: 0.9182 (mtp) cc_final: 0.8882 (mtp) REVERT: R 60 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7988 (ttm-80) REVERT: S 60 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7990 (ttm-80) REVERT: S 155 MET cc_start: 0.9190 (mtp) cc_final: 0.8893 (mtp) REVERT: T 60 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7986 (ttm-80) REVERT: T 155 MET cc_start: 0.9183 (mtp) cc_final: 0.8885 (mtp) REVERT: V 60 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7985 (ttm-80) REVERT: V 155 MET cc_start: 0.9181 (mtp) cc_final: 0.8883 (mtp) REVERT: W 60 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7983 (ttm-80) REVERT: W 155 MET cc_start: 0.9183 (mtp) cc_final: 0.8882 (mtp) REVERT: X 60 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7970 (ttm-80) REVERT: X 155 MET cc_start: 0.9188 (mtp) cc_final: 0.8890 (mtp) REVERT: Y 60 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7998 (ttm-80) outliers start: 48 outliers final: 48 residues processed: 744 average time/residue: 0.6831 time to fit residues: 603.5057 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 : 1.312 ------------------------------------------------------------------------------- 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: 10.0000 chunk 330 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 349 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 289 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 381 optimal weight: 9.9990 chunk 404 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3667 r_free = 0.3667 target = 0.149786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137366 restraints weight = 27358.858| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.74 r_work: 0.3407 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 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 = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34704 Z= 0.183 Angle : 0.602 6.604 46728 Z= 0.336 Chirality : 0.040 0.141 4920 Planarity : 0.004 0.057 6144 Dihedral : 4.419 24.286 4512 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.30 % Allowed : 9.79 % Favored : 88.91 % 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: 4.69 (0.13), residues: 4104 helix: 3.72 (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 0.007 0.001 ARG A 60 TYR 0.022 0.003 TYR J 36 PHE 0.019 0.003 PHE H 38 TRP 0.013 0.003 TRP Y 90 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (34704) covalent geometry : angle 0.60202 / 0.34 (46728) hydrogen bonds : bond 0.06101 / 4.14 ( 2688) hydrogen bonds : angle 3.83333 / 2.76 ( 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 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.442 Fit side-chains REVERT: K 60 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7941 (ttm-80) REVERT: N 60 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7943 (ttm-80) REVERT: O 60 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7936 (ttm-80) REVERT: P 60 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7939 (ttm-80) REVERT: Q 60 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7936 (ttm-80) REVERT: R 60 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7939 (ttm-80) REVERT: S 60 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7942 (ttm-80) REVERT: T 60 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7938 (ttm-80) REVERT: V 60 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7935 (ttm-80) REVERT: W 60 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: X 60 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7936 (ttm-80) REVERT: Y 60 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7944 (ttm-80) outliers start: 48 outliers final: 48 residues processed: 744 average time/residue: 0.6791 time to fit residues: 600.8110 Evaluate side-chains 795 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 747 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 255 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 395 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.149162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136730 restraints weight = 27276.078| |-----------------------------------------------------------------------------| r_work (start): 0.3502 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: 2.08 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 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 = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34704 Z= 0.206 Angle : 0.639 6.816 46728 Z= 0.356 Chirality : 0.043 0.149 4920 Planarity : 0.004 0.058 6144 Dihedral : 4.460 24.214 4512 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.30 % Allowed : 10.01 % Favored : 88.69 % 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: 4.53 (0.12), residues: 4104 helix: 3.60 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.39 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 60 TYR 0.023 0.003 TYR J 36 PHE 0.021 0.004 PHE S 38 TRP 0.013 0.003 TRP X 90 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (34704) covalent geometry : angle 0.63949 / 0.36 (46728) hydrogen bonds : bond 0.06459 / 4.38 ( 2688) hydrogen bonds : angle 3.89836 / 2.80 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15997.36 seconds wall clock time: 272 minutes 38.26 seconds (16358.26 seconds total)