Starting phenix.real_space_refine on Tue Aug 26 11:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sht_10205/08_2025/6sht_10205_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sht_10205/08_2025/6sht_10205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sht_10205/08_2025/6sht_10205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sht_10205/08_2025/6sht_10205.map" model { file = "/net/cci-nas-00/data/ceres_data/6sht_10205/08_2025/6sht_10205_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sht_10205/08_2025/6sht_10205_neut.cif" } resolution = 2.73 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= 0.001 sd= 0.015 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 192 5.16 5 C 22296 2.51 5 N 6264 2.21 5 O 8352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37152 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} Conformer: "B" Number of residues, atoms: 174, 1425 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169} bond proxies already assigned to first conformer: 1397 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2, 'water': 72} Link IDs: {None: 73} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Residues with excluded nonbonded symmetry interactions: 48 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb=" O HOH A 359 " occ=0.33 residue: pdb="FE FE B 201 " occ=0.25 residue: pdb=" O HOH B 359 " occ=0.33 residue: pdb="FE FE C 201 " occ=0.25 residue: pdb=" O HOH C 359 " occ=0.33 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb=" O HOH D 359 " occ=0.33 residue: pdb="FE FE E 201 " occ=0.25 residue: pdb=" O HOH E 359 " occ=0.33 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb=" O HOH F 359 " occ=0.33 ... (remaining 36 not shown) Time building chain proxies: 4.36, per 1000 atoms: 0.12 Number of scatterers: 37152 At special positions: 0 Unit cell: (135.36, 135.36, 135.36, 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 192 16.00 Mg 24 11.99 O 8352 8.00 N 6264 7.00 C 22296 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: 3.55 Conformation dependent library (CDL) restraints added in 2.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 120 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 40 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 120 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 40 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 120 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 40 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 120 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 40 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 120 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 40 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 120 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR F 165 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 40 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 120 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR G 165 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 40 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 120 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR H 165 " --> pdb=" O GLY H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 40 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 120 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR I 165 " --> pdb=" O GLY I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 40 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 120 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 40 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 120 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR K 165 " --> pdb=" O GLY K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 40 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 120 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR L 165 " --> pdb=" O GLY L 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 40 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 120 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR M 165 " --> pdb=" O GLY M 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 40 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 120 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR N 165 " --> pdb=" O GLY N 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 40 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 120 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR O 165 " --> pdb=" O GLY O 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 40 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 120 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR P 165 " --> pdb=" O GLY P 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 40 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 120 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR Q 165 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 120 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR R 165 " --> pdb=" O GLY R 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 40 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 120 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR S 165 " --> pdb=" O GLY S 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 40 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 120 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR T 165 " --> pdb=" O GLY T 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 40 Processing helix chain 'U' and resid 45 through 73 Processing helix chain 'U' and resid 92 through 120 Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR U 165 " --> pdb=" O GLY U 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 40 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 120 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR V 165 " --> pdb=" O GLY V 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 40 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 120 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR W 165 " --> pdb=" O GLY W 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 40 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 120 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7776 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: 6.88 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9888 1.33 - 1.46: 8088 1.46 - 1.58: 17976 1.58 - 1.71: 48 1.71 - 1.84: 312 Bond restraints: 36312 Sorted by residual: bond pdb=" CA ALA D 157 " pdb=" CB ALA D 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA M 157 " pdb=" CB ALA M 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA B 157 " pdb=" CB ALA B 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA E 157 " pdb=" CB ALA E 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA K 157 " pdb=" CB ALA K 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 ... (remaining 36307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 42168 2.15 - 4.30: 5880 4.30 - 6.44: 888 6.44 - 8.59: 144 8.59 - 10.74: 24 Bond angle restraints: 49104 Sorted by residual: angle pdb=" N HIS B 170 " pdb=" CA HIS B 170 " pdb=" C HIS B 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS D 170 " pdb=" CA HIS D 170 " pdb=" C HIS D 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS Q 170 " pdb=" CA HIS Q 170 " pdb=" C HIS Q 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS U 170 " pdb=" CA HIS U 170 " pdb=" C HIS U 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS J 170 " pdb=" CA HIS J 170 " pdb=" C HIS J 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 ... (remaining 49099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 21504 35.95 - 71.90: 1032 71.90 - 107.85: 24 107.85 - 143.80: 0 143.80 - 179.75: 24 Dihedral angle restraints: 22584 sinusoidal: 9456 harmonic: 13128 Sorted by residual: dihedral pdb=" CD BARG A 60 " pdb=" NE BARG A 60 " pdb=" CZ BARG A 60 " pdb=" NH1BARG A 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG C 60 " pdb=" NE BARG C 60 " pdb=" CZ BARG C 60 " pdb=" NH1BARG C 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 60 " pdb=" NE BARG D 60 " pdb=" CZ BARG D 60 " pdb=" NH1BARG D 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 22581 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.054: 2664 0.054 - 0.105: 1848 0.105 - 0.157: 504 0.157 - 0.209: 72 0.209 - 0.261: 24 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CA VAL I 43 " pdb=" N VAL I 43 " pdb=" C VAL I 43 " pdb=" CB VAL I 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL C 43 " pdb=" N VAL C 43 " pdb=" C VAL C 43 " pdb=" CB VAL C 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL K 43 " pdb=" N VAL K 43 " pdb=" C VAL K 43 " pdb=" CB VAL K 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5109 not shown) Planarity restraints: 6480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR F 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR F 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR L 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR L 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR L 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR L 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR G 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR G 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR G 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 134 " -0.018 2.00e-02 2.50e+03 ... (remaining 6477 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 60 0.98 - 1.96: 48 1.96 - 2.94: 16140 2.94 - 3.92: 107076 3.92 - 4.90: 208788 Warning: very small nonbonded interaction distances. Nonbonded interactions: 332112 Sorted by model distance: nonbonded pdb="FE FE D 201 " pdb="FE FE J 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE M 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE V 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE M 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE V 201 " model vdw 0.000 1.480 ... (remaining 332107 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=0.00 max=1.00 mean=0.93 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.890 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 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 : 0.015 0.083 36312 Z= 0.882 Angle : 1.547 10.740 49104 Z= 1.010 Chirality : 0.070 0.261 5112 Planarity : 0.007 0.040 6480 Dihedral : 19.276 179.750 14184 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.84 % Rotamer: Outliers : 5.56 % Allowed : 13.58 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.11), residues: 4320 helix: -1.81 (0.07), residues: 3384 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG E 40 TYR 0.038 0.007 TYR D 134 PHE 0.034 0.009 PHE T 48 TRP 0.010 0.005 TRP S 90 HIS 0.007 0.003 HIS G 125 Details of bonding type rmsd covalent geometry : bond 0.01539 (36312) covalent geometry : angle 1.54698 (49104) hydrogen bonds : bond 0.24973 ( 2640) hydrogen bonds : angle 7.00923 ( 7776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1344 time to evaluate : 1.539 Fit side-chains REVERT: A 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: A 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: A 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: B 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: B 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: B 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: C 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: C 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: C 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: D 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: D 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: D 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: E 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: E 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: E 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: F 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: F 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: F 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: G 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: G 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: G 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: H 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: H 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: H 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: I 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: I 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: I 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: J 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: J 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: J 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: K 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: K 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: K 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: L 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: L 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: L 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: M 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: M 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: M 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) REVERT: N 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: N 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: N 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: O 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: O 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: O 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: P 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: P 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: P 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: Q 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: Q 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: Q 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: R 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: R 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: R 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: S 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: S 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: S 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: T 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: T 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: T 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: U 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: U 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: U 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) REVERT: V 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: V 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: V 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: W 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: W 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: W 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: X 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: X 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: X 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) outliers start: 192 outliers final: 24 residues processed: 1392 average time/residue: 0.9276 time to fit residues: 1500.5830 Evaluate side-chains 1026 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 978 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 131 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 131 GLU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain V residue 131 GLU Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain X residue 131 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.0270 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS B 72 GLN B 95 ASN C 22 ASN C 72 GLN C 95 ASN D 57 HIS ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS F 62 HIS F 72 GLN ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 57 HIS G 72 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 GLN H 72 GLN I 72 GLN K 72 GLN L 22 ASN L 72 GLN M 22 ASN M 55 GLN M 95 ASN M 108 ASN N 8 ASN N 57 HIS ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 72 GLN Q 72 GLN R 72 GLN R 95 ASN ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS S 72 GLN T 57 HIS T 72 GLN U 57 HIS U 72 GLN U 151 ASN V 8 ASN V 72 GLN W 22 ASN W 57 HIS W 95 ASN X 72 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.099993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.078128 restraints weight = 236334.585| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.45 r_work: 0.2410 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1471 | |-----------------------------------------------------------------------------| r_final: 0.2390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.176 36312 Z= 0.406 Angle : 1.833 41.146 49104 Z= 0.926 Chirality : 0.071 0.676 5112 Planarity : 0.016 0.169 6480 Dihedral : 14.715 179.699 5136 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.24 % Favored : 95.11 % Rotamer: Outliers : 7.07 % Allowed : 18.83 % Favored : 74.10 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.11), residues: 4320 helix: -0.70 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -1.72 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.004 ARG D 40 TYR 0.125 0.010 TYR V 9 PHE 0.091 0.007 PHE N 52 TRP 0.081 0.009 TRP D 90 HIS 0.072 0.008 HIS P 148 Details of bonding type rmsd covalent geometry : bond 0.00847 (36312) covalent geometry : angle 1.83273 (49104) hydrogen bonds : bond 0.12579 ( 2640) hydrogen bonds : angle 5.58187 ( 7776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1182 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8735 (mmt-90) cc_final: 0.8468 (mmt180) REVERT: A 138 GLN cc_start: 0.9139 (tp40) cc_final: 0.8922 (tp-100) REVERT: B 138 GLN cc_start: 0.9090 (tp40) cc_final: 0.8827 (tp-100) REVERT: C 76 ARG cc_start: 0.8702 (mmt-90) cc_final: 0.8446 (mmt180) REVERT: C 138 GLN cc_start: 0.9202 (tp40) cc_final: 0.8959 (mm-40) REVERT: D 8 ASN cc_start: 0.8910 (t0) cc_final: 0.8464 (t0) REVERT: D 76 ARG cc_start: 0.8710 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: E 76 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8333 (mmt180) REVERT: E 138 GLN cc_start: 0.9079 (tp40) cc_final: 0.8872 (tp-100) REVERT: G 116 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7195 (mtpp) REVERT: G 138 GLN cc_start: 0.9174 (tp40) cc_final: 0.8957 (tp-100) REVERT: H 41 ASP cc_start: 0.8719 (p0) cc_final: 0.8057 (p0) REVERT: H 76 ARG cc_start: 0.8745 (mmt-90) cc_final: 0.8338 (mmt180) REVERT: H 106 SER cc_start: 0.8505 (p) cc_final: 0.8288 (m) REVERT: I 46 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8271 (ttmm) REVERT: I 65 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8271 (mttm) REVERT: I 76 ARG cc_start: 0.8833 (mmt-90) cc_final: 0.8459 (mmt-90) REVERT: J 46 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7770 (ttmt) REVERT: J 141 SER cc_start: 0.8911 (m) cc_final: 0.8698 (m) REVERT: K 81 ASP cc_start: 0.8252 (m-30) cc_final: 0.7927 (m-30) REVERT: K 91 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: K 138 GLN cc_start: 0.9251 (tp40) cc_final: 0.9003 (tp-100) REVERT: L 8 ASN cc_start: 0.8792 (t0) cc_final: 0.8518 (t0) REVERT: L 76 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8374 (mmt-90) REVERT: M 46 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8061 (ttmt) REVERT: M 76 ARG cc_start: 0.8691 (mmt-90) cc_final: 0.8420 (mmt180) REVERT: M 91 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: M 141 SER cc_start: 0.8835 (m) cc_final: 0.8630 (m) REVERT: N 6 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8920 (ttt90) REVERT: N 76 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8358 (mpt180) REVERT: N 116 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7181 (mtpp) REVERT: O 8 ASN cc_start: 0.8865 (t0) cc_final: 0.8501 (t0) REVERT: O 19 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7899 (mtt90) REVERT: O 46 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7619 (ttmt) REVERT: O 91 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: O 141 SER cc_start: 0.8838 (m) cc_final: 0.8600 (m) REVERT: P 76 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8463 (mmt-90) REVERT: P 138 GLN cc_start: 0.9058 (tp40) cc_final: 0.8851 (tp-100) REVERT: R 42 ASP cc_start: 0.8848 (p0) cc_final: 0.8602 (p0) REVERT: R 46 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8012 (ttmt) REVERT: R 81 ASP cc_start: 0.8253 (m-30) cc_final: 0.7962 (m-30) REVERT: R 138 GLN cc_start: 0.8991 (tp40) cc_final: 0.8728 (mm-40) REVERT: S 19 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8122 (mtm110) REVERT: S 76 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.8179 (mpt180) REVERT: T 46 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7772 (ttmt) REVERT: U 46 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8298 (ttmm) REVERT: U 138 GLN cc_start: 0.9032 (tp40) cc_final: 0.8786 (tp-100) REVERT: U 141 SER cc_start: 0.8652 (m) cc_final: 0.8411 (m) REVERT: V 6 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8899 (ttt180) REVERT: V 76 ARG cc_start: 0.8694 (mmt-90) cc_final: 0.8417 (mmt180) REVERT: W 19 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8005 (mtt90) REVERT: W 46 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8275 (ttmm) REVERT: W 76 ARG cc_start: 0.8730 (mmt-90) cc_final: 0.8487 (mmt-90) REVERT: W 106 SER cc_start: 0.8636 (p) cc_final: 0.8399 (m) REVERT: X 76 ARG cc_start: 0.8761 (mmt-90) cc_final: 0.8504 (mmt180) REVERT: X 106 SER cc_start: 0.8395 (p) cc_final: 0.8159 (m) outliers start: 244 outliers final: 64 residues processed: 1241 average time/residue: 0.7664 time to fit residues: 1113.0858 Evaluate side-chains 1071 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 997 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 162 MET Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 91 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 58 GLU Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 89 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 86 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain U residue 86 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 86 ASP Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 260 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 397 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN C 72 GLN C 102 HIS D 95 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 95 ASN F 95 ASN F 102 HIS G 95 ASN H 20 GLN H 80 GLN H 108 ASN J 80 GLN K 10 HIS K 57 HIS K 72 GLN L 8 ASN L 95 ASN M 108 ASN N 8 ASN N 102 HIS O 8 ASN P 72 GLN P 109 GLN Q 72 GLN Q 80 GLN R 10 HIS S 95 ASN T 80 GLN T 95 ASN U 95 ASN U 108 ASN V 72 GLN V 95 ASN W 72 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.108846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.085883 restraints weight = 289754.551| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.79 r_work: 0.2619 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1471 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1469 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36312 Z= 0.144 Angle : 0.553 6.332 49104 Z= 0.306 Chirality : 0.038 0.145 5112 Planarity : 0.004 0.048 6480 Dihedral : 13.052 178.909 4976 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.46 % Allowed : 0.80 % Favored : 98.74 % Rotamer: Outliers : 2.42 % Allowed : 24.43 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.12), residues: 4320 helix: 2.76 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -1.11 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 73 TYR 0.021 0.001 TYR V 134 PHE 0.015 0.002 PHE B 48 TRP 0.012 0.001 TRP I 90 HIS 0.007 0.001 HIS J 115 Details of bonding type rmsd covalent geometry : bond 0.00278 (36312) covalent geometry : angle 0.55253 (49104) hydrogen bonds : bond 0.06337 ( 2640) hydrogen bonds : angle 3.83096 ( 7776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1131 time to evaluate : 1.447 Fit side-chains REVERT: A 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7448 (p0) REVERT: A 42 ASP cc_start: 0.8649 (p0) cc_final: 0.8375 (p0) REVERT: A 46 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7953 (ttmm) REVERT: A 62 HIS cc_start: 0.8430 (m170) cc_final: 0.8210 (m170) REVERT: A 68 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7583 (ttpp) REVERT: A 76 ARG cc_start: 0.8741 (mmt-90) cc_final: 0.8491 (mpt180) REVERT: A 141 SER cc_start: 0.8831 (m) cc_final: 0.8536 (m) REVERT: B 41 ASP cc_start: 0.8435 (p0) cc_final: 0.7397 (p0) REVERT: B 46 LYS cc_start: 0.8316 (ttpp) cc_final: 0.7975 (ttmm) REVERT: B 62 HIS cc_start: 0.8411 (m170) cc_final: 0.8187 (m170) REVERT: B 68 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7520 (ttpp) REVERT: C 41 ASP cc_start: 0.8475 (p0) cc_final: 0.7531 (p0) REVERT: C 46 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7984 (ttmm) REVERT: C 68 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7447 (ttpp) REVERT: C 76 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8105 (mmt180) REVERT: C 78 PHE cc_start: 0.8980 (m-80) cc_final: 0.8555 (m-80) REVERT: C 141 SER cc_start: 0.8793 (m) cc_final: 0.8514 (m) REVERT: D 41 ASP cc_start: 0.8409 (p0) cc_final: 0.7375 (p0) REVERT: D 42 ASP cc_start: 0.8599 (p0) cc_final: 0.8363 (p0) REVERT: D 46 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7825 (ttmm) REVERT: D 62 HIS cc_start: 0.8457 (m170) cc_final: 0.8246 (m170) REVERT: D 68 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7533 (ttpp) REVERT: D 76 ARG cc_start: 0.8820 (mmt-90) cc_final: 0.8356 (mpt180) REVERT: D 78 PHE cc_start: 0.8906 (m-80) cc_final: 0.8544 (m-80) REVERT: D 141 SER cc_start: 0.8741 (m) cc_final: 0.8430 (p) REVERT: E 41 ASP cc_start: 0.8497 (p0) cc_final: 0.7459 (p0) REVERT: E 46 LYS cc_start: 0.8383 (ttpp) cc_final: 0.7977 (ttmm) REVERT: E 68 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7417 (ttpp) REVERT: E 76 ARG cc_start: 0.8756 (mmt-90) cc_final: 0.8463 (mmt180) REVERT: F 41 ASP cc_start: 0.8545 (p0) cc_final: 0.7433 (p0) REVERT: F 46 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7899 (ttmm) REVERT: F 68 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7448 (ttpp) REVERT: G 41 ASP cc_start: 0.8372 (p0) cc_final: 0.7375 (p0) REVERT: G 42 ASP cc_start: 0.8509 (p0) cc_final: 0.8218 (p0) REVERT: G 46 LYS cc_start: 0.8350 (ttpp) cc_final: 0.7993 (ttmm) REVERT: G 68 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7445 (ttpp) REVERT: G 76 ARG cc_start: 0.8782 (mmt-90) cc_final: 0.8401 (mmt180) REVERT: G 106 SER cc_start: 0.8500 (p) cc_final: 0.8262 (m) REVERT: G 141 SER cc_start: 0.8799 (m) cc_final: 0.8517 (m) REVERT: H 41 ASP cc_start: 0.8556 (p0) cc_final: 0.7613 (p0) REVERT: H 42 ASP cc_start: 0.8629 (p0) cc_final: 0.8366 (p0) REVERT: H 46 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7738 (ttpp) REVERT: H 68 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7543 (ttpp) REVERT: H 76 ARG cc_start: 0.8733 (mmt-90) cc_final: 0.8433 (mpt180) REVERT: I 46 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7912 (ttmm) REVERT: I 68 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7576 (ttpp) REVERT: I 76 ARG cc_start: 0.8758 (mmt-90) cc_final: 0.8331 (mmt180) REVERT: I 141 SER cc_start: 0.8825 (m) cc_final: 0.8610 (m) REVERT: J 8 ASN cc_start: 0.8937 (t0) cc_final: 0.8553 (t0) REVERT: J 41 ASP cc_start: 0.8308 (p0) cc_final: 0.7368 (p0) REVERT: J 42 ASP cc_start: 0.8767 (p0) cc_final: 0.8443 (p0) REVERT: J 46 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7911 (ttmm) REVERT: J 68 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7557 (ttpp) REVERT: J 76 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8433 (mmt180) REVERT: J 141 SER cc_start: 0.8785 (m) cc_final: 0.8551 (p) REVERT: K 42 ASP cc_start: 0.8668 (p0) cc_final: 0.8411 (p0) REVERT: K 46 LYS cc_start: 0.8364 (ttpp) cc_final: 0.7956 (ttmm) REVERT: K 68 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7536 (ttpp) REVERT: K 76 ARG cc_start: 0.8755 (mmt-90) cc_final: 0.8331 (mpt180) REVERT: K 81 ASP cc_start: 0.8484 (m-30) cc_final: 0.8105 (m-30) REVERT: K 106 SER cc_start: 0.8468 (p) cc_final: 0.8231 (m) REVERT: K 141 SER cc_start: 0.8766 (m) cc_final: 0.8488 (m) REVERT: L 41 ASP cc_start: 0.7986 (p0) cc_final: 0.7131 (p0) REVERT: L 42 ASP cc_start: 0.8498 (p0) cc_final: 0.8149 (p0) REVERT: L 46 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7957 (ttmm) REVERT: L 68 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7447 (ttpp) REVERT: L 76 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8230 (mpt180) REVERT: L 141 SER cc_start: 0.8745 (m) cc_final: 0.8484 (m) REVERT: M 41 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.7589 (p0) REVERT: M 46 LYS cc_start: 0.8394 (ttpp) cc_final: 0.7907 (ttmm) REVERT: M 68 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7539 (ttpp) REVERT: M 76 ARG cc_start: 0.8805 (mmt-90) cc_final: 0.8534 (mpt180) REVERT: M 141 SER cc_start: 0.8763 (m) cc_final: 0.8499 (p) REVERT: N 19 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7935 (mtt90) REVERT: N 46 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7964 (ttmm) REVERT: N 68 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7528 (ttpp) REVERT: N 76 ARG cc_start: 0.8758 (mmt-90) cc_final: 0.8391 (mmt180) REVERT: N 141 SER cc_start: 0.8775 (m) cc_final: 0.8472 (p) REVERT: O 46 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7911 (ttmm) REVERT: O 68 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7611 (ttpp) REVERT: O 76 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.8329 (mpt180) REVERT: O 141 SER cc_start: 0.8760 (m) cc_final: 0.8549 (m) REVERT: P 41 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7318 (p0) REVERT: P 46 LYS cc_start: 0.8398 (ttpp) cc_final: 0.7993 (ttmm) REVERT: P 62 HIS cc_start: 0.8391 (m170) cc_final: 0.8190 (m170) REVERT: P 68 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7632 (ttpp) REVERT: P 76 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8326 (mpt180) REVERT: P 141 SER cc_start: 0.8757 (m) cc_final: 0.8537 (m) REVERT: Q 41 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7363 (p0) REVERT: Q 42 ASP cc_start: 0.8775 (p0) cc_final: 0.8495 (p0) REVERT: Q 46 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7948 (ttmm) REVERT: Q 68 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7556 (ttpp) REVERT: R 41 ASP cc_start: 0.8023 (p0) cc_final: 0.7175 (p0) REVERT: R 46 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8083 (ttmm) REVERT: R 62 HIS cc_start: 0.8452 (m170) cc_final: 0.8239 (m170) REVERT: R 68 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7504 (ttpp) REVERT: R 76 ARG cc_start: 0.8802 (mmt-90) cc_final: 0.8432 (mpt180) REVERT: R 81 ASP cc_start: 0.8417 (m-30) cc_final: 0.8026 (m-30) REVERT: R 106 SER cc_start: 0.8534 (p) cc_final: 0.8265 (m) REVERT: R 141 SER cc_start: 0.8810 (m) cc_final: 0.8561 (m) REVERT: S 41 ASP cc_start: 0.8556 (p0) cc_final: 0.7424 (p0) REVERT: S 42 ASP cc_start: 0.8662 (p0) cc_final: 0.8363 (p0) REVERT: S 46 LYS cc_start: 0.8314 (ttpp) cc_final: 0.7993 (ttmm) REVERT: S 61 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7337 (pt0) REVERT: S 68 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7554 (ttpp) REVERT: S 76 ARG cc_start: 0.8651 (mmt-90) cc_final: 0.8231 (mpt180) REVERT: T 41 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7039 (p0) REVERT: T 46 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7875 (ttmm) REVERT: T 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7488 (ttpp) REVERT: T 76 ARG cc_start: 0.8868 (mmt-90) cc_final: 0.8487 (mmt180) REVERT: T 141 SER cc_start: 0.8789 (m) cc_final: 0.8543 (m) REVERT: U 41 ASP cc_start: 0.8341 (p0) cc_final: 0.7222 (p0) REVERT: U 42 ASP cc_start: 0.8512 (p0) cc_final: 0.8269 (p0) REVERT: U 68 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7403 (ttpp) REVERT: U 76 ARG cc_start: 0.8842 (mmt-90) cc_final: 0.8521 (mmt180) REVERT: U 109 GLN cc_start: 0.8225 (tp40) cc_final: 0.8010 (tp-100) REVERT: U 141 SER cc_start: 0.8768 (m) cc_final: 0.8521 (p) REVERT: V 41 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7547 (p0) REVERT: V 46 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7941 (ttmm) REVERT: V 68 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7607 (ttpp) REVERT: V 76 ARG cc_start: 0.8695 (mmt-90) cc_final: 0.8481 (mpt180) REVERT: V 141 SER cc_start: 0.8831 (m) cc_final: 0.8572 (m) REVERT: W 41 ASP cc_start: 0.8349 (p0) cc_final: 0.7276 (p0) REVERT: W 42 ASP cc_start: 0.8611 (p0) cc_final: 0.8327 (p0) REVERT: W 46 LYS cc_start: 0.8363 (ttpp) cc_final: 0.7945 (ttmm) REVERT: W 68 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7615 (ttpp) REVERT: W 141 SER cc_start: 0.8794 (m) cc_final: 0.8507 (m) REVERT: X 41 ASP cc_start: 0.8464 (p0) cc_final: 0.7401 (p0) REVERT: X 42 ASP cc_start: 0.8598 (p0) cc_final: 0.8364 (p0) REVERT: X 46 LYS cc_start: 0.8379 (ttpp) cc_final: 0.7980 (ttmm) REVERT: X 68 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7540 (ttpp) REVERT: X 76 ARG cc_start: 0.8730 (mmt-90) cc_final: 0.8512 (mpt180) REVERT: X 141 SER cc_start: 0.8819 (m) cc_final: 0.8535 (m) outliers start: 64 outliers final: 10 residues processed: 1148 average time/residue: 0.7805 time to fit residues: 1053.6249 Evaluate side-chains 1001 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 985 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain V residue 41 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 33 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 351 optimal weight: 5.9990 chunk 117 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 198 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 overall best weight: 2.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 95 ASN B 95 ASN C 8 ASN C 102 HIS D 8 ASN F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 95 ASN I 8 ASN K 8 ASN K 95 ASN L 8 ASN M 8 ASN O 8 ASN O 95 ASN P 8 ASN Q 8 ASN Q 95 ASN R 8 ASN R 115 HIS T 8 ASN U 8 ASN V 8 ASN X 8 ASN X 95 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.083688 restraints weight = 296808.663| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.83 r_work: 0.2594 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1469 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36312 Z= 0.162 Angle : 0.537 6.910 49104 Z= 0.294 Chirality : 0.039 0.136 5112 Planarity : 0.003 0.034 6480 Dihedral : 13.011 179.994 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 1.31 % Favored : 98.26 % Rotamer: Outliers : 2.55 % Allowed : 26.13 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.34 (0.12), residues: 4320 helix: 3.73 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.85 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 76 TYR 0.018 0.001 TYR P 134 PHE 0.016 0.002 PHE B 48 TRP 0.009 0.001 TRP Q 90 HIS 0.007 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00353 (36312) covalent geometry : angle 0.53691 (49104) hydrogen bonds : bond 0.06985 ( 2640) hydrogen bonds : angle 3.60891 ( 7776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1005 time to evaluate : 1.514 Fit side-chains REVERT: A 41 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7452 (p0) REVERT: A 42 ASP cc_start: 0.8610 (p0) cc_final: 0.8333 (p0) REVERT: A 46 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8072 (ttmm) REVERT: A 62 HIS cc_start: 0.8363 (m170) cc_final: 0.8113 (m170) REVERT: A 68 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7582 (ttpp) REVERT: A 76 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8318 (mmt180) REVERT: A 141 SER cc_start: 0.8806 (m) cc_final: 0.8483 (m) REVERT: B 41 ASP cc_start: 0.8569 (p0) cc_final: 0.7476 (p0) REVERT: B 62 HIS cc_start: 0.8341 (m170) cc_final: 0.8075 (m170) REVERT: B 68 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7586 (ttpp) REVERT: C 41 ASP cc_start: 0.8562 (p0) cc_final: 0.7680 (p0) REVERT: C 42 ASP cc_start: 0.8465 (p0) cc_final: 0.8264 (p0) REVERT: C 46 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8029 (ttmm) REVERT: C 68 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7565 (ttpp) REVERT: C 76 ARG cc_start: 0.8781 (mmt-90) cc_final: 0.8438 (mmt180) REVERT: D 41 ASP cc_start: 0.8590 (p0) cc_final: 0.7504 (p0) REVERT: D 42 ASP cc_start: 0.8629 (p0) cc_final: 0.8375 (p0) REVERT: D 46 LYS cc_start: 0.8446 (ttpp) cc_final: 0.7989 (ttmm) REVERT: D 68 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7541 (ttpp) REVERT: D 76 ARG cc_start: 0.8874 (mmt-90) cc_final: 0.8356 (mmt180) REVERT: D 141 SER cc_start: 0.8774 (m) cc_final: 0.8466 (m) REVERT: E 41 ASP cc_start: 0.8601 (p0) cc_final: 0.7501 (p0) REVERT: E 46 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8036 (ttmm) REVERT: E 68 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7528 (ttpp) REVERT: E 76 ARG cc_start: 0.8879 (mmt-90) cc_final: 0.8557 (mpt180) REVERT: F 41 ASP cc_start: 0.8563 (p0) cc_final: 0.7467 (p0) REVERT: F 61 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7487 (pt0) REVERT: F 68 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7524 (ttpp) REVERT: G 41 ASP cc_start: 0.8605 (p0) cc_final: 0.7623 (p0) REVERT: G 42 ASP cc_start: 0.8522 (p0) cc_final: 0.8228 (p0) REVERT: G 46 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8077 (ttmm) REVERT: G 68 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7529 (ttpp) REVERT: G 141 SER cc_start: 0.8806 (m) cc_final: 0.8489 (m) REVERT: H 41 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.7704 (p0) REVERT: H 42 ASP cc_start: 0.8658 (p0) cc_final: 0.8367 (p0) REVERT: H 46 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8079 (ttmm) REVERT: H 68 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7639 (ttpp) REVERT: H 76 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8498 (mpt180) REVERT: I 41 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.7556 (p0) REVERT: I 46 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8054 (ttmm) REVERT: I 68 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7533 (ttpp) REVERT: I 76 ARG cc_start: 0.8834 (mmt-90) cc_final: 0.8297 (mpt180) REVERT: I 141 SER cc_start: 0.8812 (m) cc_final: 0.8559 (m) REVERT: J 8 ASN cc_start: 0.9034 (t0) cc_final: 0.8437 (t0) REVERT: J 41 ASP cc_start: 0.8467 (p0) cc_final: 0.7551 (p0) REVERT: J 46 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7878 (ttmm) REVERT: J 68 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7543 (ttpp) REVERT: J 76 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.8343 (mmt180) REVERT: J 141 SER cc_start: 0.8788 (m) cc_final: 0.8540 (m) REVERT: K 42 ASP cc_start: 0.8636 (p0) cc_final: 0.8392 (p0) REVERT: K 46 LYS cc_start: 0.8418 (ttpp) cc_final: 0.7993 (ttmm) REVERT: K 68 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7568 (ttpp) REVERT: K 76 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.8114 (mpt180) REVERT: K 81 ASP cc_start: 0.8541 (m-30) cc_final: 0.8226 (m-30) REVERT: K 141 SER cc_start: 0.8791 (m) cc_final: 0.8450 (m) REVERT: L 41 ASP cc_start: 0.8297 (p0) cc_final: 0.7438 (p0) REVERT: L 46 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8022 (ttmm) REVERT: L 68 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7636 (ttpp) REVERT: L 76 ARG cc_start: 0.8790 (mmt-90) cc_final: 0.8359 (mpt180) REVERT: L 141 SER cc_start: 0.8777 (m) cc_final: 0.8454 (m) REVERT: M 41 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.7632 (p0) REVERT: M 42 ASP cc_start: 0.8726 (p0) cc_final: 0.8495 (p0) REVERT: M 46 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7936 (ttmm) REVERT: M 68 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7550 (ttpp) REVERT: M 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8442 (mmt180) REVERT: M 141 SER cc_start: 0.8765 (m) cc_final: 0.8509 (m) REVERT: N 46 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8089 (ttmm) REVERT: N 68 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7563 (ttpp) REVERT: N 76 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8359 (mpt180) REVERT: N 141 SER cc_start: 0.8754 (m) cc_final: 0.8435 (m) REVERT: O 42 ASP cc_start: 0.8740 (p0) cc_final: 0.8529 (p0) REVERT: O 46 LYS cc_start: 0.8466 (ttpp) cc_final: 0.7935 (ttmm) REVERT: O 68 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7644 (ttpp) REVERT: O 76 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8202 (mpt180) REVERT: O 83 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8480 (mmtt) REVERT: O 141 SER cc_start: 0.8771 (m) cc_final: 0.8522 (m) REVERT: P 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7505 (p0) REVERT: P 46 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8058 (ttmm) REVERT: P 62 HIS cc_start: 0.8353 (m170) cc_final: 0.8099 (m170) REVERT: P 68 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7676 (ttpp) REVERT: P 76 ARG cc_start: 0.8828 (mmt-90) cc_final: 0.8369 (mpt180) REVERT: P 141 SER cc_start: 0.8777 (m) cc_final: 0.8521 (m) REVERT: Q 41 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7483 (p0) REVERT: Q 42 ASP cc_start: 0.8667 (p0) cc_final: 0.8371 (p0) REVERT: Q 46 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8012 (ttmm) REVERT: Q 68 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7515 (ttpp) REVERT: R 41 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7311 (p0) REVERT: R 42 ASP cc_start: 0.8669 (p0) cc_final: 0.8421 (p0) REVERT: R 46 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8112 (ttmm) REVERT: R 62 HIS cc_start: 0.8451 (m170) cc_final: 0.8185 (m170) REVERT: R 68 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7601 (ttpp) REVERT: R 81 ASP cc_start: 0.8582 (m-30) cc_final: 0.8228 (m-30) REVERT: R 141 SER cc_start: 0.8818 (m) cc_final: 0.8528 (m) REVERT: S 41 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.7424 (p0) REVERT: S 42 ASP cc_start: 0.8590 (p0) cc_final: 0.8306 (p0) REVERT: S 68 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7590 (ttpp) REVERT: S 76 ARG cc_start: 0.8680 (mmt-90) cc_final: 0.8351 (mmt-90) REVERT: T 41 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7438 (p0) REVERT: T 42 ASP cc_start: 0.8359 (p0) cc_final: 0.8000 (p0) REVERT: T 46 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7907 (ttmm) REVERT: T 68 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7528 (ttpp) REVERT: T 76 ARG cc_start: 0.8839 (mmt-90) cc_final: 0.8367 (mmt180) REVERT: T 141 SER cc_start: 0.8800 (m) cc_final: 0.8486 (m) REVERT: U 41 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7389 (p0) REVERT: U 42 ASP cc_start: 0.8563 (p0) cc_final: 0.8306 (p0) REVERT: U 46 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8028 (ttmm) REVERT: U 68 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7575 (ttpp) REVERT: U 76 ARG cc_start: 0.8894 (mmt-90) cc_final: 0.8541 (mmt180) REVERT: U 109 GLN cc_start: 0.8175 (tp40) cc_final: 0.7945 (tp-100) REVERT: U 110 SER cc_start: 0.8842 (t) cc_final: 0.8622 (p) REVERT: U 141 SER cc_start: 0.8801 (m) cc_final: 0.8553 (m) REVERT: V 41 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.7581 (p0) REVERT: V 46 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8030 (ttmm) REVERT: V 68 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7609 (ttpp) REVERT: V 76 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8480 (mpt180) REVERT: V 141 SER cc_start: 0.8796 (m) cc_final: 0.8522 (m) REVERT: W 41 ASP cc_start: 0.8532 (p0) cc_final: 0.7440 (p0) REVERT: W 42 ASP cc_start: 0.8559 (p0) cc_final: 0.8221 (p0) REVERT: W 46 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8028 (ttmm) REVERT: W 68 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7567 (ttpp) REVERT: W 76 ARG cc_start: 0.8657 (mpt180) cc_final: 0.8360 (mmt180) REVERT: W 141 SER cc_start: 0.8805 (m) cc_final: 0.8473 (m) REVERT: X 41 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7427 (p0) REVERT: X 42 ASP cc_start: 0.8529 (p0) cc_final: 0.8285 (p0) REVERT: X 46 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8049 (ttmm) REVERT: X 68 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7618 (ttpp) REVERT: X 76 ARG cc_start: 0.8859 (mmt-90) cc_final: 0.8503 (mpt180) REVERT: X 141 SER cc_start: 0.8810 (m) cc_final: 0.8499 (m) outliers start: 70 outliers final: 38 residues processed: 1038 average time/residue: 0.8205 time to fit residues: 1006.9041 Evaluate side-chains 1015 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 964 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 174 HIS Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 180 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 337 optimal weight: 8.9990 chunk 289 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN C 8 ASN D 8 ASN F 8 ASN G 8 ASN I 8 ASN K 8 ASN L 8 ASN M 8 ASN M 138 GLN N 8 ASN O 8 ASN P 8 ASN P 95 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN T 138 GLN U 8 ASN V 8 ASN X 8 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.080490 restraints weight = 300309.908| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.75 r_work: 0.2440 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| r_final: 0.2428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 36312 Z= 0.231 Angle : 0.596 6.710 49104 Z= 0.322 Chirality : 0.042 0.148 5112 Planarity : 0.004 0.048 6480 Dihedral : 13.085 179.988 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.38 % Favored : 98.21 % Rotamer: Outliers : 3.45 % Allowed : 25.75 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.34 (0.12), residues: 4320 helix: 3.71 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.75 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 76 TYR 0.018 0.002 TYR P 134 PHE 0.020 0.002 PHE B 48 TRP 0.006 0.001 TRP Q 90 HIS 0.006 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00551 (36312) covalent geometry : angle 0.59599 (49104) hydrogen bonds : bond 0.08591 ( 2640) hydrogen bonds : angle 3.67155 ( 7776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 971 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8819 (p0) cc_final: 0.8471 (p0) REVERT: A 68 LYS cc_start: 0.8437 (mtpp) cc_final: 0.7842 (ttpp) REVERT: A 76 ARG cc_start: 0.8902 (mmt-90) cc_final: 0.8438 (mmt180) REVERT: B 46 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8215 (ttmm) REVERT: B 68 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7800 (ttpp) REVERT: C 41 ASP cc_start: 0.8661 (p0) cc_final: 0.7733 (p0) REVERT: C 42 ASP cc_start: 0.8784 (p0) cc_final: 0.8533 (p0) REVERT: C 46 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8125 (ttmm) REVERT: C 68 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7789 (ttpp) REVERT: C 76 ARG cc_start: 0.8867 (mmt-90) cc_final: 0.8544 (mmt180) REVERT: D 41 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.7689 (p0) REVERT: D 42 ASP cc_start: 0.8841 (p0) cc_final: 0.8528 (p0) REVERT: D 46 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8191 (ttmm) REVERT: D 68 LYS cc_start: 0.8381 (mtpp) cc_final: 0.7793 (ttpp) REVERT: D 76 ARG cc_start: 0.8948 (mmt-90) cc_final: 0.8406 (mmt180) REVERT: D 110 SER cc_start: 0.9078 (t) cc_final: 0.8834 (m) REVERT: E 41 ASP cc_start: 0.8677 (p0) cc_final: 0.7638 (p0) REVERT: E 68 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7731 (ttpp) REVERT: E 76 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8628 (mpt180) REVERT: E 110 SER cc_start: 0.9043 (t) cc_final: 0.8782 (m) REVERT: F 41 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.7660 (p0) REVERT: F 61 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7452 (pt0) REVERT: F 68 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7735 (ttpp) REVERT: G 42 ASP cc_start: 0.8781 (p0) cc_final: 0.8476 (p0) REVERT: G 46 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8228 (ttmm) REVERT: G 68 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7816 (ttpp) REVERT: H 42 ASP cc_start: 0.8817 (p0) cc_final: 0.8510 (p0) REVERT: H 68 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7732 (ttpp) REVERT: H 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8228 (mmt180) REVERT: I 41 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.7675 (p0) REVERT: I 68 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7753 (ttpp) REVERT: I 76 ARG cc_start: 0.8908 (mmt-90) cc_final: 0.8504 (mpt180) REVERT: I 110 SER cc_start: 0.8949 (t) cc_final: 0.8731 (p) REVERT: J 41 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7652 (p0) REVERT: J 42 ASP cc_start: 0.8785 (p0) cc_final: 0.8407 (p0) REVERT: J 46 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8126 (ttmm) REVERT: J 68 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7775 (ttpp) REVERT: J 76 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8433 (mmt180) REVERT: J 110 SER cc_start: 0.8956 (t) cc_final: 0.8725 (p) REVERT: J 141 SER cc_start: 0.8819 (m) cc_final: 0.8585 (m) REVERT: K 42 ASP cc_start: 0.8806 (p0) cc_final: 0.8495 (p0) REVERT: K 46 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8182 (ttmm) REVERT: K 68 LYS cc_start: 0.8426 (mtpp) cc_final: 0.7819 (ttpp) REVERT: K 76 ARG cc_start: 0.8845 (mmt-90) cc_final: 0.8193 (mpt180) REVERT: K 81 ASP cc_start: 0.8583 (m-30) cc_final: 0.8346 (m-30) REVERT: L 41 ASP cc_start: 0.8540 (p0) cc_final: 0.7656 (p0) REVERT: L 68 LYS cc_start: 0.8463 (mtpp) cc_final: 0.7832 (ttpp) REVERT: L 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8488 (mpt180) REVERT: M 42 ASP cc_start: 0.8836 (p0) cc_final: 0.8618 (p0) REVERT: M 46 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8142 (ttmm) REVERT: M 68 LYS cc_start: 0.8335 (mtpp) cc_final: 0.7737 (ttpp) REVERT: M 76 ARG cc_start: 0.8961 (mmt-90) cc_final: 0.8523 (mmt180) REVERT: M 141 SER cc_start: 0.8823 (m) cc_final: 0.8567 (m) REVERT: N 68 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7838 (ttpp) REVERT: N 76 ARG cc_start: 0.8890 (mmt-90) cc_final: 0.8588 (mpt180) REVERT: O 42 ASP cc_start: 0.8848 (p0) cc_final: 0.8632 (p0) REVERT: O 46 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8173 (ttmm) REVERT: O 68 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7857 (ttpp) REVERT: O 76 ARG cc_start: 0.8848 (mmt-90) cc_final: 0.8225 (mpt180) REVERT: O 83 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8478 (mmtt) REVERT: O 141 SER cc_start: 0.8833 (m) cc_final: 0.8609 (m) REVERT: P 41 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.7681 (p0) REVERT: P 68 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7837 (ttpp) REVERT: P 76 ARG cc_start: 0.8911 (mmt-90) cc_final: 0.8517 (mpt180) REVERT: P 110 SER cc_start: 0.8981 (t) cc_final: 0.8773 (p) REVERT: Q 42 ASP cc_start: 0.8768 (p0) cc_final: 0.8416 (p0) REVERT: Q 46 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8199 (ttmm) REVERT: Q 68 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7769 (ttpp) REVERT: R 41 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7474 (p0) REVERT: R 42 ASP cc_start: 0.8871 (p0) cc_final: 0.8623 (p0) REVERT: R 46 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8313 (ttmm) REVERT: R 68 LYS cc_start: 0.8426 (mtpp) cc_final: 0.7829 (ttpp) REVERT: R 76 ARG cc_start: 0.8884 (mmt-90) cc_final: 0.8184 (mmt180) REVERT: R 81 ASP cc_start: 0.8608 (m-30) cc_final: 0.8310 (m-30) REVERT: S 41 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.7716 (p0) REVERT: S 42 ASP cc_start: 0.8821 (p0) cc_final: 0.8470 (p0) REVERT: S 68 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7724 (ttpp) REVERT: S 76 ARG cc_start: 0.8820 (mmt-90) cc_final: 0.8530 (mmt-90) REVERT: T 41 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.7720 (p0) REVERT: T 42 ASP cc_start: 0.8707 (p0) cc_final: 0.8337 (p0) REVERT: T 46 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8122 (ttmm) REVERT: T 68 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7760 (ttpp) REVERT: T 76 ARG cc_start: 0.8914 (mmt-90) cc_final: 0.8386 (mmt180) REVERT: U 41 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.7713 (p0) REVERT: U 42 ASP cc_start: 0.8786 (p0) cc_final: 0.8442 (p0) REVERT: U 46 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8210 (ttmm) REVERT: U 68 LYS cc_start: 0.8378 (mtpp) cc_final: 0.7744 (ttpp) REVERT: U 76 ARG cc_start: 0.8912 (mmt-90) cc_final: 0.8528 (mmt180) REVERT: U 110 SER cc_start: 0.8942 (t) cc_final: 0.8730 (p) REVERT: V 41 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.7736 (p0) REVERT: V 68 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7773 (ttpp) REVERT: V 76 ARG cc_start: 0.8876 (mmt-90) cc_final: 0.8412 (mpt180) REVERT: V 141 SER cc_start: 0.8849 (m) cc_final: 0.8567 (m) REVERT: W 41 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.7677 (p0) REVERT: W 42 ASP cc_start: 0.8748 (p0) cc_final: 0.8386 (p0) REVERT: W 68 LYS cc_start: 0.8352 (mtpp) cc_final: 0.7742 (ttpp) REVERT: W 76 ARG cc_start: 0.8754 (mpt180) cc_final: 0.8464 (mmt180) REVERT: X 41 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7607 (p0) REVERT: X 42 ASP cc_start: 0.8764 (p0) cc_final: 0.8474 (p0) REVERT: X 46 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8214 (ttmm) REVERT: X 68 LYS cc_start: 0.8466 (mtpp) cc_final: 0.7868 (ttpp) REVERT: X 76 ARG cc_start: 0.8920 (mmt-90) cc_final: 0.8459 (mpt180) outliers start: 105 outliers final: 51 residues processed: 1019 average time/residue: 0.7831 time to fit residues: 941.9000 Evaluate side-chains 1013 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 949 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 174 HIS Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 174 HIS Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 174 HIS Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 3 SER Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 251 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 188 optimal weight: 0.2980 chunk 210 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 394 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN C 8 ASN C 102 HIS D 8 ASN F 8 ASN F 102 HIS F 115 HIS G 8 ASN I 8 ASN J 95 ASN K 8 ASN L 8 ASN M 8 ASN M 95 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN S 102 HIS T 8 ASN U 8 ASN V 8 ASN W 138 GLN X 8 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.090053 restraints weight = 314552.588| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.96 r_work: 0.2591 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1474 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 36312 Z= 0.119 Angle : 0.469 5.630 49104 Z= 0.261 Chirality : 0.036 0.125 5112 Planarity : 0.003 0.032 6480 Dihedral : 12.946 179.353 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.16 % Favored : 98.45 % Rotamer: Outliers : 2.52 % Allowed : 26.72 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.06 (0.12), residues: 4320 helix: 4.24 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.58 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 76 TYR 0.018 0.001 TYR I 37 PHE 0.013 0.002 PHE G 38 TRP 0.009 0.001 TRP N 90 HIS 0.005 0.001 HIS L 102 Details of bonding type rmsd covalent geometry : bond 0.00235 (36312) covalent geometry : angle 0.46928 (49104) hydrogen bonds : bond 0.04920 ( 2640) hydrogen bonds : angle 3.31091 ( 7776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1017 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7128 (p0) REVERT: A 42 ASP cc_start: 0.8358 (p0) cc_final: 0.8106 (p0) REVERT: A 46 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7833 (ttmm) REVERT: A 68 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7491 (ttpp) REVERT: A 76 ARG cc_start: 0.8718 (mmt-90) cc_final: 0.8342 (mmt180) REVERT: A 141 SER cc_start: 0.8680 (m) cc_final: 0.8417 (m) REVERT: B 41 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7155 (p0) REVERT: B 46 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7768 (ttmm) REVERT: B 68 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7710 (ttpm) REVERT: C 41 ASP cc_start: 0.8247 (p0) cc_final: 0.7223 (p0) REVERT: C 42 ASP cc_start: 0.8388 (p0) cc_final: 0.8183 (p0) REVERT: C 46 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7781 (ttmm) REVERT: C 68 LYS cc_start: 0.7694 (mtpp) cc_final: 0.7447 (ttpp) REVERT: C 76 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8302 (mmt180) REVERT: C 141 SER cc_start: 0.8658 (m) cc_final: 0.8398 (m) REVERT: D 41 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7170 (p0) REVERT: D 42 ASP cc_start: 0.8236 (p0) cc_final: 0.8000 (p0) REVERT: D 46 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7635 (mttp) REVERT: D 68 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7514 (ttpp) REVERT: D 76 ARG cc_start: 0.8714 (mmt-90) cc_final: 0.8318 (mmt180) REVERT: D 141 SER cc_start: 0.8679 (m) cc_final: 0.8435 (m) REVERT: E 41 ASP cc_start: 0.8184 (p0) cc_final: 0.7073 (p0) REVERT: E 46 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7804 (ttmm) REVERT: E 68 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7337 (ttpp) REVERT: E 76 ARG cc_start: 0.8780 (mmt-90) cc_final: 0.8416 (mpt180) REVERT: F 41 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7080 (p0) REVERT: F 61 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7372 (pt0) REVERT: F 68 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7373 (ttpp) REVERT: G 41 ASP cc_start: 0.8242 (p0) cc_final: 0.7141 (p0) REVERT: G 42 ASP cc_start: 0.8240 (p0) cc_final: 0.8027 (p0) REVERT: G 46 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7819 (ttmm) REVERT: G 68 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7444 (ttpp) REVERT: G 141 SER cc_start: 0.8688 (m) cc_final: 0.8456 (m) REVERT: H 41 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7325 (p0) REVERT: H 42 ASP cc_start: 0.8382 (p0) cc_final: 0.8161 (p0) REVERT: H 68 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7444 (ttpp) REVERT: H 76 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8403 (mpt180) REVERT: H 83 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8344 (mmtm) REVERT: I 41 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7040 (p0) REVERT: I 46 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7796 (ttmm) REVERT: I 68 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7419 (ttpp) REVERT: I 76 ARG cc_start: 0.8751 (mmt-90) cc_final: 0.8311 (mpt180) REVERT: I 110 SER cc_start: 0.8855 (t) cc_final: 0.8624 (p) REVERT: J 41 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7305 (p0) REVERT: J 46 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7639 (mttp) REVERT: J 68 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7374 (ttpp) REVERT: J 110 SER cc_start: 0.8864 (t) cc_final: 0.8632 (p) REVERT: J 141 SER cc_start: 0.8752 (m) cc_final: 0.8542 (m) REVERT: K 41 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7258 (p0) REVERT: K 42 ASP cc_start: 0.8291 (p0) cc_final: 0.8087 (p0) REVERT: K 46 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7791 (ttmm) REVERT: K 68 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7553 (ttpp) REVERT: K 76 ARG cc_start: 0.8659 (mmt-90) cc_final: 0.8112 (mpt180) REVERT: K 81 ASP cc_start: 0.8606 (m-30) cc_final: 0.8217 (m-30) REVERT: K 141 SER cc_start: 0.8645 (m) cc_final: 0.8371 (m) REVERT: L 41 ASP cc_start: 0.8132 (p0) cc_final: 0.7201 (p0) REVERT: L 46 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7791 (ttmm) REVERT: L 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7521 (ttpp) REVERT: L 76 ARG cc_start: 0.8696 (mmt-90) cc_final: 0.8265 (mpt180) REVERT: L 141 SER cc_start: 0.8672 (m) cc_final: 0.8447 (m) REVERT: M 41 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7148 (p0) REVERT: M 42 ASP cc_start: 0.8354 (p0) cc_final: 0.8100 (p0) REVERT: M 46 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7692 (mttp) REVERT: M 68 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7457 (ttpp) REVERT: M 76 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8065 (mmt180) REVERT: M 78 PHE cc_start: 0.8847 (m-80) cc_final: 0.8629 (m-80) REVERT: M 141 SER cc_start: 0.8764 (m) cc_final: 0.8546 (m) REVERT: N 41 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7413 (p0) REVERT: N 46 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7813 (ttmm) REVERT: N 68 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7714 (ttpm) REVERT: N 76 ARG cc_start: 0.8569 (mmt-90) cc_final: 0.8152 (mmt180) REVERT: N 141 SER cc_start: 0.8667 (m) cc_final: 0.8411 (m) REVERT: O 41 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7392 (p0) REVERT: O 42 ASP cc_start: 0.8411 (p0) cc_final: 0.8209 (p0) REVERT: O 46 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7735 (mttp) REVERT: O 68 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7428 (ttpp) REVERT: O 76 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8256 (mpt180) REVERT: O 83 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8368 (mmtt) REVERT: O 141 SER cc_start: 0.8740 (m) cc_final: 0.8524 (m) REVERT: P 41 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7124 (p0) REVERT: P 46 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7701 (mttp) REVERT: P 68 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7549 (ttpp) REVERT: P 76 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.8299 (mpt180) REVERT: P 110 SER cc_start: 0.8893 (t) cc_final: 0.8651 (p) REVERT: P 141 SER cc_start: 0.8730 (m) cc_final: 0.8522 (m) REVERT: Q 41 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7212 (p0) REVERT: Q 42 ASP cc_start: 0.8288 (p0) cc_final: 0.8019 (p0) REVERT: Q 46 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7815 (ttmm) REVERT: Q 68 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7290 (ttpp) REVERT: R 41 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7005 (p0) REVERT: R 68 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7393 (ttpp) REVERT: R 76 ARG cc_start: 0.8721 (mmt-90) cc_final: 0.8367 (mpt180) REVERT: R 81 ASP cc_start: 0.8637 (m-30) cc_final: 0.8261 (m-30) REVERT: R 141 SER cc_start: 0.8681 (m) cc_final: 0.8429 (m) REVERT: S 41 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7115 (p0) REVERT: S 46 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7636 (mttp) REVERT: S 68 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7426 (ttpp) REVERT: S 76 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8294 (mpt180) REVERT: T 41 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7079 (p0) REVERT: T 46 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7656 (mttp) REVERT: T 68 LYS cc_start: 0.7985 (mtpp) cc_final: 0.7433 (ttpp) REVERT: T 76 ARG cc_start: 0.8714 (mmt-90) cc_final: 0.8338 (mmt180) REVERT: T 141 SER cc_start: 0.8669 (m) cc_final: 0.8414 (m) REVERT: U 41 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7003 (p0) REVERT: U 46 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7693 (mttp) REVERT: U 68 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7407 (ttpp) REVERT: U 76 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8505 (mmt180) REVERT: U 110 SER cc_start: 0.8846 (t) cc_final: 0.8594 (p) REVERT: U 141 SER cc_start: 0.8739 (m) cc_final: 0.8532 (m) REVERT: V 41 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7113 (p0) REVERT: V 46 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7816 (ttmm) REVERT: V 68 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7452 (ttpp) REVERT: V 76 ARG cc_start: 0.8730 (mmt-90) cc_final: 0.8330 (mpt180) REVERT: V 141 SER cc_start: 0.8722 (m) cc_final: 0.8483 (m) REVERT: W 41 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7068 (p0) REVERT: W 46 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7783 (ttmm) REVERT: W 68 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7427 (ttpp) REVERT: W 141 SER cc_start: 0.8680 (m) cc_final: 0.8440 (m) REVERT: X 41 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7118 (p0) REVERT: X 42 ASP cc_start: 0.8269 (p0) cc_final: 0.8023 (p0) REVERT: X 46 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7837 (ttmm) REVERT: X 68 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7554 (ttpp) REVERT: X 76 ARG cc_start: 0.8761 (mmt-90) cc_final: 0.8488 (mpt180) REVERT: X 141 SER cc_start: 0.8666 (m) cc_final: 0.8421 (m) outliers start: 69 outliers final: 14 residues processed: 1035 average time/residue: 0.7514 time to fit residues: 921.0906 Evaluate side-chains 989 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 953 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 346 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 102 HIS C 8 ASN C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN I 95 ASN J 138 GLN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN Q 102 HIS R 8 ASN S 8 ASN S 102 HIS S 138 GLN T 8 ASN U 8 ASN U 102 HIS V 8 ASN V 62 HIS W 20 GLN W 102 HIS X 8 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.088612 restraints weight = 312352.819| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.85 r_work: 0.2628 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1474 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1474 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36312 Z= 0.127 Angle : 0.478 5.637 49104 Z= 0.263 Chirality : 0.036 0.126 5112 Planarity : 0.003 0.039 6480 Dihedral : 12.967 179.916 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.33 % Favored : 98.30 % Rotamer: Outliers : 2.55 % Allowed : 25.72 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.27 (0.12), residues: 4320 helix: 4.37 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.43 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 76 TYR 0.015 0.001 TYR P 134 PHE 0.013 0.002 PHE R 38 TRP 0.005 0.000 TRP N 90 HIS 0.006 0.001 HIS M 102 Details of bonding type rmsd covalent geometry : bond 0.00262 (36312) covalent geometry : angle 0.47783 (49104) hydrogen bonds : bond 0.05339 ( 2640) hydrogen bonds : angle 3.27677 ( 7776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 978 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7394 (p0) REVERT: A 46 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7852 (mttp) REVERT: A 68 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7655 (ttpp) REVERT: A 76 ARG cc_start: 0.8784 (mmt-90) cc_final: 0.8443 (mmt180) REVERT: A 141 SER cc_start: 0.8803 (m) cc_final: 0.8556 (m) REVERT: B 41 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7335 (p0) REVERT: B 46 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7805 (mttp) REVERT: B 68 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7713 (ttpp) REVERT: B 83 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8478 (mmtm) REVERT: B 110 SER cc_start: 0.8950 (t) cc_final: 0.8711 (p) REVERT: C 41 ASP cc_start: 0.8404 (p0) cc_final: 0.7523 (p0) REVERT: C 46 LYS cc_start: 0.8341 (ttpp) cc_final: 0.7861 (mttp) REVERT: C 110 SER cc_start: 0.9006 (t) cc_final: 0.8765 (p) REVERT: C 141 SER cc_start: 0.8794 (m) cc_final: 0.8557 (m) REVERT: D 41 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7328 (p0) REVERT: D 46 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7820 (mttp) REVERT: D 68 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7735 (ttpp) REVERT: D 76 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8434 (mmt180) REVERT: D 141 SER cc_start: 0.8797 (m) cc_final: 0.8560 (m) REVERT: E 41 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7140 (p0) REVERT: E 46 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7967 (ttmm) REVERT: E 68 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7693 (ttpp) REVERT: E 76 ARG cc_start: 0.8920 (mmt-90) cc_final: 0.8574 (mpt180) REVERT: F 41 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7257 (p0) REVERT: F 68 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7663 (ttpp) REVERT: G 41 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7381 (p0) REVERT: G 46 LYS cc_start: 0.8350 (ttpp) cc_final: 0.7843 (mttp) REVERT: G 61 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7555 (pt0) REVERT: G 68 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7686 (ttpp) REVERT: G 141 SER cc_start: 0.8823 (m) cc_final: 0.8586 (m) REVERT: H 41 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7464 (p0) REVERT: H 46 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7908 (mttp) REVERT: H 68 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7626 (ttpp) REVERT: H 76 ARG cc_start: 0.8838 (mmt-90) cc_final: 0.8316 (mmt180) REVERT: H 83 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8468 (mmtt) REVERT: I 41 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7108 (p0) REVERT: I 46 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7965 (ttmm) REVERT: I 68 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7629 (ttpp) REVERT: I 76 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8440 (mpt180) REVERT: I 110 SER cc_start: 0.8935 (t) cc_final: 0.8725 (p) REVERT: J 8 ASN cc_start: 0.8969 (t0) cc_final: 0.8497 (t0) REVERT: J 41 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7307 (p0) REVERT: J 46 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7783 (mttp) REVERT: J 68 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7642 (ttpp) REVERT: J 110 SER cc_start: 0.8919 (t) cc_final: 0.8692 (p) REVERT: J 141 SER cc_start: 0.8870 (m) cc_final: 0.8649 (m) REVERT: K 41 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7268 (p0) REVERT: K 42 ASP cc_start: 0.8320 (p0) cc_final: 0.8077 (p0) REVERT: K 46 LYS cc_start: 0.8335 (ttpp) cc_final: 0.7813 (mttp) REVERT: K 68 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7797 (ttpp) REVERT: K 76 ARG cc_start: 0.8759 (mmt-90) cc_final: 0.8252 (mpt180) REVERT: K 81 ASP cc_start: 0.8639 (m-30) cc_final: 0.8307 (m-30) REVERT: K 110 SER cc_start: 0.8964 (t) cc_final: 0.8746 (p) REVERT: K 141 SER cc_start: 0.8783 (m) cc_final: 0.8527 (m) REVERT: L 41 ASP cc_start: 0.8251 (p0) cc_final: 0.7389 (p0) REVERT: L 46 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7992 (ttmm) REVERT: L 68 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7710 (ttpp) REVERT: L 76 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8456 (mpt180) REVERT: L 141 SER cc_start: 0.8789 (m) cc_final: 0.8562 (m) REVERT: M 41 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7352 (p0) REVERT: M 46 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7931 (mttp) REVERT: M 68 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7656 (ttpp) REVERT: M 76 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8212 (mmt180) REVERT: M 78 PHE cc_start: 0.8939 (m-80) cc_final: 0.8678 (m-80) REVERT: M 141 SER cc_start: 0.8861 (m) cc_final: 0.8656 (m) REVERT: N 41 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7498 (p0) REVERT: N 46 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7936 (ttmm) REVERT: N 68 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7743 (ttpp) REVERT: N 76 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.8266 (mmt180) REVERT: N 141 SER cc_start: 0.8801 (m) cc_final: 0.8554 (m) REVERT: O 41 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7233 (p0) REVERT: O 46 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7899 (mttp) REVERT: O 68 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7658 (ttpp) REVERT: O 76 ARG cc_start: 0.8809 (mmt-90) cc_final: 0.8384 (mpt180) REVERT: O 83 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8483 (mmtt) REVERT: O 110 SER cc_start: 0.8939 (t) cc_final: 0.8735 (p) REVERT: P 41 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7352 (p0) REVERT: P 46 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7867 (mttp) REVERT: P 68 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7699 (ttpp) REVERT: P 76 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8488 (mpt180) REVERT: P 110 SER cc_start: 0.8973 (t) cc_final: 0.8748 (p) REVERT: Q 41 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7334 (p0) REVERT: Q 46 LYS cc_start: 0.8364 (ttpp) cc_final: 0.7866 (mttp) REVERT: Q 68 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7557 (ttpp) REVERT: Q 110 SER cc_start: 0.8980 (t) cc_final: 0.8776 (p) REVERT: R 41 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7252 (p0) REVERT: R 68 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7624 (ttpp) REVERT: R 76 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8522 (mpt180) REVERT: R 81 ASP cc_start: 0.8667 (m-30) cc_final: 0.8319 (m-30) REVERT: R 141 SER cc_start: 0.8811 (m) cc_final: 0.8578 (m) REVERT: S 41 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7153 (p0) REVERT: S 46 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7841 (mttp) REVERT: S 68 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7666 (ttpp) REVERT: S 76 ARG cc_start: 0.8661 (mmt-90) cc_final: 0.8333 (mmt180) REVERT: T 41 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7176 (p0) REVERT: T 42 ASP cc_start: 0.8358 (p0) cc_final: 0.8107 (p0) REVERT: T 46 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7882 (mttp) REVERT: T 68 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7669 (ttpp) REVERT: T 76 ARG cc_start: 0.8821 (mmt-90) cc_final: 0.8455 (mmt180) REVERT: T 141 SER cc_start: 0.8818 (m) cc_final: 0.8585 (m) REVERT: U 41 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7063 (p0) REVERT: U 46 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7869 (mttp) REVERT: U 68 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7644 (ttpp) REVERT: U 76 ARG cc_start: 0.8880 (mmt-90) cc_final: 0.8579 (mmt180) REVERT: U 110 SER cc_start: 0.8977 (t) cc_final: 0.8745 (p) REVERT: V 41 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7290 (p0) REVERT: V 46 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7840 (mttp) REVERT: V 61 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7740 (pt0) REVERT: V 68 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7664 (ttpp) REVERT: V 76 ARG cc_start: 0.8757 (mmt-90) cc_final: 0.8445 (mpt180) REVERT: V 83 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8455 (mmtt) REVERT: V 141 SER cc_start: 0.8827 (m) cc_final: 0.8608 (m) REVERT: W 41 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7131 (p0) REVERT: W 46 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7957 (ttmm) REVERT: W 68 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7599 (ttpp) REVERT: W 110 SER cc_start: 0.8984 (t) cc_final: 0.8777 (p) REVERT: W 141 SER cc_start: 0.8772 (m) cc_final: 0.8525 (m) REVERT: X 41 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7213 (p0) REVERT: X 46 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7871 (mttp) REVERT: X 68 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7727 (ttpp) REVERT: X 76 ARG cc_start: 0.8818 (mmt-90) cc_final: 0.8460 (mpt180) REVERT: X 83 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8499 (mmtt) REVERT: X 141 SER cc_start: 0.8795 (m) cc_final: 0.8548 (m) outliers start: 70 outliers final: 26 residues processed: 1002 average time/residue: 0.7131 time to fit residues: 848.3323 Evaluate side-chains 996 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 943 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 83 LYS Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 88 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 330 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 102 HIS C 8 ASN C 62 HIS C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 62 HIS G 102 HIS I 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN O 102 HIS P 8 ASN Q 8 ASN R 8 ASN S 8 ASN S 102 HIS T 8 ASN U 8 ASN U 102 HIS V 8 ASN V 62 HIS W 102 HIS X 8 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.113104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.089584 restraints weight = 305192.004| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.93 r_work: 0.2648 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1474 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36312 Z= 0.122 Angle : 0.468 6.222 49104 Z= 0.258 Chirality : 0.036 0.125 5112 Planarity : 0.003 0.039 6480 Dihedral : 12.948 179.906 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.53 % Favored : 98.13 % Rotamer: Outliers : 2.44 % Allowed : 25.98 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.36 (0.12), residues: 4320 helix: 4.43 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.38 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 76 TYR 0.016 0.001 TYR I 37 PHE 0.013 0.002 PHE R 38 TRP 0.005 0.000 TRP N 90 HIS 0.006 0.001 HIS J 102 Details of bonding type rmsd covalent geometry : bond 0.00252 (36312) covalent geometry : angle 0.46845 (49104) hydrogen bonds : bond 0.05056 ( 2640) hydrogen bonds : angle 3.22382 ( 7776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 956 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7038 (p0) REVERT: A 46 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7730 (mttp) REVERT: A 68 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7524 (ttpp) REVERT: A 76 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8225 (mmt-90) REVERT: A 141 SER cc_start: 0.8740 (m) cc_final: 0.8477 (m) REVERT: B 41 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7156 (p0) REVERT: B 46 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7709 (mttp) REVERT: B 68 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7623 (ttpp) REVERT: B 83 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (mmtm) REVERT: B 110 SER cc_start: 0.8844 (t) cc_final: 0.8615 (p) REVERT: C 41 ASP cc_start: 0.8281 (p0) cc_final: 0.7446 (p0) REVERT: C 46 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7738 (mttp) REVERT: C 110 SER cc_start: 0.8919 (t) cc_final: 0.8660 (p) REVERT: C 141 SER cc_start: 0.8716 (m) cc_final: 0.8469 (m) REVERT: D 41 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7304 (p0) REVERT: D 46 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7706 (mttp) REVERT: D 68 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7626 (ttpp) REVERT: D 76 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.8338 (mmt180) REVERT: D 141 SER cc_start: 0.8726 (m) cc_final: 0.8472 (m) REVERT: E 41 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7077 (p0) REVERT: E 46 LYS cc_start: 0.8252 (ttpp) cc_final: 0.7722 (mttp) REVERT: E 68 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7605 (ttpp) REVERT: E 76 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8455 (mpt180) REVERT: F 41 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7127 (p0) REVERT: F 68 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7634 (ttpp) REVERT: G 41 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7116 (p0) REVERT: G 46 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7726 (mttp) REVERT: G 68 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7588 (ttpp) REVERT: G 141 SER cc_start: 0.8730 (m) cc_final: 0.8495 (m) REVERT: H 41 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7312 (p0) REVERT: H 46 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7749 (mttp) REVERT: H 68 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7502 (ttpp) REVERT: H 76 ARG cc_start: 0.8705 (mmt-90) cc_final: 0.8239 (mmt180) REVERT: H 83 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8394 (mmtt) REVERT: I 41 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7051 (p0) REVERT: I 46 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7681 (mttp) REVERT: I 68 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7448 (ttpp) REVERT: I 76 ARG cc_start: 0.8733 (mmt-90) cc_final: 0.8352 (mpt180) REVERT: I 110 SER cc_start: 0.8857 (t) cc_final: 0.8627 (p) REVERT: J 41 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7192 (p0) REVERT: J 46 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7749 (mttp) REVERT: J 68 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7602 (ttpp) REVERT: J 110 SER cc_start: 0.8841 (t) cc_final: 0.8572 (p) REVERT: J 141 SER cc_start: 0.8801 (m) cc_final: 0.8590 (m) REVERT: K 41 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7192 (p0) REVERT: K 42 ASP cc_start: 0.8215 (p0) cc_final: 0.7969 (p0) REVERT: K 46 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7693 (mttp) REVERT: K 68 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7707 (ttpp) REVERT: K 76 ARG cc_start: 0.8686 (mmt-90) cc_final: 0.8206 (mpt180) REVERT: K 81 ASP cc_start: 0.8614 (m-30) cc_final: 0.8243 (m-30) REVERT: K 110 SER cc_start: 0.8897 (t) cc_final: 0.8657 (p) REVERT: K 141 SER cc_start: 0.8684 (m) cc_final: 0.8421 (m) REVERT: L 41 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7258 (p0) REVERT: L 46 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7851 (ttmm) REVERT: L 68 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7793 (ttpm) REVERT: L 76 ARG cc_start: 0.8673 (mmt-90) cc_final: 0.8343 (mpt180) REVERT: L 141 SER cc_start: 0.8731 (m) cc_final: 0.8504 (m) REVERT: M 41 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7126 (p0) REVERT: M 46 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7791 (mttp) REVERT: M 68 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7548 (ttpp) REVERT: M 76 ARG cc_start: 0.8804 (mmt-90) cc_final: 0.8168 (mmt180) REVERT: M 78 PHE cc_start: 0.8881 (m-80) cc_final: 0.8667 (m-80) REVERT: M 141 SER cc_start: 0.8799 (m) cc_final: 0.8587 (m) REVERT: N 41 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7448 (p0) REVERT: N 46 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7688 (mttp) REVERT: N 68 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7641 (ttpp) REVERT: N 76 ARG cc_start: 0.8618 (mmt-90) cc_final: 0.8211 (mmt180) REVERT: N 141 SER cc_start: 0.8713 (m) cc_final: 0.8443 (m) REVERT: O 41 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7312 (p0) REVERT: O 46 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7782 (mttp) REVERT: O 68 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7688 (ttpt) REVERT: O 76 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.8308 (mpt180) REVERT: O 83 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8408 (mmtt) REVERT: O 110 SER cc_start: 0.8870 (t) cc_final: 0.8644 (p) REVERT: P 41 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7228 (p0) REVERT: P 46 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7752 (mttp) REVERT: P 76 ARG cc_start: 0.8741 (mmt-90) cc_final: 0.8279 (mpt180) REVERT: P 110 SER cc_start: 0.8887 (t) cc_final: 0.8636 (p) REVERT: Q 41 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7040 (p0) REVERT: Q 46 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7753 (mttp) REVERT: Q 68 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7541 (ttpp) REVERT: Q 110 SER cc_start: 0.8884 (t) cc_final: 0.8664 (p) REVERT: R 41 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7152 (p0) REVERT: R 46 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7805 (mttp) REVERT: R 68 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7615 (ttpp) REVERT: R 76 ARG cc_start: 0.8775 (mmt-90) cc_final: 0.8100 (mmt180) REVERT: R 81 ASP cc_start: 0.8687 (m-30) cc_final: 0.8317 (m-30) REVERT: R 141 SER cc_start: 0.8707 (m) cc_final: 0.8450 (m) REVERT: S 41 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7045 (p0) REVERT: S 46 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7698 (mttp) REVERT: S 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7534 (ttpp) REVERT: S 76 ARG cc_start: 0.8605 (mmt-90) cc_final: 0.8284 (mmt180) REVERT: T 41 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7049 (p0) REVERT: T 46 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7735 (mttp) REVERT: T 68 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7519 (ttpp) REVERT: T 76 ARG cc_start: 0.8768 (mmt-90) cc_final: 0.8342 (mmt180) REVERT: T 141 SER cc_start: 0.8720 (m) cc_final: 0.8454 (m) REVERT: U 41 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7015 (p0) REVERT: U 46 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7743 (mttp) REVERT: U 68 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7510 (ttpp) REVERT: U 76 ARG cc_start: 0.8834 (mmt-90) cc_final: 0.8524 (mmt180) REVERT: U 110 SER cc_start: 0.8904 (t) cc_final: 0.8656 (p) REVERT: V 41 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7088 (p0) REVERT: V 46 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7680 (mttp) REVERT: V 61 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7563 (pt0) REVERT: V 68 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7640 (ttpp) REVERT: V 76 ARG cc_start: 0.8741 (mmt-90) cc_final: 0.8363 (mpt180) REVERT: V 83 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8402 (mmtt) REVERT: V 141 SER cc_start: 0.8759 (m) cc_final: 0.8513 (m) REVERT: W 41 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7139 (p0) REVERT: W 46 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7702 (mttp) REVERT: W 68 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7606 (ttpp) REVERT: W 110 SER cc_start: 0.8931 (t) cc_final: 0.8697 (p) REVERT: W 141 SER cc_start: 0.8710 (m) cc_final: 0.8470 (m) REVERT: X 41 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7059 (p0) REVERT: X 46 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7753 (mttp) REVERT: X 68 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7681 (ttpp) REVERT: X 76 ARG cc_start: 0.8800 (mmt-90) cc_final: 0.8367 (mmt-90) REVERT: X 83 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8453 (mmtt) REVERT: X 141 SER cc_start: 0.8720 (m) cc_final: 0.8450 (m) outliers start: 66 outliers final: 31 residues processed: 983 average time/residue: 0.7274 time to fit residues: 852.1197 Evaluate side-chains 1000 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 940 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 159 GLU Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 83 LYS Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 180 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 360 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 102 HIS C 8 ASN C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN O 102 HIS P 8 ASN Q 8 ASN R 8 ASN R 102 HIS S 8 ASN S 102 HIS T 8 ASN U 8 ASN U 102 HIS V 8 ASN V 62 HIS W 102 HIS X 8 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.090620 restraints weight = 325038.532| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.01 r_work: 0.2658 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36312 Z= 0.117 Angle : 0.459 6.099 49104 Z= 0.254 Chirality : 0.036 0.124 5112 Planarity : 0.003 0.035 6480 Dihedral : 12.932 179.857 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.57 % Favored : 98.09 % Rotamer: Outliers : 2.16 % Allowed : 25.90 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.45 (0.12), residues: 4320 helix: 4.48 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.32 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 76 TYR 0.016 0.001 TYR P 134 PHE 0.013 0.002 PHE B 38 TRP 0.005 0.000 TRP N 90 HIS 0.006 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00239 (36312) covalent geometry : angle 0.45852 (49104) hydrogen bonds : bond 0.04782 ( 2640) hydrogen bonds : angle 3.17744 ( 7776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 975 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7121 (p0) REVERT: A 46 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7703 (mttp) REVERT: A 68 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7604 (ttpp) REVERT: A 76 ARG cc_start: 0.8736 (mmt-90) cc_final: 0.8433 (mmt180) REVERT: A 110 SER cc_start: 0.8871 (t) cc_final: 0.8654 (p) REVERT: A 141 SER cc_start: 0.8721 (m) cc_final: 0.8453 (m) REVERT: B 8 ASN cc_start: 0.8982 (t0) cc_final: 0.8488 (t0) REVERT: B 41 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7094 (p0) REVERT: B 46 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7674 (mttp) REVERT: B 68 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7644 (ttpp) REVERT: B 83 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (mmtt) REVERT: B 110 SER cc_start: 0.8841 (t) cc_final: 0.8603 (p) REVERT: C 41 ASP cc_start: 0.8214 (p0) cc_final: 0.7447 (p0) REVERT: C 46 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7717 (mttp) REVERT: C 110 SER cc_start: 0.8904 (t) cc_final: 0.8673 (p) REVERT: C 141 SER cc_start: 0.8712 (m) cc_final: 0.8467 (m) REVERT: D 41 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7163 (p0) REVERT: D 46 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7694 (mttp) REVERT: D 68 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7642 (ttpp) REVERT: D 76 ARG cc_start: 0.8771 (mmt-90) cc_final: 0.8346 (mmt180) REVERT: D 141 SER cc_start: 0.8720 (m) cc_final: 0.8485 (m) REVERT: E 41 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7019 (p0) REVERT: E 46 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7689 (mttp) REVERT: E 68 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7623 (ttpp) REVERT: E 76 ARG cc_start: 0.8844 (mmt-90) cc_final: 0.8483 (mpt180) REVERT: F 41 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7048 (p0) REVERT: F 68 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7625 (ttpp) REVERT: G 41 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7200 (p0) REVERT: G 46 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7704 (mttp) REVERT: G 68 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7612 (ttpp) REVERT: G 141 SER cc_start: 0.8720 (m) cc_final: 0.8479 (m) REVERT: H 41 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7256 (p0) REVERT: H 46 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7776 (mttp) REVERT: H 68 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7636 (ttpp) REVERT: H 76 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8233 (mmt180) REVERT: H 83 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8397 (mmtt) REVERT: H 110 SER cc_start: 0.8911 (t) cc_final: 0.8693 (p) REVERT: I 41 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.6977 (p0) REVERT: I 46 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7674 (mttp) REVERT: I 68 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7519 (ttpp) REVERT: I 76 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8385 (mpt180) REVERT: I 110 SER cc_start: 0.8848 (t) cc_final: 0.8613 (p) REVERT: J 41 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7246 (p0) REVERT: J 46 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7721 (mttp) REVERT: J 68 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7549 (ttpp) REVERT: J 110 SER cc_start: 0.8834 (t) cc_final: 0.8589 (p) REVERT: J 141 SER cc_start: 0.8789 (m) cc_final: 0.8586 (m) REVERT: K 41 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7065 (p0) REVERT: K 42 ASP cc_start: 0.8148 (p0) cc_final: 0.7906 (p0) REVERT: K 46 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7674 (mttp) REVERT: K 68 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7704 (ttpp) REVERT: K 76 ARG cc_start: 0.8652 (mmt-90) cc_final: 0.8217 (mpt180) REVERT: K 81 ASP cc_start: 0.8618 (m-30) cc_final: 0.8241 (m-30) REVERT: K 110 SER cc_start: 0.8898 (t) cc_final: 0.8659 (p) REVERT: K 141 SER cc_start: 0.8689 (m) cc_final: 0.8416 (m) REVERT: L 41 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7139 (p0) REVERT: L 46 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7680 (mttp) REVERT: L 68 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7598 (ttpp) REVERT: L 76 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.8372 (mpt180) REVERT: L 141 SER cc_start: 0.8727 (m) cc_final: 0.8481 (m) REVERT: M 41 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7058 (p0) REVERT: M 46 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7782 (mttp) REVERT: M 68 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7597 (ttpp) REVERT: M 76 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8190 (mmt180) REVERT: M 78 PHE cc_start: 0.8883 (m-80) cc_final: 0.8665 (m-80) REVERT: M 141 SER cc_start: 0.8802 (m) cc_final: 0.8586 (m) REVERT: N 41 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7321 (p0) REVERT: N 46 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7663 (mttp) REVERT: N 68 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7631 (ttpp) REVERT: N 76 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.8206 (mmt180) REVERT: N 141 SER cc_start: 0.8705 (m) cc_final: 0.8466 (m) REVERT: O 41 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7241 (p0) REVERT: O 46 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7784 (mttp) REVERT: O 68 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7639 (ttpp) REVERT: O 76 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8317 (mpt180) REVERT: O 83 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8410 (mmtt) REVERT: O 110 SER cc_start: 0.8835 (t) cc_final: 0.8597 (p) REVERT: P 41 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7210 (p0) REVERT: P 46 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7716 (mttp) REVERT: P 76 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8321 (mpt180) REVERT: P 110 SER cc_start: 0.8877 (t) cc_final: 0.8624 (p) REVERT: Q 41 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7180 (p0) REVERT: Q 46 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7706 (mttp) REVERT: Q 68 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7576 (ttpp) REVERT: Q 110 SER cc_start: 0.8882 (t) cc_final: 0.8655 (p) REVERT: R 41 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7160 (p0) REVERT: R 46 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7797 (mttp) REVERT: R 68 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7607 (ttpp) REVERT: R 76 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8429 (mpt180) REVERT: R 81 ASP cc_start: 0.8649 (m-30) cc_final: 0.8255 (m-30) REVERT: R 141 SER cc_start: 0.8715 (m) cc_final: 0.8464 (m) REVERT: S 41 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7025 (p0) REVERT: S 46 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7672 (mttp) REVERT: S 68 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7535 (ttpp) REVERT: S 76 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.8297 (mmt180) REVERT: T 41 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.6885 (p0) REVERT: T 46 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7709 (mttp) REVERT: T 68 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7612 (ttpp) REVERT: T 76 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8330 (mmt180) REVERT: T 141 SER cc_start: 0.8717 (m) cc_final: 0.8482 (m) REVERT: U 41 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.6978 (p0) REVERT: U 46 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7701 (mttp) REVERT: U 68 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7589 (ttpp) REVERT: U 76 ARG cc_start: 0.8845 (mmt-90) cc_final: 0.8527 (mmt180) REVERT: U 110 SER cc_start: 0.8867 (t) cc_final: 0.8582 (p) REVERT: V 41 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7104 (p0) REVERT: V 46 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7667 (mttp) REVERT: V 61 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7536 (pt0) REVERT: V 68 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7606 (ttpp) REVERT: V 76 ARG cc_start: 0.8733 (mmt-90) cc_final: 0.8320 (mmt180) REVERT: V 83 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8381 (mmtt) REVERT: V 110 SER cc_start: 0.8878 (t) cc_final: 0.8638 (p) REVERT: V 141 SER cc_start: 0.8742 (m) cc_final: 0.8507 (m) REVERT: W 41 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7112 (p0) REVERT: W 46 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7718 (mttp) REVERT: W 68 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7636 (ttpp) REVERT: W 110 SER cc_start: 0.8895 (t) cc_final: 0.8648 (p) REVERT: W 141 SER cc_start: 0.8725 (m) cc_final: 0.8487 (m) REVERT: X 41 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7009 (p0) REVERT: X 46 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7704 (mttp) REVERT: X 68 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7668 (ttpp) REVERT: X 76 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8406 (mpt180) REVERT: X 141 SER cc_start: 0.8729 (m) cc_final: 0.8498 (m) outliers start: 55 outliers final: 25 residues processed: 998 average time/residue: 0.7123 time to fit residues: 842.3967 Evaluate side-chains 1006 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 954 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 159 GLU Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 375 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 305 optimal weight: 0.0040 chunk 236 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 260 optimal weight: 0.6980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 102 HIS C 8 ASN C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN K 8 ASN L 8 ASN M 8 ASN M 102 HIS N 8 ASN O 8 ASN O 102 HIS P 8 ASN Q 8 ASN R 8 ASN R 102 HIS S 8 ASN S 102 HIS T 8 ASN U 8 ASN U 102 HIS V 8 ASN V 62 HIS W 102 HIS X 8 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.113385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.089905 restraints weight = 305025.321| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.93 r_work: 0.2652 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36312 Z= 0.122 Angle : 0.467 5.532 49104 Z= 0.258 Chirality : 0.036 0.125 5112 Planarity : 0.003 0.032 6480 Dihedral : 12.940 179.990 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.72 % Favored : 97.99 % Rotamer: Outliers : 2.24 % Allowed : 25.72 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.45 (0.12), residues: 4320 helix: 4.47 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.29 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 76 TYR 0.017 0.001 TYR P 134 PHE 0.013 0.002 PHE R 38 TRP 0.004 0.000 TRP N 90 HIS 0.006 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00253 (36312) covalent geometry : angle 0.46720 (49104) hydrogen bonds : bond 0.04982 ( 2640) hydrogen bonds : angle 3.19072 ( 7776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 957 time to evaluate : 1.543 Fit side-chains REVERT: A 41 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7080 (p0) REVERT: A 46 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7729 (mttp) REVERT: A 68 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7647 (ttpp) REVERT: A 76 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.8419 (mmt180) REVERT: A 110 SER cc_start: 0.8891 (t) cc_final: 0.8677 (p) REVERT: A 141 SER cc_start: 0.8733 (m) cc_final: 0.8491 (m) REVERT: B 8 ASN cc_start: 0.8994 (t0) cc_final: 0.8498 (t0) REVERT: B 41 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7205 (p0) REVERT: B 46 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7705 (mttp) REVERT: B 68 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7662 (ttpp) REVERT: B 83 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8425 (mmtt) REVERT: B 110 SER cc_start: 0.8847 (t) cc_final: 0.8587 (p) REVERT: C 41 ASP cc_start: 0.8256 (p0) cc_final: 0.7464 (p0) REVERT: C 46 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7751 (mttp) REVERT: C 110 SER cc_start: 0.8908 (t) cc_final: 0.8681 (p) REVERT: C 141 SER cc_start: 0.8731 (m) cc_final: 0.8475 (m) REVERT: D 41 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7284 (p0) REVERT: D 46 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7724 (mttp) REVERT: D 68 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7672 (ttpp) REVERT: D 76 ARG cc_start: 0.8779 (mmt-90) cc_final: 0.8355 (mmt180) REVERT: D 141 SER cc_start: 0.8726 (m) cc_final: 0.8476 (m) REVERT: E 41 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7040 (p0) REVERT: E 46 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7723 (mttp) REVERT: E 68 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7614 (ttpp) REVERT: E 76 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8487 (mpt180) REVERT: F 41 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7064 (p0) REVERT: F 46 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7628 (mttp) REVERT: F 68 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7658 (ttpp) REVERT: G 41 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7211 (p0) REVERT: G 46 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7724 (mttp) REVERT: G 68 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7642 (ttpp) REVERT: G 141 SER cc_start: 0.8735 (m) cc_final: 0.8493 (m) REVERT: H 41 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7273 (p0) REVERT: H 46 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7785 (mttp) REVERT: H 68 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7670 (ttpp) REVERT: H 76 ARG cc_start: 0.8744 (mmt-90) cc_final: 0.8231 (mmt180) REVERT: H 83 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8400 (mmtt) REVERT: H 110 SER cc_start: 0.8930 (t) cc_final: 0.8715 (p) REVERT: I 41 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.6993 (p0) REVERT: I 46 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7715 (mttp) REVERT: I 68 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7567 (ttpp) REVERT: I 76 ARG cc_start: 0.8725 (mmt-90) cc_final: 0.8369 (mpt180) REVERT: I 110 SER cc_start: 0.8856 (t) cc_final: 0.8630 (p) REVERT: J 8 ASN cc_start: 0.8959 (t0) cc_final: 0.8488 (t0) REVERT: J 41 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7301 (p0) REVERT: J 46 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7753 (mttp) REVERT: J 68 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7612 (ttpp) REVERT: J 110 SER cc_start: 0.8825 (t) cc_final: 0.8547 (p) REVERT: J 141 SER cc_start: 0.8788 (m) cc_final: 0.8586 (m) REVERT: K 41 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7105 (p0) REVERT: K 42 ASP cc_start: 0.8173 (p0) cc_final: 0.7945 (p0) REVERT: K 46 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7705 (mttp) REVERT: K 68 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7702 (ttpp) REVERT: K 76 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8215 (mpt180) REVERT: K 81 ASP cc_start: 0.8614 (m-30) cc_final: 0.8241 (m-30) REVERT: K 110 SER cc_start: 0.8901 (t) cc_final: 0.8667 (p) REVERT: K 141 SER cc_start: 0.8706 (m) cc_final: 0.8455 (m) REVERT: L 41 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7293 (p0) REVERT: L 46 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7705 (mttp) REVERT: L 68 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7611 (ttpp) REVERT: L 76 ARG cc_start: 0.8673 (mmt-90) cc_final: 0.8372 (mpt180) REVERT: L 141 SER cc_start: 0.8748 (m) cc_final: 0.8516 (m) REVERT: M 41 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7119 (p0) REVERT: M 46 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7804 (mttp) REVERT: M 68 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7619 (ttpp) REVERT: M 76 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8170 (mmt180) REVERT: M 78 PHE cc_start: 0.8890 (m-80) cc_final: 0.8667 (m-80) REVERT: M 141 SER cc_start: 0.8797 (m) cc_final: 0.8584 (m) REVERT: N 41 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7372 (p0) REVERT: N 46 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7685 (mttp) REVERT: N 68 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7647 (ttpp) REVERT: N 76 ARG cc_start: 0.8680 (mmt-90) cc_final: 0.8362 (mpt180) REVERT: N 141 SER cc_start: 0.8718 (m) cc_final: 0.8457 (m) REVERT: O 41 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7249 (p0) REVERT: O 46 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7798 (mttp) REVERT: O 68 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7644 (ttpp) REVERT: O 76 ARG cc_start: 0.8756 (mmt-90) cc_final: 0.8298 (mpt180) REVERT: O 83 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8416 (mmtt) REVERT: O 110 SER cc_start: 0.8840 (t) cc_final: 0.8607 (p) REVERT: P 41 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7212 (p0) REVERT: P 46 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7744 (mttp) REVERT: P 76 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8334 (mpt180) REVERT: P 110 SER cc_start: 0.8897 (t) cc_final: 0.8647 (p) REVERT: Q 41 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7133 (p0) REVERT: Q 46 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7723 (mttp) REVERT: Q 68 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7616 (ttpp) REVERT: Q 110 SER cc_start: 0.8879 (t) cc_final: 0.8657 (p) REVERT: R 41 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7200 (p0) REVERT: R 46 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7787 (mttp) REVERT: R 68 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7603 (ttpp) REVERT: R 76 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8430 (mpt180) REVERT: R 81 ASP cc_start: 0.8640 (m-30) cc_final: 0.8262 (m-30) REVERT: R 141 SER cc_start: 0.8715 (m) cc_final: 0.8462 (m) REVERT: S 41 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7030 (p0) REVERT: S 46 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7700 (mttp) REVERT: S 68 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7544 (ttpp) REVERT: S 76 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8300 (mmt180) REVERT: T 41 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7118 (p0) REVERT: T 46 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7740 (mttp) REVERT: T 68 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7622 (ttpp) REVERT: T 76 ARG cc_start: 0.8764 (mmt-90) cc_final: 0.8376 (mmt180) REVERT: T 141 SER cc_start: 0.8713 (m) cc_final: 0.8455 (m) REVERT: U 41 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7021 (p0) REVERT: U 46 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7717 (mttp) REVERT: U 68 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7640 (ttpp) REVERT: U 76 ARG cc_start: 0.8834 (mmt-90) cc_final: 0.8500 (mmt180) REVERT: U 78 PHE cc_start: 0.8896 (m-80) cc_final: 0.8627 (m-80) REVERT: U 110 SER cc_start: 0.8880 (t) cc_final: 0.8594 (p) REVERT: V 41 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7151 (p0) REVERT: V 46 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7699 (mttp) REVERT: V 61 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7520 (pt0) REVERT: V 68 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7617 (ttpp) REVERT: V 76 ARG cc_start: 0.8744 (mmt-90) cc_final: 0.8361 (mpt180) REVERT: V 83 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8389 (mmtt) REVERT: V 110 SER cc_start: 0.8898 (t) cc_final: 0.8655 (p) REVERT: V 141 SER cc_start: 0.8745 (m) cc_final: 0.8517 (m) REVERT: W 41 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7134 (p0) REVERT: W 46 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7735 (mttp) REVERT: W 68 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7640 (ttpp) REVERT: W 110 SER cc_start: 0.8926 (t) cc_final: 0.8687 (p) REVERT: W 141 SER cc_start: 0.8729 (m) cc_final: 0.8476 (m) REVERT: X 41 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7099 (p0) REVERT: X 46 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7747 (mttp) REVERT: X 68 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7681 (ttpp) REVERT: X 76 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8373 (mpt180) REVERT: X 83 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8464 (mmtt) REVERT: X 141 SER cc_start: 0.8725 (m) cc_final: 0.8466 (m) outliers start: 58 outliers final: 29 residues processed: 986 average time/residue: 0.7240 time to fit residues: 847.6838 Evaluate side-chains 1006 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 949 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 83 LYS Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 159 GLU Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 83 LYS Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 chunk 406 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 chunk 252 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 102 HIS C 8 ASN C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 8 ASN K 8 ASN L 8 ASN M 8 ASN M 102 HIS N 8 ASN O 8 ASN O 102 HIS P 8 ASN Q 8 ASN Q 102 HIS R 8 ASN R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 62 HIS W 102 HIS X 8 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.091967 restraints weight = 314013.803| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.96 r_work: 0.2690 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36312 Z= 0.113 Angle : 0.457 5.527 49104 Z= 0.253 Chirality : 0.035 0.122 5112 Planarity : 0.003 0.033 6480 Dihedral : 12.912 179.728 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.74 % Favored : 97.99 % Rotamer: Outliers : 2.13 % Allowed : 26.16 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.53 (0.12), residues: 4320 helix: 4.53 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.24 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 76 TYR 0.018 0.001 TYR P 134 PHE 0.013 0.002 PHE R 38 TRP 0.007 0.000 TRP N 90 HIS 0.006 0.001 HIS Q 102 Details of bonding type rmsd covalent geometry : bond 0.00228 (36312) covalent geometry : angle 0.45738 (49104) hydrogen bonds : bond 0.04546 ( 2640) hydrogen bonds : angle 3.15012 ( 7776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16265.70 seconds wall clock time: 276 minutes 45.36 seconds (16605.36 seconds total)