Starting phenix.real_space_refine on Tue Sep 15 06:12:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sht_10205/09_2026/6sht_10205_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sht_10205/09_2026/6sht_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_10205/09_2026/6sht_10205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sht_10205/09_2026/6sht_10205.map" model { file = "/net/cci-nas-00/data/ceres_data/6sht_10205/09_2026/6sht_10205_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sht_10205/09_2026/6sht_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.45, 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: 2.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 0.74 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: 6.73 Time building geometry restraints manager: 3.60 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: 0.14 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: 1.450 Set stop_for_unknowns flag: 0.010 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.410 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 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 are 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/Z covalent geometry : bond 0.01539 / 0.88 (36312) covalent geometry : angle 1.54698 / 1.01 (49104) hydrogen bonds : bond 0.24973 / 16.53 ( 2640) hydrogen bonds : angle 7.00923 / 5.12 ( 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 : 1.391 Fit side-chains REVERT: A 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: A 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8607 (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: 0.9089 (mmt-90) cc_final: 0.8607 (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: 0.9089 (mmt-90) cc_final: 0.8607 (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: 0.9362 (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: 0.9362 (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: 0.9362 (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: 0.8210 time to fit residues: 1338.4566 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 : 1.379 ------------------------------------------------------------------------------- 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: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN B 72 GLN C 72 GLN D 72 GLN E 72 GLN F 72 GLN G 72 GLN H 72 GLN I 72 GLN J 72 GLN K 72 GLN L 72 GLN M 72 GLN N 72 GLN O 72 GLN P 72 GLN Q 72 GLN R 72 GLN S 72 GLN T 72 GLN U 72 GLN V 72 GLN W 72 GLN X 72 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.087406 restraints weight = 285655.209| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.63 r_work: 0.2566 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (12 function evaluations) r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 36312 Z= 0.142 Angle : 0.567 5.194 49104 Z= 0.315 Chirality : 0.039 0.141 5112 Planarity : 0.004 0.022 6480 Dihedral : 13.177 178.263 5136 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.58 % Allowed : 0.00 % Favored : 99.42 % Rotamer: Outliers : 1.23 % Allowed : 20.99 % Favored : 77.78 % 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 are not related in a simple way. whole: 2.96 (0.12), residues: 4320 helix: 2.58 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.51 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 6 TYR 0.017 0.001 TYR F 134 PHE 0.011 0.001 PHE M 38 TRP 0.004 0.001 TRP N 90 HIS 0.003 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (36312) covalent geometry : angle 0.56690 / 0.31 (49104) hydrogen bonds : bond 0.06332 / 4.21 ( 2640) hydrogen bonds : angle 3.79224 / 2.75 ( 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 1152 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1128 time to evaluate : 1.496 Fit side-chains REVERT: A 41 ASP cc_start: 0.8463 (p0) cc_final: 0.7511 (p0) REVERT: A 46 LYS cc_start: 0.8250 (ttpp) cc_final: 0.7917 (ttmm) REVERT: A 62 HIS cc_start: 0.8482 (m170) cc_final: 0.8261 (m170) REVERT: A 68 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7550 (ttpp) REVERT: A 76 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8640 (mmt180) REVERT: B 41 ASP cc_start: 0.8476 (p0) cc_final: 0.7534 (p0) REVERT: B 46 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7909 (ttmm) REVERT: B 62 HIS cc_start: 0.8487 (m170) cc_final: 0.8270 (m170) REVERT: B 68 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7549 (ttpp) REVERT: B 76 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8648 (mmt180) REVERT: C 41 ASP cc_start: 0.8469 (p0) cc_final: 0.7524 (p0) REVERT: C 46 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7925 (ttmm) REVERT: C 62 HIS cc_start: 0.8489 (m170) cc_final: 0.8267 (m170) REVERT: C 68 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7562 (ttpp) REVERT: C 76 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8660 (mmt180) REVERT: D 41 ASP cc_start: 0.8476 (p0) cc_final: 0.7536 (p0) REVERT: D 46 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7903 (ttmm) REVERT: D 62 HIS cc_start: 0.8491 (m170) cc_final: 0.8267 (m170) REVERT: D 68 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7552 (ttpp) REVERT: D 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8648 (mmt180) REVERT: E 41 ASP cc_start: 0.8476 (p0) cc_final: 0.7534 (p0) REVERT: E 46 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7909 (ttmm) REVERT: E 62 HIS cc_start: 0.8487 (m170) cc_final: 0.8271 (m170) REVERT: E 68 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7549 (ttpp) REVERT: E 76 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8648 (mmt180) REVERT: F 41 ASP cc_start: 0.8463 (p0) cc_final: 0.7511 (p0) REVERT: F 46 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7917 (ttmm) REVERT: F 62 HIS cc_start: 0.8482 (m170) cc_final: 0.8261 (m170) REVERT: F 68 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7550 (ttpp) REVERT: F 76 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8640 (mmt180) REVERT: G 41 ASP cc_start: 0.8463 (p0) cc_final: 0.7511 (p0) REVERT: G 46 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7917 (ttmm) REVERT: G 62 HIS cc_start: 0.8482 (m170) cc_final: 0.8261 (m170) REVERT: G 68 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7550 (ttpp) REVERT: G 76 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8640 (mmt180) REVERT: H 41 ASP cc_start: 0.8476 (p0) cc_final: 0.7534 (p0) REVERT: H 46 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7909 (ttmm) REVERT: H 62 HIS cc_start: 0.8487 (m170) cc_final: 0.8270 (m170) REVERT: H 68 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7549 (ttpp) REVERT: H 76 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8648 (mmt180) REVERT: I 41 ASP cc_start: 0.8472 (p0) cc_final: 0.7526 (p0) REVERT: I 46 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7922 (ttmm) REVERT: I 62 HIS cc_start: 0.8484 (m170) cc_final: 0.8266 (m170) REVERT: I 68 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7551 (ttpp) REVERT: I 76 ARG cc_start: 0.8907 (mmt-90) cc_final: 0.8657 (mmt180) REVERT: J 41 ASP cc_start: 0.8465 (p0) cc_final: 0.7523 (p0) REVERT: J 46 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7904 (ttmm) REVERT: J 62 HIS cc_start: 0.8494 (m170) cc_final: 0.8272 (m170) REVERT: J 68 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7558 (ttpp) REVERT: J 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: K 41 ASP cc_start: 0.8472 (p0) cc_final: 0.7526 (p0) REVERT: K 46 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7921 (ttmm) REVERT: K 62 HIS cc_start: 0.8484 (m170) cc_final: 0.8266 (m170) REVERT: K 68 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7551 (ttpp) REVERT: K 76 ARG cc_start: 0.8907 (mmt-90) cc_final: 0.8657 (mmt180) REVERT: L 41 ASP cc_start: 0.8464 (p0) cc_final: 0.7523 (p0) REVERT: L 46 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7904 (ttmm) REVERT: L 62 HIS cc_start: 0.8494 (m170) cc_final: 0.8272 (m170) REVERT: L 68 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7558 (ttpp) REVERT: L 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: M 41 ASP cc_start: 0.8477 (p0) cc_final: 0.7533 (p0) REVERT: M 46 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7900 (ttmm) REVERT: M 62 HIS cc_start: 0.8483 (m170) cc_final: 0.8261 (m170) REVERT: M 68 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7559 (ttpp) REVERT: M 76 ARG cc_start: 0.8908 (mmt-90) cc_final: 0.8661 (mmt180) REVERT: N 41 ASP cc_start: 0.8468 (p0) cc_final: 0.7526 (p0) REVERT: N 46 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7912 (ttmm) REVERT: N 62 HIS cc_start: 0.8483 (m170) cc_final: 0.8260 (m170) REVERT: N 68 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7556 (ttpp) REVERT: N 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: O 41 ASP cc_start: 0.8475 (p0) cc_final: 0.7536 (p0) REVERT: O 46 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7903 (ttmm) REVERT: O 62 HIS cc_start: 0.8492 (m170) cc_final: 0.8267 (m170) REVERT: O 68 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7552 (ttpp) REVERT: O 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8648 (mmt180) REVERT: P 41 ASP cc_start: 0.8469 (p0) cc_final: 0.7524 (p0) REVERT: P 46 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7925 (ttmm) REVERT: P 62 HIS cc_start: 0.8489 (m170) cc_final: 0.8267 (m170) REVERT: P 68 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7561 (ttpp) REVERT: P 76 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8660 (mmt180) REVERT: Q 41 ASP cc_start: 0.8475 (p0) cc_final: 0.7536 (p0) REVERT: Q 46 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7903 (ttmm) REVERT: Q 62 HIS cc_start: 0.8492 (m170) cc_final: 0.8267 (m170) REVERT: Q 68 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7552 (ttpp) REVERT: Q 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8648 (mmt180) REVERT: R 41 ASP cc_start: 0.8469 (p0) cc_final: 0.7524 (p0) REVERT: R 46 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7925 (ttmm) REVERT: R 62 HIS cc_start: 0.8489 (m170) cc_final: 0.8267 (m170) REVERT: R 68 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7561 (ttpp) REVERT: R 76 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8660 (mmt180) REVERT: S 41 ASP cc_start: 0.8465 (p0) cc_final: 0.7523 (p0) REVERT: S 46 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7904 (ttmm) REVERT: S 62 HIS cc_start: 0.8494 (m170) cc_final: 0.8272 (m170) REVERT: S 68 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7558 (ttpp) REVERT: S 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: T 41 ASP cc_start: 0.8472 (p0) cc_final: 0.7526 (p0) REVERT: T 46 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7921 (ttmm) REVERT: T 62 HIS cc_start: 0.8484 (m170) cc_final: 0.8266 (m170) REVERT: T 68 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7551 (ttpp) REVERT: T 76 ARG cc_start: 0.8907 (mmt-90) cc_final: 0.8657 (mmt180) REVERT: U 41 ASP cc_start: 0.8477 (p0) cc_final: 0.7533 (p0) REVERT: U 46 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7900 (ttmm) REVERT: U 62 HIS cc_start: 0.8484 (m170) cc_final: 0.8261 (m170) REVERT: U 68 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7559 (ttpp) REVERT: U 76 ARG cc_start: 0.8908 (mmt-90) cc_final: 0.8661 (mmt180) REVERT: V 41 ASP cc_start: 0.8468 (p0) cc_final: 0.7526 (p0) REVERT: V 46 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7912 (ttmm) REVERT: V 62 HIS cc_start: 0.8483 (m170) cc_final: 0.8260 (m170) REVERT: V 68 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7556 (ttpp) REVERT: V 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: W 41 ASP cc_start: 0.8468 (p0) cc_final: 0.7527 (p0) REVERT: W 46 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7912 (ttmm) REVERT: W 62 HIS cc_start: 0.8483 (m170) cc_final: 0.8260 (m170) REVERT: W 68 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7556 (ttpp) REVERT: W 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: X 41 ASP cc_start: 0.8477 (p0) cc_final: 0.7533 (p0) REVERT: X 46 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7900 (ttmm) REVERT: X 62 HIS cc_start: 0.8483 (m170) cc_final: 0.8261 (m170) REVERT: X 68 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7559 (ttpp) REVERT: X 76 ARG cc_start: 0.8908 (mmt-90) cc_final: 0.8661 (mmt180) outliers start: 24 outliers final: 0 residues processed: 1152 average time/residue: 0.8344 time to fit residues: 1134.0705 Evaluate side-chains 1008 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1008 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 260 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 397 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 377 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 95 ASN B 8 ASN B 95 ASN C 8 ASN C 95 ASN D 8 ASN D 95 ASN E 8 ASN E 95 ASN F 8 ASN F 95 ASN G 8 ASN G 95 ASN H 8 ASN H 95 ASN I 8 ASN I 95 ASN J 8 ASN J 95 ASN K 8 ASN K 95 ASN L 8 ASN L 95 ASN M 8 ASN M 95 ASN N 8 ASN N 95 ASN O 8 ASN O 95 ASN P 8 ASN P 95 ASN Q 8 ASN Q 95 ASN R 8 ASN R 95 ASN S 8 ASN S 95 ASN T 8 ASN T 95 ASN U 8 ASN U 95 ASN V 8 ASN V 95 ASN W 8 ASN W 95 ASN X 8 ASN X 95 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.103723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.081253 restraints weight = 295263.513| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.79 r_work: 0.2501 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 36312 Z= 0.209 Angle : 0.586 5.266 49104 Z= 0.319 Chirality : 0.041 0.142 5112 Planarity : 0.004 0.025 6480 Dihedral : 13.012 179.015 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.58 % Allowed : 1.16 % Favored : 98.26 % Rotamer: Outliers : 3.70 % Allowed : 24.07 % Favored : 72.22 % 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 are not related in a simple way. whole: 4.22 (0.12), residues: 4320 helix: 3.52 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.42 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 40 TYR 0.016 0.002 TYR L 134 PHE 0.015 0.002 PHE K 38 TRP 0.002 0.001 TRP C 90 HIS 0.005 0.001 HIS Q 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (36312) covalent geometry : angle 0.58621 / 0.32 (49104) hydrogen bonds : bond 0.08279 / 5.50 ( 2640) hydrogen bonds : angle 3.67845 / 2.67 ( 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 1104 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 984 time to evaluate : 1.783 Fit side-chains REVERT: A 41 ASP cc_start: 0.8594 (p0) cc_final: 0.7697 (p0) REVERT: A 68 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7680 (ttpp) REVERT: A 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8529 (mmt180) REVERT: B 41 ASP cc_start: 0.8603 (p0) cc_final: 0.7710 (p0) REVERT: B 68 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7670 (ttpp) REVERT: B 76 ARG cc_start: 0.8945 (mmt-90) cc_final: 0.8520 (mmt180) REVERT: C 41 ASP cc_start: 0.8600 (p0) cc_final: 0.7709 (p0) REVERT: C 68 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7676 (ttpp) REVERT: C 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8526 (mmt180) REVERT: D 41 ASP cc_start: 0.8598 (p0) cc_final: 0.7704 (p0) REVERT: D 68 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7667 (ttpp) REVERT: D 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8525 (mmt180) REVERT: E 41 ASP cc_start: 0.8603 (p0) cc_final: 0.7711 (p0) REVERT: E 68 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7669 (ttpp) REVERT: E 76 ARG cc_start: 0.8944 (mmt-90) cc_final: 0.8519 (mmt180) REVERT: F 41 ASP cc_start: 0.8593 (p0) cc_final: 0.7696 (p0) REVERT: F 68 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7680 (ttpp) REVERT: F 76 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8528 (mmt180) REVERT: G 41 ASP cc_start: 0.8593 (p0) cc_final: 0.7696 (p0) REVERT: G 68 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7680 (ttpp) REVERT: G 76 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8528 (mmt180) REVERT: H 41 ASP cc_start: 0.8603 (p0) cc_final: 0.7710 (p0) REVERT: H 68 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7669 (ttpp) REVERT: H 76 ARG cc_start: 0.8945 (mmt-90) cc_final: 0.8520 (mmt180) REVERT: I 41 ASP cc_start: 0.8605 (p0) cc_final: 0.7713 (p0) REVERT: I 68 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7658 (ttpp) REVERT: I 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8523 (mmt180) REVERT: J 41 ASP cc_start: 0.8590 (p0) cc_final: 0.7697 (p0) REVERT: J 68 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7669 (ttpp) REVERT: J 76 ARG cc_start: 0.8945 (mmt-90) cc_final: 0.8519 (mmt180) REVERT: K 41 ASP cc_start: 0.8605 (p0) cc_final: 0.7713 (p0) REVERT: K 68 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7659 (ttpp) REVERT: K 76 ARG cc_start: 0.8948 (mmt-90) cc_final: 0.8522 (mmt180) REVERT: L 41 ASP cc_start: 0.8590 (p0) cc_final: 0.7697 (p0) REVERT: L 68 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7669 (ttpp) REVERT: L 76 ARG cc_start: 0.8946 (mmt-90) cc_final: 0.8519 (mmt180) REVERT: M 41 ASP cc_start: 0.8597 (p0) cc_final: 0.7708 (p0) REVERT: M 68 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7668 (ttpp) REVERT: M 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8521 (mmt180) REVERT: N 41 ASP cc_start: 0.8600 (p0) cc_final: 0.7710 (p0) REVERT: N 68 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7665 (ttpp) REVERT: N 76 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8519 (mmt180) REVERT: O 41 ASP cc_start: 0.8597 (p0) cc_final: 0.7702 (p0) REVERT: O 68 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7667 (ttpp) REVERT: O 76 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8524 (mmt180) REVERT: P 41 ASP cc_start: 0.8601 (p0) cc_final: 0.7709 (p0) REVERT: P 68 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7677 (ttpp) REVERT: P 76 ARG cc_start: 0.8950 (mmt-90) cc_final: 0.8527 (mmt180) REVERT: Q 41 ASP cc_start: 0.8596 (p0) cc_final: 0.7702 (p0) REVERT: Q 68 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7666 (ttpp) REVERT: Q 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8524 (mmt180) REVERT: R 41 ASP cc_start: 0.8602 (p0) cc_final: 0.7710 (p0) REVERT: R 68 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7677 (ttpp) REVERT: R 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8526 (mmt180) REVERT: S 41 ASP cc_start: 0.8590 (p0) cc_final: 0.7696 (p0) REVERT: S 68 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7668 (ttpp) REVERT: S 76 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8520 (mmt180) REVERT: T 41 ASP cc_start: 0.8604 (p0) cc_final: 0.7713 (p0) REVERT: T 68 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7659 (ttpp) REVERT: T 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8522 (mmt180) REVERT: U 41 ASP cc_start: 0.8597 (p0) cc_final: 0.7707 (p0) REVERT: U 68 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7668 (ttpp) REVERT: U 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8521 (mmt180) REVERT: V 41 ASP cc_start: 0.8600 (p0) cc_final: 0.7710 (p0) REVERT: V 68 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7665 (ttpp) REVERT: V 76 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8520 (mmt180) REVERT: W 41 ASP cc_start: 0.8600 (p0) cc_final: 0.7710 (p0) REVERT: W 68 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7665 (ttpp) REVERT: W 76 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8519 (mmt180) REVERT: X 41 ASP cc_start: 0.8597 (p0) cc_final: 0.7707 (p0) REVERT: X 68 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7668 (ttpp) REVERT: X 76 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8521 (mmt180) outliers start: 120 outliers final: 72 residues processed: 1032 average time/residue: 0.7720 time to fit residues: 951.0018 Evaluate side-chains 987 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 915 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 119 THR 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 C residue 159 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 159 GLU 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 61 GLU Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 159 GLU Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 159 GLU Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 159 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 33 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 351 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 8 ASN C 8 ASN D 8 ASN E 8 ASN F 8 ASN G 8 ASN H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN W 8 ASN X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.104937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.082306 restraints weight = 307050.461| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.82 r_work: 0.2533 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 36312 Z= 0.179 Angle : 0.547 5.121 49104 Z= 0.298 Chirality : 0.040 0.140 5112 Planarity : 0.003 0.025 6480 Dihedral : 13.043 179.833 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.58 % Allowed : 1.16 % Favored : 98.26 % Rotamer: Outliers : 4.32 % Allowed : 24.69 % Favored : 70.99 % 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 are not related in a simple way. whole: 4.61 (0.12), residues: 4320 helix: 3.87 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.56 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 40 TYR 0.015 0.002 TYR C 134 PHE 0.014 0.002 PHE D 38 TRP 0.002 0.001 TRP N 90 HIS 0.005 0.001 HIS L 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (36312) covalent geometry : angle 0.54679 / 0.30 (49104) hydrogen bonds : bond 0.07374 / 4.90 ( 2640) hydrogen bonds : angle 3.54289 / 2.57 ( 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 1128 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 984 time to evaluate : 1.492 Fit side-chains REVERT: A 41 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7633 (p0) REVERT: A 46 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8135 (ttmm) REVERT: A 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7719 (ttpp) REVERT: A 76 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8561 (mmt180) REVERT: B 41 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7629 (p0) REVERT: B 46 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8129 (ttmm) REVERT: B 68 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7708 (ttpp) REVERT: B 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8557 (mmt180) REVERT: C 41 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7640 (p0) REVERT: C 46 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8143 (ttmm) REVERT: C 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7720 (ttpp) REVERT: C 76 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8551 (mmt180) REVERT: D 41 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7630 (p0) REVERT: D 46 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8124 (ttmm) REVERT: D 68 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7715 (ttpp) REVERT: D 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8553 (mmt180) REVERT: E 41 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7629 (p0) REVERT: E 46 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8128 (ttmm) REVERT: E 68 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7709 (ttpp) REVERT: E 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8557 (mmt180) REVERT: F 41 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7633 (p0) REVERT: F 46 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8135 (ttmm) REVERT: F 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7719 (ttpp) REVERT: F 76 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8561 (mmt180) REVERT: G 41 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7633 (p0) REVERT: G 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8135 (ttmm) REVERT: G 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7719 (ttpp) REVERT: G 76 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8561 (mmt180) REVERT: H 41 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7629 (p0) REVERT: H 46 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8128 (ttmm) REVERT: H 68 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7709 (ttpp) REVERT: H 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8557 (mmt180) REVERT: I 41 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.7639 (p0) REVERT: I 46 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8140 (ttmm) REVERT: I 68 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7699 (ttpp) REVERT: I 76 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8561 (mmt180) REVERT: J 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7631 (p0) REVERT: J 46 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8133 (ttmm) REVERT: J 68 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7712 (ttpp) REVERT: J 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8550 (mmt180) REVERT: K 41 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.7639 (p0) REVERT: K 46 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8140 (ttmm) REVERT: K 68 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7700 (ttpp) REVERT: K 76 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8561 (mmt180) REVERT: L 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7632 (p0) REVERT: L 46 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8133 (ttmm) REVERT: L 68 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7712 (ttpp) REVERT: L 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8550 (mmt180) REVERT: M 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7631 (p0) REVERT: M 46 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8114 (ttmm) REVERT: M 68 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7708 (ttpp) REVERT: M 76 ARG cc_start: 0.8937 (mmt-90) cc_final: 0.8557 (mmt180) REVERT: N 41 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7630 (p0) REVERT: N 46 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8121 (ttmm) REVERT: N 68 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7695 (ttpp) REVERT: N 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8550 (mmt180) REVERT: O 41 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7630 (p0) REVERT: O 46 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8125 (ttmm) REVERT: O 68 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7715 (ttpp) REVERT: O 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8553 (mmt180) REVERT: P 41 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7640 (p0) REVERT: P 46 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8142 (ttmm) REVERT: P 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7720 (ttpp) REVERT: P 76 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8551 (mmt180) REVERT: Q 41 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7630 (p0) REVERT: Q 46 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8125 (ttmm) REVERT: Q 68 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7715 (ttpp) REVERT: Q 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8553 (mmt180) REVERT: R 41 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7640 (p0) REVERT: R 46 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8143 (ttmm) REVERT: R 68 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7720 (ttpp) REVERT: R 76 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8551 (mmt180) REVERT: S 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7631 (p0) REVERT: S 46 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8133 (ttmm) REVERT: S 68 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7712 (ttpp) REVERT: S 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8550 (mmt180) REVERT: T 41 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.7639 (p0) REVERT: T 46 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8140 (ttmm) REVERT: T 68 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7700 (ttpp) REVERT: T 76 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8561 (mmt180) REVERT: U 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7631 (p0) REVERT: U 46 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8113 (ttmm) REVERT: U 68 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7708 (ttpp) REVERT: U 76 ARG cc_start: 0.8937 (mmt-90) cc_final: 0.8557 (mmt180) REVERT: V 41 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7630 (p0) REVERT: V 46 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8121 (ttmm) REVERT: V 68 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7696 (ttpp) REVERT: V 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8550 (mmt180) REVERT: W 41 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7630 (p0) REVERT: W 46 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8121 (ttmm) REVERT: W 68 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7695 (ttpp) REVERT: W 76 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8550 (mmt180) REVERT: X 41 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7631 (p0) REVERT: X 46 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8113 (ttmm) REVERT: X 68 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7708 (ttpp) REVERT: X 76 ARG cc_start: 0.8937 (mmt-90) cc_final: 0.8557 (mmt180) outliers start: 144 outliers final: 72 residues processed: 1056 average time/residue: 0.7995 time to fit residues: 1003.2885 Evaluate side-chains 1008 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 912 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 67 MET 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 67 MET Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 67 MET 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 67 MET 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 K residue 67 MET Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 116 LYS 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 116 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 116 LYS Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 116 LYS 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 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 116 LYS 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 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 116 LYS 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: 3.9990 chunk 202 optimal weight: 0.7980 chunk 354 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 363 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 8 ASN C 8 ASN D 8 ASN E 8 ASN F 8 ASN G 8 ASN H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN W 8 ASN X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.106067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.083334 restraints weight = 307416.583| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.87 r_work: 0.2531 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 36312 Z= 0.169 Angle : 0.526 5.115 49104 Z= 0.288 Chirality : 0.039 0.139 5112 Planarity : 0.003 0.025 6480 Dihedral : 13.030 179.940 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.58 % Allowed : 1.16 % Favored : 98.26 % Rotamer: Outliers : 4.32 % Allowed : 23.46 % Favored : 72.22 % 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 are not related in a simple way. whole: 4.80 (0.12), residues: 4320 helix: 3.94 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.28 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 40 TYR 0.014 0.001 TYR E 134 PHE 0.013 0.002 PHE C 38 TRP 0.002 0.001 TRP O 90 HIS 0.006 0.001 HIS G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (36312) covalent geometry : angle 0.52630 / 0.29 (49104) hydrogen bonds : bond 0.07093 / 4.72 ( 2640) hydrogen bonds : angle 3.46813 / 2.52 ( 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 1104 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 960 time to evaluate : 1.529 Fit side-chains REVERT: A 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7683 (p0) REVERT: A 46 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8098 (ttmm) REVERT: A 68 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7761 (ttpp) REVERT: A 76 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8591 (mmt180) REVERT: B 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7672 (p0) REVERT: B 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8094 (ttmm) REVERT: B 68 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7746 (ttpp) REVERT: B 76 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: C 41 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7685 (p0) REVERT: C 46 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8105 (ttmm) REVERT: C 68 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7757 (ttpp) REVERT: C 76 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8582 (mmt180) REVERT: D 41 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7669 (p0) REVERT: D 46 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8087 (ttmm) REVERT: D 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7748 (ttpp) REVERT: D 76 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: E 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7672 (p0) REVERT: E 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8094 (ttmm) REVERT: E 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7747 (ttpp) REVERT: E 76 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: F 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7683 (p0) REVERT: F 46 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8097 (ttmm) REVERT: F 68 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7761 (ttpp) REVERT: F 76 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8591 (mmt180) REVERT: G 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7683 (p0) REVERT: G 46 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8097 (ttmm) REVERT: G 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7761 (ttpp) REVERT: G 76 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8591 (mmt180) REVERT: H 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7672 (p0) REVERT: H 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8094 (ttmm) REVERT: H 68 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7746 (ttpp) REVERT: H 76 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: I 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7676 (p0) REVERT: I 46 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8093 (ttmm) REVERT: I 68 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7736 (ttpp) REVERT: I 76 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: J 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7678 (p0) REVERT: J 46 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8103 (ttmm) REVERT: J 68 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7753 (ttpp) REVERT: J 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8583 (mmt180) REVERT: K 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7676 (p0) REVERT: K 46 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8093 (ttmm) REVERT: K 68 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7736 (ttpp) REVERT: K 76 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: L 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7678 (p0) REVERT: L 46 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8103 (ttmm) REVERT: L 68 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7753 (ttpp) REVERT: L 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: M 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7676 (p0) REVERT: M 46 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8080 (ttmm) REVERT: M 68 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7740 (ttpp) REVERT: M 76 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8580 (mmt180) REVERT: N 41 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7682 (p0) REVERT: N 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8089 (ttmm) REVERT: N 68 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7742 (ttpp) REVERT: N 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: O 41 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7669 (p0) REVERT: O 46 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8087 (ttmm) REVERT: O 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7748 (ttpp) REVERT: O 76 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: P 41 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7685 (p0) REVERT: P 46 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8105 (ttmm) REVERT: P 68 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7757 (ttpp) REVERT: P 76 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8582 (mmt180) REVERT: Q 41 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7669 (p0) REVERT: Q 46 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8087 (ttmm) REVERT: Q 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7748 (ttpp) REVERT: Q 76 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: R 41 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7685 (p0) REVERT: R 46 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8105 (ttmm) REVERT: R 68 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7757 (ttpp) REVERT: R 76 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8582 (mmt180) REVERT: S 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7678 (p0) REVERT: S 46 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8103 (ttmm) REVERT: S 68 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7753 (ttpp) REVERT: S 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: T 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7676 (p0) REVERT: T 46 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8093 (ttmm) REVERT: T 68 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7736 (ttpp) REVERT: T 76 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8584 (mmt180) REVERT: U 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7676 (p0) REVERT: U 46 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8080 (ttmm) REVERT: U 68 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7740 (ttpp) REVERT: U 76 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8580 (mmt180) REVERT: V 41 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7681 (p0) REVERT: V 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8089 (ttmm) REVERT: V 68 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7742 (ttpp) REVERT: V 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: W 41 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7681 (p0) REVERT: W 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8089 (ttmm) REVERT: W 68 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7742 (ttpp) REVERT: W 76 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8587 (mmt180) REVERT: X 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7676 (p0) REVERT: X 46 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8080 (ttmm) REVERT: X 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7740 (ttpp) REVERT: X 76 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8580 (mmt180) outliers start: 144 outliers final: 120 residues processed: 1008 average time/residue: 0.7822 time to fit residues: 939.7794 Evaluate side-chains 1080 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 936 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 67 MET 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 41 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 67 MET 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 61 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 67 MET 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 67 MET Chi-restraints excluded: chain J residue 116 LYS 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 61 GLU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 116 LYS 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 61 GLU Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 159 GLU Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 116 LYS 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 61 GLU Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 116 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 61 GLU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 116 LYS Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 159 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 251 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 394 optimal weight: 6.9990 chunk 236 optimal weight: 0.0170 chunk 36 optimal weight: 5.9990 chunk 307 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 8 ASN C 8 ASN D 8 ASN E 8 ASN F 8 ASN G 8 ASN H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN W 8 ASN X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.081111 restraints weight = 316843.168| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.78 r_work: 0.2474 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 36312 Z= 0.212 Angle : 0.562 5.113 49104 Z= 0.307 Chirality : 0.041 0.146 5112 Planarity : 0.003 0.025 6480 Dihedral : 13.003 179.225 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.58 % Allowed : 1.74 % Favored : 97.67 % Rotamer: Outliers : 5.56 % Allowed : 23.46 % Favored : 70.99 % 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 are not related in a simple way. whole: 4.70 (0.12), residues: 4320 helix: 3.93 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.48 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 40 TYR 0.015 0.002 TYR U 134 PHE 0.016 0.002 PHE M 38 TRP 0.002 0.001 TRP M 90 HIS 0.005 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (36312) covalent geometry : angle 0.56190 / 0.31 (49104) hydrogen bonds : bond 0.08127 / 5.40 ( 2640) hydrogen bonds : angle 3.54372 / 2.57 ( 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 1152 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 960 time to evaluate : 1.401 Fit side-chains REVERT: A 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7745 (p0) REVERT: A 46 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8208 (ttmm) REVERT: A 68 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7857 (ttpp) REVERT: A 76 ARG cc_start: 0.8980 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: A 110 SER cc_start: 0.8993 (t) cc_final: 0.8779 (p) REVERT: B 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7745 (p0) REVERT: B 46 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8205 (ttmm) REVERT: B 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7841 (ttpp) REVERT: B 76 ARG cc_start: 0.8977 (mmt-90) cc_final: 0.8635 (mmt180) REVERT: B 110 SER cc_start: 0.8990 (t) cc_final: 0.8776 (p) REVERT: C 41 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7751 (p0) REVERT: C 46 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8220 (ttmm) REVERT: C 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7843 (ttpp) REVERT: C 76 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: C 110 SER cc_start: 0.8996 (t) cc_final: 0.8782 (p) REVERT: D 41 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7739 (p0) REVERT: D 46 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8199 (ttmm) REVERT: D 68 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7846 (ttpp) REVERT: D 76 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: D 110 SER cc_start: 0.8988 (t) cc_final: 0.8775 (p) REVERT: E 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7745 (p0) REVERT: E 46 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8205 (ttmm) REVERT: E 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7841 (ttpp) REVERT: E 76 ARG cc_start: 0.8977 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: E 110 SER cc_start: 0.8990 (t) cc_final: 0.8776 (p) REVERT: F 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7745 (p0) REVERT: F 46 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8208 (ttmm) REVERT: F 68 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7857 (ttpp) REVERT: F 76 ARG cc_start: 0.8980 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: F 110 SER cc_start: 0.8993 (t) cc_final: 0.8780 (p) REVERT: G 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7745 (p0) REVERT: G 46 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8208 (ttmm) REVERT: G 68 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7857 (ttpp) REVERT: G 76 ARG cc_start: 0.8979 (mmt-90) cc_final: 0.8637 (mmt180) REVERT: G 110 SER cc_start: 0.8993 (t) cc_final: 0.8780 (p) REVERT: H 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7745 (p0) REVERT: H 46 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8205 (ttmm) REVERT: H 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7841 (ttpp) REVERT: H 76 ARG cc_start: 0.8977 (mmt-90) cc_final: 0.8635 (mmt180) REVERT: H 110 SER cc_start: 0.8990 (t) cc_final: 0.8776 (p) REVERT: I 41 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7742 (p0) REVERT: I 46 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8215 (ttmm) REVERT: I 68 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7826 (ttpp) REVERT: I 76 ARG cc_start: 0.8983 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: I 110 SER cc_start: 0.8997 (t) cc_final: 0.8783 (p) REVERT: J 41 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7745 (p0) REVERT: J 46 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8209 (ttmm) REVERT: J 68 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7848 (ttpp) REVERT: J 76 ARG cc_start: 0.8978 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: J 110 SER cc_start: 0.8986 (t) cc_final: 0.8772 (p) REVERT: K 41 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7742 (p0) REVERT: K 46 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8215 (ttmm) REVERT: K 68 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7826 (ttpp) REVERT: K 76 ARG cc_start: 0.8983 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: K 110 SER cc_start: 0.8997 (t) cc_final: 0.8783 (p) REVERT: L 41 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.7745 (p0) REVERT: L 46 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8209 (ttmm) REVERT: L 68 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7848 (ttpp) REVERT: L 76 ARG cc_start: 0.8978 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: L 110 SER cc_start: 0.8985 (t) cc_final: 0.8772 (p) REVERT: M 41 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7741 (p0) REVERT: M 46 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8204 (ttmm) REVERT: M 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7840 (ttpp) REVERT: M 76 ARG cc_start: 0.8982 (mmt-90) cc_final: 0.8637 (mmt180) REVERT: M 110 SER cc_start: 0.8990 (t) cc_final: 0.8776 (p) REVERT: N 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7749 (p0) REVERT: N 46 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8208 (ttmm) REVERT: N 68 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7839 (ttpp) REVERT: N 76 ARG cc_start: 0.8984 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: N 110 SER cc_start: 0.8992 (t) cc_final: 0.8780 (p) REVERT: O 41 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7740 (p0) REVERT: O 46 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8199 (ttmm) REVERT: O 68 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7846 (ttpp) REVERT: O 76 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: O 110 SER cc_start: 0.8988 (t) cc_final: 0.8775 (p) REVERT: P 41 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7750 (p0) REVERT: P 46 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8220 (ttmm) REVERT: P 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7843 (ttpp) REVERT: P 76 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: P 110 SER cc_start: 0.8996 (t) cc_final: 0.8782 (p) REVERT: Q 41 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7739 (p0) REVERT: Q 46 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8199 (ttmm) REVERT: Q 68 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7846 (ttpp) REVERT: Q 76 ARG cc_start: 0.8975 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: Q 110 SER cc_start: 0.8988 (t) cc_final: 0.8775 (p) REVERT: R 41 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.7750 (p0) REVERT: R 46 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8220 (ttmm) REVERT: R 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7843 (ttpp) REVERT: R 76 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: R 110 SER cc_start: 0.8996 (t) cc_final: 0.8782 (p) REVERT: S 41 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.7745 (p0) REVERT: S 46 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8209 (ttmm) REVERT: S 68 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7848 (ttpp) REVERT: S 76 ARG cc_start: 0.8978 (mmt-90) cc_final: 0.8634 (mmt180) REVERT: S 110 SER cc_start: 0.8986 (t) cc_final: 0.8772 (p) REVERT: T 41 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7742 (p0) REVERT: T 46 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8215 (ttmm) REVERT: T 68 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7826 (ttpp) REVERT: T 76 ARG cc_start: 0.8983 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: T 110 SER cc_start: 0.8997 (t) cc_final: 0.8783 (p) REVERT: U 41 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7741 (p0) REVERT: U 46 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8204 (ttmm) REVERT: U 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7840 (ttpp) REVERT: U 76 ARG cc_start: 0.8982 (mmt-90) cc_final: 0.8637 (mmt180) REVERT: U 110 SER cc_start: 0.8990 (t) cc_final: 0.8776 (p) REVERT: V 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7748 (p0) REVERT: V 46 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8208 (ttmm) REVERT: V 68 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7839 (ttpp) REVERT: V 76 ARG cc_start: 0.8984 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: V 110 SER cc_start: 0.8992 (t) cc_final: 0.8779 (p) REVERT: W 41 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7749 (p0) REVERT: W 46 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8208 (ttmm) REVERT: W 68 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7839 (ttpp) REVERT: W 76 ARG cc_start: 0.8984 (mmt-90) cc_final: 0.8638 (mmt180) REVERT: W 110 SER cc_start: 0.8992 (t) cc_final: 0.8779 (p) REVERT: X 41 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7741 (p0) REVERT: X 46 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8204 (ttmm) REVERT: X 68 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7840 (ttpp) REVERT: X 76 ARG cc_start: 0.8982 (mmt-90) cc_final: 0.8637 (mmt180) REVERT: X 110 SER cc_start: 0.8990 (t) cc_final: 0.8776 (p) outliers start: 192 outliers final: 144 residues processed: 1032 average time/residue: 0.7968 time to fit residues: 974.9730 Evaluate side-chains 1104 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 936 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 106 SER 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 41 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 106 SER 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 61 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 106 SER 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 67 MET Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 116 LYS 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 61 GLU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 116 LYS 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 61 GLU Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 159 GLU Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 106 SER Chi-restraints excluded: chain U residue 116 LYS 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 61 GLU Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 106 SER Chi-restraints excluded: chain V residue 116 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 61 GLU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 116 LYS Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 159 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 287 optimal weight: 0.6980 chunk 231 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 8 ASN C 8 ASN D 8 ASN E 8 ASN F 8 ASN G 8 ASN H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN W 8 ASN X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.106533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.083850 restraints weight = 313467.096| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.86 r_work: 0.2496 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 36312 Z= 0.167 Angle : 0.517 5.105 49104 Z= 0.284 Chirality : 0.039 0.136 5112 Planarity : 0.003 0.025 6480 Dihedral : 13.014 179.742 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.58 % Allowed : 0.80 % Favored : 98.62 % Rotamer: Outliers : 4.94 % Allowed : 23.46 % Favored : 71.60 % 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 are not related in a simple way. whole: 4.92 (0.12), residues: 4320 helix: 4.00 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.12 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 40 TYR 0.014 0.001 TYR M 134 PHE 0.013 0.002 PHE R 38 TRP 0.002 0.001 TRP B 90 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (36312) covalent geometry : angle 0.51667 / 0.28 (49104) hydrogen bonds : bond 0.07007 / 4.66 ( 2640) hydrogen bonds : angle 3.44029 / 2.50 ( 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 1128 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 960 time to evaluate : 1.484 Fit side-chains REVERT: A 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7660 (p0) REVERT: A 46 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8092 (ttmm) REVERT: A 68 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7729 (ttpp) REVERT: A 76 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8610 (mmt180) REVERT: A 110 SER cc_start: 0.8918 (t) cc_final: 0.8691 (p) REVERT: B 41 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7649 (p0) REVERT: B 46 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8084 (ttmm) REVERT: B 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7708 (ttpp) REVERT: B 76 ARG cc_start: 0.8935 (mmt-90) cc_final: 0.8611 (mmt180) REVERT: B 110 SER cc_start: 0.8911 (t) cc_final: 0.8685 (p) REVERT: C 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7661 (p0) REVERT: C 46 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8098 (ttmm) REVERT: C 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7721 (ttpp) REVERT: C 76 ARG cc_start: 0.8941 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: C 110 SER cc_start: 0.8936 (t) cc_final: 0.8711 (p) REVERT: D 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7659 (p0) REVERT: D 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8075 (ttmm) REVERT: D 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7720 (ttpp) REVERT: D 76 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8617 (mmt180) REVERT: D 110 SER cc_start: 0.8923 (t) cc_final: 0.8698 (p) REVERT: E 41 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7649 (p0) REVERT: E 46 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8084 (ttmm) REVERT: E 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7708 (ttpp) REVERT: E 76 ARG cc_start: 0.8935 (mmt-90) cc_final: 0.8611 (mmt180) REVERT: E 110 SER cc_start: 0.8911 (t) cc_final: 0.8684 (p) REVERT: F 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7660 (p0) REVERT: F 46 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8092 (ttmm) REVERT: F 68 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7729 (ttpp) REVERT: F 76 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8610 (mmt180) REVERT: F 110 SER cc_start: 0.8918 (t) cc_final: 0.8692 (p) REVERT: G 41 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7660 (p0) REVERT: G 46 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8093 (ttmm) REVERT: G 68 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7729 (ttpp) REVERT: G 76 ARG cc_start: 0.8936 (mmt-90) cc_final: 0.8611 (mmt180) REVERT: G 110 SER cc_start: 0.8918 (t) cc_final: 0.8691 (p) REVERT: H 41 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7649 (p0) REVERT: H 46 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8084 (ttmm) REVERT: H 68 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7708 (ttpp) REVERT: H 76 ARG cc_start: 0.8935 (mmt-90) cc_final: 0.8611 (mmt180) REVERT: H 110 SER cc_start: 0.8911 (t) cc_final: 0.8684 (p) REVERT: I 41 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7655 (p0) REVERT: I 46 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8093 (ttmm) REVERT: I 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7706 (ttpp) REVERT: I 76 ARG cc_start: 0.8942 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: I 110 SER cc_start: 0.8931 (t) cc_final: 0.8704 (p) REVERT: J 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7658 (p0) REVERT: J 46 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8102 (ttmm) REVERT: J 68 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7727 (ttpp) REVERT: J 76 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8616 (mmt180) REVERT: J 110 SER cc_start: 0.8918 (t) cc_final: 0.8694 (p) REVERT: K 41 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7655 (p0) REVERT: K 46 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8093 (ttmm) REVERT: K 68 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7705 (ttpp) REVERT: K 76 ARG cc_start: 0.8942 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: K 110 SER cc_start: 0.8931 (t) cc_final: 0.8704 (p) REVERT: L 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7658 (p0) REVERT: L 46 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8102 (ttmm) REVERT: L 68 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7727 (ttpp) REVERT: L 76 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8616 (mmt180) REVERT: L 110 SER cc_start: 0.8918 (t) cc_final: 0.8693 (p) REVERT: M 41 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7649 (p0) REVERT: M 46 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8078 (ttmm) REVERT: M 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7717 (ttpp) REVERT: M 76 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8617 (mmt180) REVERT: M 110 SER cc_start: 0.8930 (t) cc_final: 0.8704 (p) REVERT: N 41 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7672 (p0) REVERT: N 46 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8085 (ttmm) REVERT: N 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7712 (ttpp) REVERT: N 76 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8631 (mmt180) REVERT: N 110 SER cc_start: 0.8926 (t) cc_final: 0.8699 (p) REVERT: O 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7659 (p0) REVERT: O 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8075 (ttmm) REVERT: O 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7720 (ttpp) REVERT: O 76 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: O 110 SER cc_start: 0.8923 (t) cc_final: 0.8698 (p) REVERT: P 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7660 (p0) REVERT: P 46 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8098 (ttmm) REVERT: P 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7721 (ttpp) REVERT: P 76 ARG cc_start: 0.8941 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: P 110 SER cc_start: 0.8937 (t) cc_final: 0.8712 (p) REVERT: Q 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7659 (p0) REVERT: Q 46 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8076 (ttmm) REVERT: Q 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7720 (ttpp) REVERT: Q 76 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8617 (mmt180) REVERT: Q 110 SER cc_start: 0.8923 (t) cc_final: 0.8698 (p) REVERT: R 41 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7660 (p0) REVERT: R 46 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8098 (ttmm) REVERT: R 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7721 (ttpp) REVERT: R 76 ARG cc_start: 0.8941 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: R 110 SER cc_start: 0.8937 (t) cc_final: 0.8712 (p) REVERT: S 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7658 (p0) REVERT: S 46 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8102 (ttmm) REVERT: S 68 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7727 (ttpp) REVERT: S 76 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8616 (mmt180) REVERT: S 110 SER cc_start: 0.8918 (t) cc_final: 0.8693 (p) REVERT: T 41 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7655 (p0) REVERT: T 46 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8093 (ttmm) REVERT: T 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7706 (ttpp) REVERT: T 76 ARG cc_start: 0.8942 (mmt-90) cc_final: 0.8618 (mmt180) REVERT: T 110 SER cc_start: 0.8931 (t) cc_final: 0.8704 (p) REVERT: U 41 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7649 (p0) REVERT: U 46 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8078 (ttmm) REVERT: U 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7717 (ttpp) REVERT: U 76 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8617 (mmt180) REVERT: U 110 SER cc_start: 0.8930 (t) cc_final: 0.8704 (p) REVERT: V 41 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7672 (p0) REVERT: V 46 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8085 (ttmm) REVERT: V 68 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7713 (ttpp) REVERT: V 76 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8631 (mmt180) REVERT: V 110 SER cc_start: 0.8926 (t) cc_final: 0.8699 (p) REVERT: W 41 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7671 (p0) REVERT: W 46 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8085 (ttmm) REVERT: W 68 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7712 (ttpp) REVERT: W 76 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8631 (mmt180) REVERT: W 110 SER cc_start: 0.8926 (t) cc_final: 0.8699 (p) REVERT: X 41 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7650 (p0) REVERT: X 46 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8078 (ttmm) REVERT: X 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7717 (ttpp) REVERT: X 76 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8617 (mmt180) REVERT: X 110 SER cc_start: 0.8930 (t) cc_final: 0.8704 (p) outliers start: 168 outliers final: 144 residues processed: 1008 average time/residue: 0.7912 time to fit residues: 948.9116 Evaluate side-chains 1104 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 936 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 106 SER 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 41 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 106 SER 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 61 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 106 SER 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 67 MET Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 116 LYS 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 61 GLU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 116 LYS 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 61 GLU Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 159 GLU Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 106 SER Chi-restraints excluded: chain U residue 116 LYS 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 61 GLU Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 106 SER Chi-restraints excluded: chain V residue 116 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 61 GLU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 116 LYS Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 159 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 88 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 8 ASN C 8 ASN D 8 ASN E 8 ASN F 8 ASN G 8 ASN H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN S 8 ASN T 8 ASN U 8 ASN V 8 ASN W 8 ASN X 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.106780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.084229 restraints weight = 302980.308| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.81 r_work: 0.2513 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 36312 Z= 0.167 Angle : 0.515 5.101 49104 Z= 0.284 Chirality : 0.039 0.135 5112 Planarity : 0.003 0.025 6480 Dihedral : 13.005 179.704 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.94 % Allowed : 23.46 % Favored : 71.60 % 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 are not related in a simple way. whole: 4.99 (0.12), residues: 4320 helix: 4.03 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.05 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 40 TYR 0.015 0.001 TYR J 134 PHE 0.014 0.002 PHE M 38 TRP 0.002 0.001 TRP I 90 HIS 0.006 0.001 HIS J 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (36312) covalent geometry : angle 0.51516 / 0.28 (49104) hydrogen bonds : bond 0.07019 / 4.67 ( 2640) hydrogen bonds : angle 3.43003 / 2.49 ( 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 1104 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 936 time to evaluate : 1.430 Fit side-chains REVERT: A 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7679 (p0) REVERT: A 46 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8120 (ttmm) REVERT: A 68 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7755 (ttpp) REVERT: A 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: A 110 SER cc_start: 0.8947 (t) cc_final: 0.8725 (p) REVERT: B 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7670 (p0) REVERT: B 46 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8115 (ttmm) REVERT: B 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7734 (ttpp) REVERT: B 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: B 110 SER cc_start: 0.8940 (t) cc_final: 0.8718 (p) REVERT: C 41 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7682 (p0) REVERT: C 46 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8124 (ttmm) REVERT: C 68 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7746 (ttpp) REVERT: C 76 ARG cc_start: 0.8957 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: C 110 SER cc_start: 0.8967 (t) cc_final: 0.8747 (p) REVERT: D 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7690 (p0) REVERT: D 46 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8107 (ttmm) REVERT: D 68 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7743 (ttpp) REVERT: D 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8646 (mmt180) REVERT: D 110 SER cc_start: 0.8951 (t) cc_final: 0.8731 (p) REVERT: E 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7670 (p0) REVERT: E 46 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8115 (ttmm) REVERT: E 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7734 (ttpp) REVERT: E 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: E 110 SER cc_start: 0.8940 (t) cc_final: 0.8718 (p) REVERT: F 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7679 (p0) REVERT: F 46 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8120 (ttmm) REVERT: F 68 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7755 (ttpp) REVERT: F 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: F 110 SER cc_start: 0.8947 (t) cc_final: 0.8725 (p) REVERT: G 41 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7680 (p0) REVERT: G 46 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8120 (ttmm) REVERT: G 68 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7755 (ttpp) REVERT: G 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: G 110 SER cc_start: 0.8947 (t) cc_final: 0.8725 (p) REVERT: H 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7670 (p0) REVERT: H 46 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8115 (ttmm) REVERT: H 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7734 (ttpp) REVERT: H 76 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8639 (mmt180) REVERT: H 110 SER cc_start: 0.8940 (t) cc_final: 0.8718 (p) REVERT: I 41 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7675 (p0) REVERT: I 46 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8123 (ttmm) REVERT: I 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7731 (ttpp) REVERT: I 76 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8653 (mmt180) REVERT: I 110 SER cc_start: 0.8957 (t) cc_final: 0.8734 (p) REVERT: J 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7691 (p0) REVERT: J 46 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8129 (ttmm) REVERT: J 68 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7755 (ttpp) REVERT: J 76 ARG cc_start: 0.8959 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: J 110 SER cc_start: 0.8945 (t) cc_final: 0.8725 (p) REVERT: K 41 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7676 (p0) REVERT: K 46 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8122 (ttmm) REVERT: K 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7731 (ttpp) REVERT: K 76 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8652 (mmt180) REVERT: K 110 SER cc_start: 0.8957 (t) cc_final: 0.8734 (p) REVERT: L 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7691 (p0) REVERT: L 46 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8130 (ttmm) REVERT: L 68 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7755 (ttpp) REVERT: L 76 ARG cc_start: 0.8959 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: L 110 SER cc_start: 0.8945 (t) cc_final: 0.8725 (p) REVERT: M 41 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7675 (p0) REVERT: M 46 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8110 (ttmm) REVERT: M 68 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7743 (ttpp) REVERT: M 76 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8653 (mmt180) REVERT: M 110 SER cc_start: 0.8949 (t) cc_final: 0.8726 (p) REVERT: N 41 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7705 (p0) REVERT: N 46 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8118 (ttmm) REVERT: N 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7733 (ttpp) REVERT: N 76 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8656 (mmt180) REVERT: N 110 SER cc_start: 0.8961 (t) cc_final: 0.8737 (p) REVERT: O 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7690 (p0) REVERT: O 46 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8107 (ttmm) REVERT: O 68 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7742 (ttpp) REVERT: O 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8646 (mmt180) REVERT: O 110 SER cc_start: 0.8952 (t) cc_final: 0.8731 (p) REVERT: P 41 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7683 (p0) REVERT: P 46 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8125 (ttmm) REVERT: P 68 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7747 (ttpp) REVERT: P 76 ARG cc_start: 0.8957 (mmt-90) cc_final: 0.8646 (mmt180) REVERT: P 110 SER cc_start: 0.8968 (t) cc_final: 0.8747 (p) REVERT: Q 41 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7690 (p0) REVERT: Q 46 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8106 (ttmm) REVERT: Q 68 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7743 (ttpp) REVERT: Q 76 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8646 (mmt180) REVERT: Q 110 SER cc_start: 0.8951 (t) cc_final: 0.8731 (p) REVERT: R 41 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7682 (p0) REVERT: R 46 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8124 (ttmm) REVERT: R 68 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7746 (ttpp) REVERT: R 76 ARG cc_start: 0.8957 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: R 110 SER cc_start: 0.8968 (t) cc_final: 0.8747 (p) REVERT: S 41 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7691 (p0) REVERT: S 46 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8130 (ttmm) REVERT: S 68 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7755 (ttpp) REVERT: S 76 ARG cc_start: 0.8959 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: S 110 SER cc_start: 0.8945 (t) cc_final: 0.8725 (p) REVERT: T 41 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7676 (p0) REVERT: T 46 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8122 (ttmm) REVERT: T 68 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7731 (ttpp) REVERT: T 76 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8652 (mmt180) REVERT: T 110 SER cc_start: 0.8957 (t) cc_final: 0.8734 (p) REVERT: U 41 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7674 (p0) REVERT: U 46 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8110 (ttmm) REVERT: U 68 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7742 (ttpp) REVERT: U 76 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8653 (mmt180) REVERT: U 110 SER cc_start: 0.8949 (t) cc_final: 0.8726 (p) REVERT: V 41 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7705 (p0) REVERT: V 46 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8118 (ttmm) REVERT: V 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7733 (ttpp) REVERT: V 76 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8656 (mmt180) REVERT: V 110 SER cc_start: 0.8961 (t) cc_final: 0.8737 (p) REVERT: W 41 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7705 (p0) REVERT: W 46 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8118 (ttmm) REVERT: W 68 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7733 (ttpp) REVERT: W 76 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8656 (mmt180) REVERT: W 110 SER cc_start: 0.8960 (t) cc_final: 0.8737 (p) REVERT: X 41 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7674 (p0) REVERT: X 46 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8110 (ttmm) REVERT: X 68 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7742 (ttpp) REVERT: X 76 ARG cc_start: 0.8962 (mmt-90) cc_final: 0.8653 (mmt180) REVERT: X 110 SER cc_start: 0.8949 (t) cc_final: 0.8726 (p) outliers start: 168 outliers final: 144 residues processed: 984 average time/residue: 0.7737 time to fit residues: 908.2903 Evaluate side-chains 1104 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 936 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 106 SER 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 41 ASP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 106 SER 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 61 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 106 SER 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 67 MET Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 116 LYS 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 61 GLU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 116 LYS 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 61 GLU Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 159 GLU Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 106 SER Chi-restraints excluded: chain U residue 116 LYS 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 61 GLU Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 106 SER Chi-restraints excluded: chain V residue 116 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 61 GLU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 116 LYS Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 159 GLU 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: 0.0050 chunk 250 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 360 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 8 ASN D 8 ASN D 102 HIS E 8 ASN F 8 ASN F 102 HIS G 8 ASN H 8 ASN I 8 ASN J 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 T 8 ASN T 102 HIS U 8 ASN V 8 ASN V 102 HIS W 8 ASN X 8 ASN X 102 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.113554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.090626 restraints weight = 326230.761| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.00 r_work: 0.2638 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1476 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 36312 Z= 0.119 Angle : 0.458 5.085 49104 Z= 0.255 Chirality : 0.036 0.124 5112 Planarity : 0.003 0.025 6480 Dihedral : 12.976 179.797 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.45 % Allowed : 24.95 % Favored : 71.60 % 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 are not related in a simple way. whole: 5.37 (0.12), residues: 4320 helix: 4.38 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.16 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 76 TYR 0.014 0.001 TYR Q 134 PHE 0.011 0.002 PHE G 38 TRP 0.003 0.001 TRP L 90 HIS 0.005 0.001 HIS J 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (36312) covalent geometry : angle 0.45822 / 0.25 (49104) hydrogen bonds : bond 0.05017 / 3.34 ( 2640) hydrogen bonds : angle 3.22250 / 2.34 ( 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 1046 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 936 time to evaluate : 1.436 Fit side-chains REVERT: A 41 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7352 (p0) REVERT: A 46 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7762 (mttp) REVERT: A 68 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7666 (ttpp) REVERT: A 76 ARG cc_start: 0.8884 (mmt-90) cc_final: 0.8470 (mmt-90) REVERT: A 110 SER cc_start: 0.8904 (t) cc_final: 0.8660 (p) REVERT: B 41 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7341 (p0) REVERT: B 46 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7752 (mttp) REVERT: B 68 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7644 (ttpp) REVERT: B 76 ARG cc_start: 0.8886 (mmt-90) cc_final: 0.8473 (mmt-90) REVERT: B 110 SER cc_start: 0.8914 (t) cc_final: 0.8670 (p) REVERT: C 41 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7346 (p0) REVERT: C 46 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7769 (mttp) REVERT: C 68 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7645 (ttpp) REVERT: C 76 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8483 (mmt-90) REVERT: C 110 SER cc_start: 0.8918 (t) cc_final: 0.8673 (p) REVERT: D 41 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7318 (p0) REVERT: D 46 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7749 (mttp) REVERT: D 68 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7644 (ttpp) REVERT: D 76 ARG cc_start: 0.8886 (mmt-90) cc_final: 0.8473 (mmt-90) REVERT: D 110 SER cc_start: 0.8916 (t) cc_final: 0.8671 (p) REVERT: E 41 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7344 (p0) REVERT: E 46 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7755 (mttp) REVERT: E 68 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7644 (ttpp) REVERT: E 76 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8472 (mmt-90) REVERT: E 110 SER cc_start: 0.8915 (t) cc_final: 0.8671 (p) REVERT: F 41 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7348 (p0) REVERT: F 46 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7763 (mttp) REVERT: F 68 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7670 (ttpp) REVERT: F 76 ARG cc_start: 0.8882 (mmt-90) cc_final: 0.8469 (mmt-90) REVERT: F 110 SER cc_start: 0.8902 (t) cc_final: 0.8656 (p) REVERT: G 41 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7349 (p0) REVERT: G 46 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7762 (mttp) REVERT: G 68 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7667 (ttpp) REVERT: G 76 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8466 (mmt-90) REVERT: G 110 SER cc_start: 0.8905 (t) cc_final: 0.8660 (p) REVERT: H 41 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7344 (p0) REVERT: H 46 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7754 (mttp) REVERT: H 68 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7639 (ttpp) REVERT: H 76 ARG cc_start: 0.8891 (mmt-90) cc_final: 0.8475 (mmt-90) REVERT: H 110 SER cc_start: 0.8916 (t) cc_final: 0.8671 (p) REVERT: I 41 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7336 (p0) REVERT: I 46 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7749 (mttp) REVERT: I 68 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7655 (ttpp) REVERT: I 76 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: I 110 SER cc_start: 0.8918 (t) cc_final: 0.8674 (p) REVERT: J 41 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7342 (p0) REVERT: J 46 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7765 (mttp) REVERT: J 68 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7652 (ttpp) REVERT: J 76 ARG cc_start: 0.8902 (mmt-90) cc_final: 0.8491 (mmt-90) REVERT: J 110 SER cc_start: 0.8913 (t) cc_final: 0.8672 (p) REVERT: K 41 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7338 (p0) REVERT: K 46 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7750 (mttp) REVERT: K 68 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7657 (ttpp) REVERT: K 76 ARG cc_start: 0.8897 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: K 110 SER cc_start: 0.8917 (t) cc_final: 0.8673 (p) REVERT: L 41 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7344 (p0) REVERT: L 46 LYS cc_start: 0.8282 (ttpp) cc_final: 0.7768 (mttp) REVERT: L 68 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7654 (ttpp) REVERT: L 76 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8490 (mmt-90) REVERT: L 110 SER cc_start: 0.8908 (t) cc_final: 0.8666 (p) REVERT: M 41 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7341 (p0) REVERT: M 46 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7744 (mttp) REVERT: M 68 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7649 (ttpp) REVERT: M 76 ARG cc_start: 0.8898 (mmt-90) cc_final: 0.8485 (mmt-90) REVERT: M 110 SER cc_start: 0.8921 (t) cc_final: 0.8676 (p) REVERT: N 41 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7284 (p0) REVERT: N 46 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7754 (mttp) REVERT: N 68 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7641 (ttpp) REVERT: N 76 ARG cc_start: 0.8898 (mmt-90) cc_final: 0.8482 (mmt-90) REVERT: N 110 SER cc_start: 0.8923 (t) cc_final: 0.8677 (p) REVERT: O 41 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7319 (p0) REVERT: O 46 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7747 (mttp) REVERT: O 68 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7645 (ttpp) REVERT: O 76 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8474 (mmt-90) REVERT: O 110 SER cc_start: 0.8915 (t) cc_final: 0.8670 (p) REVERT: P 41 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7335 (p0) REVERT: P 46 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7768 (mttp) REVERT: P 68 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7642 (ttpp) REVERT: P 76 ARG cc_start: 0.8895 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: P 110 SER cc_start: 0.8918 (t) cc_final: 0.8672 (p) REVERT: Q 41 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7323 (p0) REVERT: Q 46 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7746 (mttp) REVERT: Q 68 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7640 (ttpp) REVERT: Q 76 ARG cc_start: 0.8887 (mmt-90) cc_final: 0.8472 (mmt-90) REVERT: Q 110 SER cc_start: 0.8916 (t) cc_final: 0.8671 (p) REVERT: R 41 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7334 (p0) REVERT: R 46 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7769 (mttp) REVERT: R 68 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7644 (ttpp) REVERT: R 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: R 110 SER cc_start: 0.8921 (t) cc_final: 0.8675 (p) REVERT: S 41 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7344 (p0) REVERT: S 46 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7765 (mttp) REVERT: S 68 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7651 (ttpp) REVERT: S 76 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8488 (mmt-90) REVERT: S 110 SER cc_start: 0.8912 (t) cc_final: 0.8672 (p) REVERT: T 41 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7336 (p0) REVERT: T 46 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7750 (mttp) REVERT: T 68 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7660 (ttpp) REVERT: T 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8483 (mmt-90) REVERT: T 110 SER cc_start: 0.8915 (t) cc_final: 0.8671 (p) REVERT: U 41 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7341 (p0) REVERT: U 46 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7745 (mttp) REVERT: U 68 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7647 (ttpp) REVERT: U 76 ARG cc_start: 0.8898 (mmt-90) cc_final: 0.8487 (mmt-90) REVERT: U 110 SER cc_start: 0.8920 (t) cc_final: 0.8675 (p) REVERT: V 41 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7284 (p0) REVERT: V 46 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7754 (mttp) REVERT: V 68 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7641 (ttpp) REVERT: V 76 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8485 (mmt-90) REVERT: V 110 SER cc_start: 0.8921 (t) cc_final: 0.8675 (p) REVERT: W 41 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7285 (p0) REVERT: W 46 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7756 (mttp) REVERT: W 68 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7643 (ttpp) REVERT: W 76 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8480 (mmt-90) REVERT: W 110 SER cc_start: 0.8924 (t) cc_final: 0.8679 (p) REVERT: X 41 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7339 (p0) REVERT: X 46 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7747 (mttp) REVERT: X 68 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7644 (ttpp) REVERT: X 76 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8479 (mmt-90) REVERT: X 110 SER cc_start: 0.8919 (t) cc_final: 0.8675 (p) outliers start: 110 outliers final: 38 residues processed: 950 average time/residue: 0.7776 time to fit residues: 881.9148 Evaluate side-chains 974 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 912 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 106 SER Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 106 SER 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 106 SER Chi-restraints excluded: chain X residue 159 GLU 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: 10.0000 chunk 134 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 8 ASN D 8 ASN D 102 HIS E 8 ASN F 8 ASN G 8 ASN G 102 HIS H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN L 102 HIS M 8 ASN N 8 ASN O 8 ASN P 8 ASN Q 8 ASN R 8 ASN R 102 HIS S 8 ASN T 8 ASN T 102 HIS U 8 ASN V 8 ASN V 102 HIS W 8 ASN W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.079947 restraints weight = 305126.859| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.78 r_work: 0.2477 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1472 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 36312 Z= 0.258 Angle : 0.597 5.123 49104 Z= 0.325 Chirality : 0.043 0.150 5112 Planarity : 0.004 0.027 6480 Dihedral : 12.939 178.238 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.70 % Allowed : 23.46 % Favored : 72.84 % 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 are not related in a simple way. whole: 4.80 (0.12), residues: 4320 helix: 3.94 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.15 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 40 TYR 0.016 0.002 TYR J 134 PHE 0.017 0.003 PHE S 38 TRP 0.002 0.001 TRP F 90 HIS 0.006 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (36312) covalent geometry : angle 0.59742 / 0.33 (49104) hydrogen bonds : bond 0.08733 / 5.81 ( 2640) hydrogen bonds : angle 3.53588 / 2.57 ( 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 1032 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 912 time to evaluate : 1.428 Fit side-chains REVERT: A 41 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7817 (p0) REVERT: A 46 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8283 (ttmm) REVERT: A 68 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7907 (ttpp) REVERT: A 76 ARG cc_start: 0.9016 (mmt-90) cc_final: 0.8690 (mmt180) REVERT: A 110 SER cc_start: 0.9017 (t) cc_final: 0.8813 (p) REVERT: B 41 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.7814 (p0) REVERT: B 46 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8273 (ttmm) REVERT: B 68 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7892 (ttpp) REVERT: B 76 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8677 (mmt180) REVERT: B 110 SER cc_start: 0.9011 (t) cc_final: 0.8806 (p) REVERT: C 41 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7824 (p0) REVERT: C 46 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8288 (ttmm) REVERT: C 68 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7898 (ttpp) REVERT: C 76 ARG cc_start: 0.9011 (mmt-90) cc_final: 0.8684 (mmt180) REVERT: C 110 SER cc_start: 0.9021 (t) cc_final: 0.8818 (p) REVERT: D 41 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.7806 (p0) REVERT: D 46 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8267 (ttmm) REVERT: D 68 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7906 (ttpp) REVERT: D 76 ARG cc_start: 0.9005 (mmt-90) cc_final: 0.8675 (mmt180) REVERT: D 110 SER cc_start: 0.9005 (t) cc_final: 0.8801 (p) REVERT: E 41 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.7816 (p0) REVERT: E 46 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8272 (ttmm) REVERT: E 68 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7890 (ttpp) REVERT: E 76 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8680 (mmt180) REVERT: E 110 SER cc_start: 0.9013 (t) cc_final: 0.8807 (p) REVERT: F 41 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7817 (p0) REVERT: F 46 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8285 (ttmm) REVERT: F 68 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7907 (ttpp) REVERT: F 76 ARG cc_start: 0.9012 (mmt-90) cc_final: 0.8684 (mmt180) REVERT: F 110 SER cc_start: 0.9013 (t) cc_final: 0.8810 (p) REVERT: G 41 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7817 (p0) REVERT: G 46 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8285 (ttmm) REVERT: G 68 LYS cc_start: 0.8364 (mtpp) cc_final: 0.7905 (ttpp) REVERT: G 76 ARG cc_start: 0.9016 (mmt-90) cc_final: 0.8689 (mmt180) REVERT: G 110 SER cc_start: 0.9016 (t) cc_final: 0.8813 (p) REVERT: H 41 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.7818 (p0) REVERT: H 46 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8273 (ttmm) REVERT: H 68 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7887 (ttpp) REVERT: H 76 ARG cc_start: 0.9008 (mmt-90) cc_final: 0.8680 (mmt180) REVERT: H 110 SER cc_start: 0.9013 (t) cc_final: 0.8807 (p) REVERT: I 41 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7821 (p0) REVERT: I 46 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8274 (ttmm) REVERT: I 68 LYS cc_start: 0.8352 (mtpp) cc_final: 0.7885 (ttpp) REVERT: I 76 ARG cc_start: 0.9013 (mmt-90) cc_final: 0.8683 (mmt180) REVERT: I 110 SER cc_start: 0.9023 (t) cc_final: 0.8817 (p) REVERT: J 41 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.7808 (p0) REVERT: J 46 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8273 (ttmm) REVERT: J 68 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7908 (ttpp) REVERT: J 76 ARG cc_start: 0.9016 (mmt-90) cc_final: 0.8686 (mmt180) REVERT: J 110 SER cc_start: 0.9012 (t) cc_final: 0.8809 (p) REVERT: K 41 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.7818 (p0) REVERT: K 46 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8277 (ttmm) REVERT: K 68 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7888 (ttpp) REVERT: K 76 ARG cc_start: 0.9013 (mmt-90) cc_final: 0.8683 (mmt180) REVERT: K 110 SER cc_start: 0.9022 (t) cc_final: 0.8816 (p) REVERT: L 41 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7811 (p0) REVERT: L 46 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8270 (ttmm) REVERT: L 68 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7912 (ttpp) REVERT: L 76 ARG cc_start: 0.9017 (mmt-90) cc_final: 0.8690 (mmt180) REVERT: L 110 SER cc_start: 0.9011 (t) cc_final: 0.8808 (p) REVERT: M 41 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7816 (p0) REVERT: M 46 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8279 (ttmm) REVERT: M 68 LYS cc_start: 0.8368 (mtpp) cc_final: 0.7900 (ttpp) REVERT: M 76 ARG cc_start: 0.9016 (mmt-90) cc_final: 0.8683 (mmt180) REVERT: M 110 SER cc_start: 0.9017 (t) cc_final: 0.8811 (p) REVERT: N 41 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.7825 (p0) REVERT: N 46 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8268 (ttmm) REVERT: N 68 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7900 (ttpp) REVERT: N 76 ARG cc_start: 0.9018 (mmt-90) cc_final: 0.8688 (mmt180) REVERT: N 110 SER cc_start: 0.9020 (t) cc_final: 0.8814 (p) REVERT: O 41 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7804 (p0) REVERT: O 46 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8263 (ttmm) REVERT: O 68 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7903 (ttpp) REVERT: O 76 ARG cc_start: 0.9007 (mmt-90) cc_final: 0.8676 (mmt180) REVERT: O 110 SER cc_start: 0.9004 (t) cc_final: 0.8799 (p) REVERT: P 41 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7825 (p0) REVERT: P 46 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8291 (ttmm) REVERT: P 68 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7893 (ttpp) REVERT: P 76 ARG cc_start: 0.9010 (mmt-90) cc_final: 0.8682 (mmt180) REVERT: P 110 SER cc_start: 0.9021 (t) cc_final: 0.8817 (p) REVERT: Q 41 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7806 (p0) REVERT: Q 46 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8264 (ttmm) REVERT: Q 68 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7905 (ttpp) REVERT: Q 76 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8676 (mmt180) REVERT: Q 110 SER cc_start: 0.9006 (t) cc_final: 0.8802 (p) REVERT: R 41 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7824 (p0) REVERT: R 46 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8295 (ttmm) REVERT: R 68 LYS cc_start: 0.8361 (mtpp) cc_final: 0.7897 (ttpp) REVERT: R 76 ARG cc_start: 0.9012 (mmt-90) cc_final: 0.8683 (mmt180) REVERT: R 110 SER cc_start: 0.9019 (t) cc_final: 0.8815 (p) REVERT: S 41 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7806 (p0) REVERT: S 46 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8266 (ttmm) REVERT: S 68 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7912 (ttpp) REVERT: S 76 ARG cc_start: 0.9016 (mmt-90) cc_final: 0.8688 (mmt180) REVERT: S 110 SER cc_start: 0.9012 (t) cc_final: 0.8810 (p) REVERT: T 41 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7820 (p0) REVERT: T 46 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8275 (ttmm) REVERT: T 68 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7890 (ttpp) REVERT: T 76 ARG cc_start: 0.9012 (mmt-90) cc_final: 0.8683 (mmt180) REVERT: T 110 SER cc_start: 0.9019 (t) cc_final: 0.8813 (p) REVERT: U 41 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7815 (p0) REVERT: U 46 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8276 (ttmm) REVERT: U 68 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7900 (ttpp) REVERT: U 76 ARG cc_start: 0.9017 (mmt-90) cc_final: 0.8686 (mmt180) REVERT: U 110 SER cc_start: 0.9016 (t) cc_final: 0.8810 (p) REVERT: V 41 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7823 (p0) REVERT: V 46 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8269 (ttmm) REVERT: V 68 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7901 (ttpp) REVERT: V 76 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8685 (mmt180) REVERT: V 110 SER cc_start: 0.9018 (t) cc_final: 0.8813 (p) REVERT: W 41 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.7825 (p0) REVERT: W 46 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8269 (ttmm) REVERT: W 68 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7903 (ttpp) REVERT: W 76 ARG cc_start: 0.9017 (mmt-90) cc_final: 0.8688 (mmt180) REVERT: W 110 SER cc_start: 0.9019 (t) cc_final: 0.8814 (p) REVERT: X 41 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.7815 (p0) REVERT: X 46 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8279 (ttmm) REVERT: X 68 LYS cc_start: 0.8370 (mtpp) cc_final: 0.7903 (ttpp) REVERT: X 76 ARG cc_start: 0.9015 (mmt-90) cc_final: 0.8685 (mmt180) REVERT: X 110 SER cc_start: 0.9014 (t) cc_final: 0.8808 (p) outliers start: 120 outliers final: 72 residues processed: 936 average time/residue: 0.7601 time to fit residues: 849.9165 Evaluate side-chains 1008 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 912 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 106 SER 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 106 SER Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 116 LYS Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 106 SER Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 159 GLU Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 116 LYS Chi-restraints excluded: chain S residue 159 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 106 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 106 SER Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 106 SER Chi-restraints excluded: chain V residue 116 LYS Chi-restraints excluded: chain V residue 159 GLU Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 106 SER Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 116 LYS Chi-restraints excluded: chain X residue 159 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 300 optimal weight: 8.9990 chunk 406 optimal weight: 0.8980 chunk 268 optimal weight: 0.1980 chunk 252 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 309 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 8 ASN C 102 HIS D 8 ASN D 102 HIS E 8 ASN F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 8 ASN I 8 ASN J 8 ASN K 8 ASN L 8 ASN M 8 ASN N 8 ASN O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 8 ASN R 8 ASN S 8 ASN T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 102 HIS W 8 ASN 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 = 0.3168 r_free = 0.3168 target = 0.113711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.090882 restraints weight = 314318.776| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.01 r_work: 0.2625 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1488 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 36312 Z= 0.127 Angle : 0.508 5.536 49104 Z= 0.280 Chirality : 0.036 0.117 5112 Planarity : 0.004 0.044 6480 Dihedral : 12.813 177.160 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.73 % Allowed : 24.43 % Favored : 72.84 % 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 are not related in a simple way. whole: 5.16 (0.12), residues: 4320 helix: 4.21 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.12 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 19 TYR 0.016 0.001 TYR H 134 PHE 0.015 0.002 PHE L 38 TRP 0.004 0.001 TRP R 90 HIS 0.006 0.001 HIS F 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (36312) covalent geometry : angle 0.50844 / 0.28 (49104) hydrogen bonds : bond 0.05088 / 3.38 ( 2640) hydrogen bonds : angle 3.29870 / 2.39 ( 7776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16846.13 seconds wall clock time: 286 minutes 54.40 seconds (17214.40 seconds total)