Starting phenix.real_space_refine on Tue Aug 26 01:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpk_44780/08_2025/9bpk_44780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpk_44780/08_2025/9bpk_44780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bpk_44780/08_2025/9bpk_44780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpk_44780/08_2025/9bpk_44780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bpk_44780/08_2025/9bpk_44780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpk_44780/08_2025/9bpk_44780.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 21000 2.51 5 N 5760 2.21 5 O 6312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 240 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33192 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "D" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "J" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "N" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "P" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "R" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "T" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "V" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "X" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Time building chain proxies: 6.71, per 1000 atoms: 0.20 Number of scatterers: 33192 At special positions: 0 Unit cell: (134.93, 134.93, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6312 8.00 N 5760 7.00 C 21000 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 41 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 158 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 158 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 125 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 158 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'E' and resid 13 through 41 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 125 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 158 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'F' and resid 13 through 43 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 158 Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 162 through 175 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 158 Processing helix chain 'H' and resid 162 through 175 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 158 Processing helix chain 'I' and resid 162 through 175 Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 158 Processing helix chain 'J' and resid 162 through 175 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 158 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 158 Processing helix chain 'L' and resid 162 through 175 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 125 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 158 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'N' and resid 13 through 41 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 158 Processing helix chain 'N' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 158 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 158 Processing helix chain 'P' and resid 162 through 175 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 158 Processing helix chain 'Q' and resid 162 through 174 Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 125 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 158 Processing helix chain 'R' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 158 Processing helix chain 'S' and resid 162 through 174 Processing helix chain 'T' and resid 13 through 42 removed outlier: 3.533A pdb=" N ASP T 42 " --> pdb=" O GLY T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 125 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 158 Processing helix chain 'T' and resid 162 through 174 Processing helix chain 'U' and resid 13 through 42 removed outlier: 3.511A pdb=" N ASP U 42 " --> pdb=" O GLY U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 158 Processing helix chain 'U' and resid 162 through 175 Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 158 Processing helix chain 'V' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 158 Processing helix chain 'W' and resid 162 through 175 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 158 Processing helix chain 'X' and resid 163 through 174 2688 hydrogen bonds defined for protein. 8064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8580 1.33 - 1.45: 6351 1.45 - 1.57: 18669 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 33816 Sorted by residual: bond pdb=" CZ ARG G 157 " pdb=" NH2 ARG G 157 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" CZ ARG L 157 " pdb=" NH2 ARG L 157 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG F 157 " pdb=" NH2 ARG F 157 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" CZ ARG E 172 " pdb=" NH2 ARG E 172 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" CZ ARG B 157 " pdb=" NH2 ARG B 157 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.11e+01 ... (remaining 33811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 28056 1.49 - 2.99: 13084 2.99 - 4.48: 3732 4.48 - 5.98: 495 5.98 - 7.47: 113 Bond angle restraints: 45480 Sorted by residual: angle pdb=" C ASP T 126 " pdb=" N PRO T 127 " pdb=" CA PRO T 127 " ideal model delta sigma weight residual 119.32 125.89 -6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" CB HIS R 53 " pdb=" CG HIS R 53 " pdb=" CD2 HIS R 53 " ideal model delta sigma weight residual 131.20 124.17 7.03 1.30e+00 5.92e-01 2.93e+01 angle pdb=" CB HIS J 151 " pdb=" CG HIS J 151 " pdb=" CD2 HIS J 151 " ideal model delta sigma weight residual 131.20 124.68 6.52 1.30e+00 5.92e-01 2.52e+01 angle pdb=" C ASP D 126 " pdb=" N PRO D 127 " pdb=" CA PRO D 127 " ideal model delta sigma weight residual 119.32 125.03 -5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" CB HIS C 128 " pdb=" CG HIS C 128 " pdb=" CD2 HIS C 128 " ideal model delta sigma weight residual 131.20 124.69 6.51 1.30e+00 5.92e-01 2.51e+01 ... (remaining 45475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18521 17.98 - 35.97: 1427 35.97 - 53.95: 314 53.95 - 71.93: 140 71.93 - 89.91: 22 Dihedral angle restraints: 20424 sinusoidal: 8472 harmonic: 11952 Sorted by residual: dihedral pdb=" C LEU P 144 " pdb=" N LEU P 144 " pdb=" CA LEU P 144 " pdb=" CB LEU P 144 " ideal model delta harmonic sigma weight residual -122.60 -136.80 14.20 0 2.50e+00 1.60e-01 3.23e+01 dihedral pdb=" C LYS I 176 " pdb=" N LYS I 176 " pdb=" CA LYS I 176 " pdb=" CB LYS I 176 " ideal model delta harmonic sigma weight residual -122.60 -136.44 13.84 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C LYS M 176 " pdb=" N LYS M 176 " pdb=" CA LYS M 176 " pdb=" CB LYS M 176 " ideal model delta harmonic sigma weight residual -122.60 -135.91 13.31 0 2.50e+00 1.60e-01 2.84e+01 ... (remaining 20421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3717 0.113 - 0.227: 1041 0.227 - 0.340: 102 0.340 - 0.453: 9 0.453 - 0.567: 3 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA LEU P 144 " pdb=" N LEU P 144 " pdb=" C LEU P 144 " pdb=" CB LEU P 144 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA LEU G 144 " pdb=" N LEU G 144 " pdb=" C LEU G 144 " pdb=" CB LEU G 144 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA LYS I 176 " pdb=" N LYS I 176 " pdb=" C LYS I 176 " pdb=" CB LYS I 176 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 4869 not shown) Planarity restraints: 5952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 34 " 0.142 2.00e-02 2.50e+03 8.17e-02 1.33e+02 pdb=" CG TYR J 34 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR J 34 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR J 34 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR J 34 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR J 34 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR J 34 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR J 34 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 34 " -0.139 2.00e-02 2.50e+03 8.16e-02 1.33e+02 pdb=" CG TYR M 34 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR M 34 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TYR M 34 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR M 34 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR M 34 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR M 34 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR M 34 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR W 32 " -0.145 2.00e-02 2.50e+03 8.03e-02 1.29e+02 pdb=" CG TYR W 32 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR W 32 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR W 32 " 0.073 2.00e-02 2.50e+03 pdb=" CE1 TYR W 32 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR W 32 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR W 32 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR W 32 " -0.127 2.00e-02 2.50e+03 ... (remaining 5949 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 14855 2.96 - 3.45: 39129 3.45 - 3.93: 66472 3.93 - 4.42: 73641 4.42 - 4.90: 119044 Nonbonded interactions: 313141 Sorted by model distance: nonbonded pdb=" OH TYR N 27 " pdb=" OE2 GLU N 141 " model vdw 2.480 3.040 nonbonded pdb=" OH TYR F 34 " pdb=" OE1 GLU F 107 " model vdw 2.522 3.040 nonbonded pdb=" OH TYR B 34 " pdb=" OE1 GLU B 107 " model vdw 2.529 3.040 nonbonded pdb=" OH TYR K 27 " pdb=" OE2 GLU K 141 " model vdw 2.532 3.040 nonbonded pdb=" OH TYR L 34 " pdb=" OE1 GLU L 107 " model vdw 2.533 3.040 ... (remaining 313136 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: 0.00 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.100 Find NCS groups from input model: 0.510 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.011 0.045 33816 Z= 0.717 Angle : 1.780 7.472 45480 Z= 1.207 Chirality : 0.095 0.567 4872 Planarity : 0.018 0.147 5952 Dihedral : 14.963 89.914 12744 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.99 % Favored : 97.75 % Rotamer: Outliers : 3.45 % Allowed : 4.31 % Favored : 92.24 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.12), residues: 4080 helix: 0.74 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : -1.54 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG M 172 TYR 0.145 0.028 TYR W 32 PHE 0.102 0.022 PHE U 41 TRP 0.036 0.015 TRP N 93 HIS 0.014 0.003 HIS M 151 Details of bonding type rmsd covalent geometry : bond 0.01137 (33816) covalent geometry : angle 1.77967 (45480) hydrogen bonds : bond 0.09911 ( 2688) hydrogen bonds : angle 5.49395 ( 8064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1035 time to evaluate : 0.912 Fit side-chains REVERT: A 34 TYR cc_start: 0.7539 (m-80) cc_final: 0.7334 (m-10) REVERT: C 34 TYR cc_start: 0.7620 (m-80) cc_final: 0.7418 (m-10) REVERT: C 107 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5650 (tp30) REVERT: E 34 TYR cc_start: 0.7654 (m-80) cc_final: 0.7377 (m-10) REVERT: L 141 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5833 (mm-30) REVERT: N 43 ARG cc_start: 0.7437 (mtp180) cc_final: 0.6887 (mtm180) REVERT: Q 107 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5699 (tp30) REVERT: T 34 TYR cc_start: 0.7662 (m-80) cc_final: 0.7290 (m-10) REVERT: T 79 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7142 (mmp80) REVERT: X 34 TYR cc_start: 0.7602 (m-80) cc_final: 0.7286 (m-10) outliers start: 120 outliers final: 26 residues processed: 1100 average time/residue: 0.8229 time to fit residues: 1035.3775 Evaluate side-chains 580 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 551 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain J residue 15 ASP Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain L residue 15 ASP Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain W residue 15 ASP 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: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 29 GLN D 29 GLN E 7 GLN E 29 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 29 GLN G 29 GLN G 73 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 GLN H 29 GLN I 7 GLN I 29 GLN J 7 GLN K 29 GLN L 7 GLN L 29 GLN M 29 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 29 GLN O 7 GLN O 29 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN P 29 GLN Q 29 GLN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN R 75 GLN S 29 GLN T 7 GLN T 29 GLN U 7 GLN U 29 GLN V 7 GLN V 29 GLN V 74 ASN W 29 GLN ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080448 restraints weight = 54726.733| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.42 r_work: 0.3134 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33816 Z= 0.149 Angle : 0.597 6.755 45480 Z= 0.314 Chirality : 0.036 0.122 4872 Planarity : 0.004 0.035 5952 Dihedral : 5.406 92.847 4580 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.23 % Favored : 98.58 % Rotamer: Outliers : 3.39 % Allowed : 11.67 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.13), residues: 4080 helix: 2.55 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.20 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 56 TYR 0.030 0.002 TYR D 66 PHE 0.015 0.002 PHE X 39 TRP 0.007 0.001 TRP A 93 HIS 0.006 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00336 (33816) covalent geometry : angle 0.59708 (45480) hydrogen bonds : bond 0.04054 ( 2688) hydrogen bonds : angle 3.77175 ( 8064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 882 time to evaluate : 0.938 Fit side-chains REVERT: A 49 GLU cc_start: 0.8117 (tp30) cc_final: 0.7872 (tp30) REVERT: A 107 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8323 (tp30) REVERT: A 112 GLN cc_start: 0.9055 (tp40) cc_final: 0.8846 (tp-100) REVERT: A 125 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 22 SER cc_start: 0.9235 (m) cc_final: 0.8972 (p) REVERT: B 42 ASP cc_start: 0.8323 (t0) cc_final: 0.7691 (t0) REVERT: B 49 GLU cc_start: 0.8142 (tp30) cc_final: 0.7786 (tm-30) REVERT: B 61 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8161 (mm-30) REVERT: B 125 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8582 (p) REVERT: C 22 SER cc_start: 0.9239 (m) cc_final: 0.9010 (p) REVERT: C 42 ASP cc_start: 0.8359 (t0) cc_final: 0.8147 (t0) REVERT: C 49 GLU cc_start: 0.8101 (tp30) cc_final: 0.7742 (tm-30) REVERT: C 61 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8036 (mm-30) REVERT: C 68 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8610 (mtm-85) REVERT: D 61 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 71 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8773 (ttmm) REVERT: D 112 GLN cc_start: 0.9063 (tp40) cc_final: 0.8858 (tp40) REVERT: E 15 ASP cc_start: 0.8670 (p0) cc_final: 0.8407 (p0) REVERT: E 42 ASP cc_start: 0.8334 (t0) cc_final: 0.7756 (t0) REVERT: F 49 GLU cc_start: 0.8105 (tp30) cc_final: 0.7728 (tm-30) REVERT: F 61 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8142 (mm-30) REVERT: F 125 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8584 (p) REVERT: G 22 SER cc_start: 0.9232 (m) cc_final: 0.8982 (p) REVERT: G 49 GLU cc_start: 0.8145 (tp30) cc_final: 0.7804 (tm-30) REVERT: G 61 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8169 (mm-30) REVERT: G 125 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8609 (p) REVERT: G 172 ARG cc_start: 0.8958 (mmp-170) cc_final: 0.8757 (mmm160) REVERT: H 15 ASP cc_start: 0.8678 (p0) cc_final: 0.8318 (p0) REVERT: H 61 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7954 (mm-30) REVERT: H 104 MET cc_start: 0.9095 (ttp) cc_final: 0.8870 (ttp) REVERT: I 49 GLU cc_start: 0.8109 (tp30) cc_final: 0.7765 (tm-30) REVERT: I 61 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8164 (mm-30) REVERT: I 68 ARG cc_start: 0.8818 (mtm110) cc_final: 0.8610 (mtm-85) REVERT: I 125 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8569 (p) REVERT: J 22 SER cc_start: 0.9225 (m) cc_final: 0.9023 (p) REVERT: J 49 GLU cc_start: 0.8064 (tp30) cc_final: 0.7711 (tm-30) REVERT: J 61 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: J 68 ARG cc_start: 0.8856 (ttm110) cc_final: 0.8647 (mtm-85) REVERT: J 176 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8133 (pttm) REVERT: K 49 GLU cc_start: 0.8114 (tp30) cc_final: 0.7765 (tm-30) REVERT: K 61 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8156 (mm-30) REVERT: K 125 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8577 (p) REVERT: L 45 ASP cc_start: 0.8949 (p0) cc_final: 0.8748 (p0) REVERT: L 49 GLU cc_start: 0.8071 (tp30) cc_final: 0.7750 (tm-30) REVERT: L 61 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8202 (mm-30) REVERT: L 71 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8803 (ttmm) REVERT: L 112 GLN cc_start: 0.9047 (tp40) cc_final: 0.8845 (tp40) REVERT: L 172 ARG cc_start: 0.8921 (mmp-170) cc_final: 0.8718 (mmm160) REVERT: M 61 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8057 (mm-30) REVERT: M 112 GLN cc_start: 0.9095 (tp40) cc_final: 0.8890 (tp40) REVERT: N 49 GLU cc_start: 0.8098 (tp30) cc_final: 0.7764 (tm-30) REVERT: N 61 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8041 (mm-30) REVERT: N 125 THR cc_start: 0.9058 (m) cc_final: 0.8597 (p) REVERT: O 15 ASP cc_start: 0.8607 (p0) cc_final: 0.8397 (p0) REVERT: O 125 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8574 (p) REVERT: P 61 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8134 (mm-30) REVERT: P 64 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8441 (mm-30) REVERT: P 68 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8559 (mtm-85) REVERT: P 125 THR cc_start: 0.9026 (m) cc_final: 0.8567 (p) REVERT: P 172 ARG cc_start: 0.8975 (mmp-170) cc_final: 0.8748 (mmm160) REVERT: Q 34 TYR cc_start: 0.9344 (m-10) cc_final: 0.9080 (m-10) REVERT: Q 49 GLU cc_start: 0.8097 (tp30) cc_final: 0.7743 (tm-30) REVERT: Q 61 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8111 (mm-30) REVERT: Q 107 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: Q 124 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8725 (mmt-90) REVERT: Q 125 THR cc_start: 0.9041 (m) cc_final: 0.8582 (p) REVERT: R 61 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: R 112 GLN cc_start: 0.9047 (tp40) cc_final: 0.8743 (tp40) REVERT: S 61 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8012 (mm-30) REVERT: S 125 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8603 (p) REVERT: T 42 ASP cc_start: 0.8351 (t0) cc_final: 0.7757 (t0) REVERT: T 176 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7877 (pptt) REVERT: U 42 ASP cc_start: 0.8434 (t0) cc_final: 0.7820 (t0) REVERT: U 49 GLU cc_start: 0.8200 (tp30) cc_final: 0.7881 (tm-30) REVERT: U 61 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8090 (mm-30) REVERT: U 112 GLN cc_start: 0.9059 (tp40) cc_final: 0.8852 (tp40) REVERT: U 125 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8574 (p) REVERT: V 43 ARG cc_start: 0.8839 (mtm180) cc_final: 0.8617 (mtm180) REVERT: V 61 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8064 (mm-30) REVERT: W 22 SER cc_start: 0.9214 (m) cc_final: 0.8998 (p) REVERT: W 68 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8703 (mtm-85) REVERT: W 112 GLN cc_start: 0.8967 (tp40) cc_final: 0.8732 (tp40) REVERT: W 125 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8599 (p) REVERT: X 49 GLU cc_start: 0.8146 (tp30) cc_final: 0.7779 (tm-30) REVERT: X 61 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: X 124 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8493 (mmt-90) outliers start: 118 outliers final: 28 residues processed: 925 average time/residue: 0.7126 time to fit residues: 770.8335 Evaluate side-chains 704 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 660 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain J residue 15 ASP Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 15 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain L residue 15 ASP Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain R residue 15 ASP Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain S residue 15 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain V residue 15 ASP Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 382 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 377 optimal weight: 0.7980 chunk 362 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 29 GLN C 29 GLN D 11 ASN D 29 GLN E 29 GLN E 136 HIS F 29 GLN G 29 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN I 29 GLN J 29 GLN K 29 GLN L 29 GLN M 29 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN O 29 GLN O 112 GLN P 29 GLN P 112 GLN Q 29 GLN Q 112 GLN S 29 GLN T 29 GLN T 112 GLN U 29 GLN V 29 GLN V 112 GLN V 136 HIS W 29 GLN X 29 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.079822 restraints weight = 55136.791| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.43 r_work: 0.3110 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33816 Z= 0.145 Angle : 0.541 7.949 45480 Z= 0.281 Chirality : 0.036 0.117 4872 Planarity : 0.004 0.037 5952 Dihedral : 4.665 64.183 4559 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.77 % Rotamer: Outliers : 1.90 % Allowed : 17.13 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.13), residues: 4080 helix: 2.86 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 56 TYR 0.026 0.002 TYR C 66 PHE 0.014 0.002 PHE V 41 TRP 0.004 0.001 TRP A 93 HIS 0.006 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00319 (33816) covalent geometry : angle 0.54141 (45480) hydrogen bonds : bond 0.03547 ( 2688) hydrogen bonds : angle 3.62505 ( 8064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 772 time to evaluate : 1.051 Fit side-chains REVERT: A 42 ASP cc_start: 0.8350 (t0) cc_final: 0.7636 (t0) REVERT: A 49 GLU cc_start: 0.8217 (tp30) cc_final: 0.7955 (tp30) REVERT: A 61 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 112 GLN cc_start: 0.9017 (tp40) cc_final: 0.8640 (tp40) REVERT: A 125 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 22 SER cc_start: 0.9207 (m) cc_final: 0.8992 (p) REVERT: B 49 GLU cc_start: 0.8070 (tp30) cc_final: 0.7674 (tm-30) REVERT: B 61 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8117 (mm-30) REVERT: C 22 SER cc_start: 0.9218 (m) cc_final: 0.8986 (p) REVERT: C 42 ASP cc_start: 0.8334 (t0) cc_final: 0.7998 (t0) REVERT: C 49 GLU cc_start: 0.7993 (tp30) cc_final: 0.7643 (tm-30) REVERT: C 61 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8005 (mm-30) REVERT: C 112 GLN cc_start: 0.9054 (tp40) cc_final: 0.8679 (tp40) REVERT: C 148 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.9012 (mtp) REVERT: D 42 ASP cc_start: 0.8296 (t70) cc_final: 0.8015 (t0) REVERT: D 61 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8105 (mm-30) REVERT: D 84 ASP cc_start: 0.8766 (m-30) cc_final: 0.8526 (m-30) REVERT: D 112 GLN cc_start: 0.9042 (tp40) cc_final: 0.8836 (tp40) REVERT: D 125 THR cc_start: 0.8786 (m) cc_final: 0.8293 (p) REVERT: E 22 SER cc_start: 0.9207 (m) cc_final: 0.8992 (p) REVERT: E 42 ASP cc_start: 0.8295 (t0) cc_final: 0.7498 (t0) REVERT: F 42 ASP cc_start: 0.8301 (t0) cc_final: 0.7617 (t0) REVERT: F 49 GLU cc_start: 0.8112 (tp30) cc_final: 0.7741 (tm-30) REVERT: F 61 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8028 (mm-30) REVERT: F 125 THR cc_start: 0.9017 (m) cc_final: 0.8529 (p) REVERT: G 22 SER cc_start: 0.9246 (m) cc_final: 0.9018 (p) REVERT: G 49 GLU cc_start: 0.8048 (tp30) cc_final: 0.7698 (tm-30) REVERT: G 61 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8103 (mm-30) REVERT: G 125 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8529 (p) REVERT: G 140 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: H 42 ASP cc_start: 0.8240 (t0) cc_final: 0.7544 (t0) REVERT: H 61 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7930 (mm-30) REVERT: H 148 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8770 (mpp) REVERT: I 42 ASP cc_start: 0.8341 (t0) cc_final: 0.7613 (t0) REVERT: I 49 GLU cc_start: 0.8088 (tp30) cc_final: 0.7699 (tm-30) REVERT: I 61 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8143 (mm-30) REVERT: I 68 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8609 (mtm-85) REVERT: I 125 THR cc_start: 0.9032 (m) cc_final: 0.8512 (p) REVERT: J 22 SER cc_start: 0.9201 (m) cc_final: 0.9001 (p) REVERT: J 42 ASP cc_start: 0.8318 (t0) cc_final: 0.8111 (t0) REVERT: J 49 GLU cc_start: 0.8051 (tp30) cc_final: 0.7679 (tm-30) REVERT: J 61 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: J 84 ASP cc_start: 0.8846 (m-30) cc_final: 0.8614 (m-30) REVERT: J 176 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8200 (pttm) REVERT: K 42 ASP cc_start: 0.8293 (t0) cc_final: 0.7565 (t0) REVERT: K 49 GLU cc_start: 0.8039 (tp30) cc_final: 0.7669 (tm-30) REVERT: K 61 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8092 (mm-30) REVERT: K 84 ASP cc_start: 0.8705 (m-30) cc_final: 0.8463 (m-30) REVERT: K 125 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8492 (p) REVERT: L 42 ASP cc_start: 0.8325 (t0) cc_final: 0.7648 (t0) REVERT: L 49 GLU cc_start: 0.8106 (tp30) cc_final: 0.7729 (tm-30) REVERT: L 61 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8119 (mm-30) REVERT: L 71 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8789 (ttmm) REVERT: M 42 ASP cc_start: 0.8292 (t0) cc_final: 0.7585 (t0) REVERT: M 49 GLU cc_start: 0.8100 (tp30) cc_final: 0.7745 (tm-30) REVERT: M 61 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8023 (mm-30) REVERT: M 63 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8189 (ttp80) REVERT: N 49 GLU cc_start: 0.8141 (tp30) cc_final: 0.7796 (tm-30) REVERT: N 61 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8062 (mm-30) REVERT: N 71 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8814 (ttmm) REVERT: N 107 GLU cc_start: 0.8707 (tp30) cc_final: 0.8473 (tp30) REVERT: N 125 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8531 (p) REVERT: O 42 ASP cc_start: 0.8345 (t0) cc_final: 0.7620 (t0) REVERT: O 49 GLU cc_start: 0.8102 (tp30) cc_final: 0.7751 (tm-30) REVERT: O 125 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8503 (p) REVERT: P 42 ASP cc_start: 0.8324 (t0) cc_final: 0.7602 (t0) REVERT: P 49 GLU cc_start: 0.8167 (tp30) cc_final: 0.7834 (tm-30) REVERT: P 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8103 (mm-30) REVERT: P 68 ARG cc_start: 0.8807 (mtm110) cc_final: 0.8573 (mtm-85) REVERT: P 125 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8473 (p) REVERT: Q 49 GLU cc_start: 0.8049 (tp30) cc_final: 0.7662 (tm-30) REVERT: Q 61 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8108 (mm-30) REVERT: Q 107 GLU cc_start: 0.8310 (tp30) cc_final: 0.7959 (tp30) REVERT: Q 125 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8534 (p) REVERT: R 49 GLU cc_start: 0.8073 (tp30) cc_final: 0.7737 (tm-30) REVERT: R 61 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: R 84 ASP cc_start: 0.8765 (m-30) cc_final: 0.8470 (m-30) REVERT: S 42 ASP cc_start: 0.8273 (t0) cc_final: 0.7567 (t0) REVERT: S 61 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7965 (mm-30) REVERT: S 125 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8523 (p) REVERT: T 42 ASP cc_start: 0.8350 (t0) cc_final: 0.7564 (t0) REVERT: T 49 GLU cc_start: 0.8072 (tp30) cc_final: 0.7732 (tm-30) REVERT: T 61 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8277 (mm-30) REVERT: T 176 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7931 (pptt) REVERT: U 42 ASP cc_start: 0.8377 (t0) cc_final: 0.7592 (t0) REVERT: U 49 GLU cc_start: 0.8151 (tp30) cc_final: 0.7800 (tm-30) REVERT: U 61 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8166 (mm-30) REVERT: U 125 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8501 (p) REVERT: V 49 GLU cc_start: 0.8030 (tp30) cc_final: 0.7673 (tm-30) REVERT: V 61 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7978 (mm-30) REVERT: V 84 ASP cc_start: 0.8922 (m-30) cc_final: 0.8702 (m-30) REVERT: W 22 SER cc_start: 0.9225 (m) cc_final: 0.8998 (p) REVERT: W 125 THR cc_start: 0.8998 (m) cc_final: 0.8506 (p) REVERT: X 42 ASP cc_start: 0.8301 (t0) cc_final: 0.7550 (t0) REVERT: X 49 GLU cc_start: 0.8081 (tp30) cc_final: 0.7720 (tm-30) REVERT: X 61 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: X 124 ARG cc_start: 0.8828 (mmt-90) cc_final: 0.8609 (mmt-90) outliers start: 66 outliers final: 9 residues processed: 802 average time/residue: 0.6768 time to fit residues: 638.4609 Evaluate side-chains 667 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 641 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 190 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN D 29 GLN E 29 GLN F 29 GLN H 29 GLN I 29 GLN J 29 GLN K 29 GLN L 29 GLN M 29 GLN M 75 GLN N 29 GLN O 29 GLN P 29 GLN Q 29 GLN S 29 GLN S 136 HIS T 29 GLN U 29 GLN V 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.089806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.077106 restraints weight = 54951.184| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.52 r_work: 0.3033 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33816 Z= 0.194 Angle : 0.548 10.465 45480 Z= 0.281 Chirality : 0.037 0.168 4872 Planarity : 0.004 0.039 5952 Dihedral : 4.450 66.892 4524 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.08 % Favored : 98.75 % Rotamer: Outliers : 2.53 % Allowed : 18.45 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.31 (0.13), residues: 4080 helix: 2.82 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.83 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 56 TYR 0.026 0.002 TYR N 66 PHE 0.017 0.002 PHE P 41 TRP 0.004 0.001 TRP X 93 HIS 0.005 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00425 (33816) covalent geometry : angle 0.54761 (45480) hydrogen bonds : bond 0.03823 ( 2688) hydrogen bonds : angle 3.68604 ( 8064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 668 time to evaluate : 1.156 Fit side-chains REVERT: A 42 ASP cc_start: 0.8414 (t0) cc_final: 0.7675 (t0) REVERT: A 49 GLU cc_start: 0.8232 (tp30) cc_final: 0.7979 (tp30) REVERT: A 57 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 61 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 71 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8823 (ttmm) REVERT: A 125 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 22 SER cc_start: 0.9216 (m) cc_final: 0.8981 (p) REVERT: B 42 ASP cc_start: 0.8409 (t70) cc_final: 0.7576 (t0) REVERT: B 49 GLU cc_start: 0.8139 (tp30) cc_final: 0.7775 (tm-30) REVERT: B 61 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8167 (mm-30) REVERT: C 22 SER cc_start: 0.9213 (m) cc_final: 0.8970 (p) REVERT: C 42 ASP cc_start: 0.8452 (t0) cc_final: 0.7683 (t0) REVERT: C 49 GLU cc_start: 0.8147 (tp30) cc_final: 0.7769 (tm-30) REVERT: C 61 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 148 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.9041 (mtp) REVERT: D 42 ASP cc_start: 0.8391 (t70) cc_final: 0.8133 (t0) REVERT: D 49 GLU cc_start: 0.8666 (tt0) cc_final: 0.8459 (tp30) REVERT: D 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8140 (mm-30) REVERT: D 71 LYS cc_start: 0.9156 (ttpt) cc_final: 0.8849 (ttmm) REVERT: D 125 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8462 (p) REVERT: E 22 SER cc_start: 0.9202 (m) cc_final: 0.8973 (p) REVERT: E 42 ASP cc_start: 0.8371 (t0) cc_final: 0.7539 (t0) REVERT: E 49 GLU cc_start: 0.8185 (tp30) cc_final: 0.7982 (tp30) REVERT: E 148 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.9007 (mtp) REVERT: F 42 ASP cc_start: 0.8403 (t0) cc_final: 0.7770 (t0) REVERT: F 49 GLU cc_start: 0.8169 (tp30) cc_final: 0.7930 (tp30) REVERT: F 61 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8108 (mm-30) REVERT: F 125 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8586 (p) REVERT: G 22 SER cc_start: 0.9214 (m) cc_final: 0.8957 (p) REVERT: G 49 GLU cc_start: 0.8131 (tp30) cc_final: 0.7770 (tm-30) REVERT: G 61 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8122 (mm-30) REVERT: G 91 ASP cc_start: 0.8713 (p0) cc_final: 0.8399 (m-30) REVERT: G 125 THR cc_start: 0.9036 (m) cc_final: 0.8515 (p) REVERT: G 140 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: H 42 ASP cc_start: 0.8374 (t0) cc_final: 0.7630 (t0) REVERT: H 49 GLU cc_start: 0.8166 (tp30) cc_final: 0.7825 (tm-30) REVERT: H 61 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8086 (mm-30) REVERT: H 124 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8503 (mmt-90) REVERT: H 148 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8719 (mpp) REVERT: I 42 ASP cc_start: 0.8435 (t0) cc_final: 0.7680 (t0) REVERT: I 49 GLU cc_start: 0.8168 (tp30) cc_final: 0.7943 (tp30) REVERT: I 61 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8147 (mm-30) REVERT: I 68 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8583 (mtm-85) REVERT: I 125 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8534 (p) REVERT: J 22 SER cc_start: 0.9212 (m) cc_final: 0.8991 (p) REVERT: J 42 ASP cc_start: 0.8431 (t0) cc_final: 0.7690 (t0) REVERT: J 49 GLU cc_start: 0.8153 (tp30) cc_final: 0.7911 (tp30) REVERT: J 61 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: J 176 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8131 (pttm) REVERT: K 42 ASP cc_start: 0.8414 (t0) cc_final: 0.7668 (t0) REVERT: K 49 GLU cc_start: 0.8154 (tp30) cc_final: 0.7905 (tp30) REVERT: K 61 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8163 (mm-30) REVERT: K 125 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8563 (p) REVERT: L 42 ASP cc_start: 0.8397 (t0) cc_final: 0.7804 (t0) REVERT: L 49 GLU cc_start: 0.8182 (tp30) cc_final: 0.7964 (tp30) REVERT: L 61 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8194 (mm-30) REVERT: L 71 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8841 (ttmm) REVERT: M 42 ASP cc_start: 0.8471 (t0) cc_final: 0.7683 (t0) REVERT: M 49 GLU cc_start: 0.8188 (tp30) cc_final: 0.7962 (tp30) REVERT: M 61 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8143 (mm-30) REVERT: M 63 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8173 (ttp80) REVERT: N 42 ASP cc_start: 0.8431 (t0) cc_final: 0.7694 (t0) REVERT: N 49 GLU cc_start: 0.8170 (tp30) cc_final: 0.7949 (tp30) REVERT: N 61 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8132 (mm-30) REVERT: N 71 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8816 (ttmm) REVERT: N 125 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8576 (p) REVERT: O 15 ASP cc_start: 0.8765 (p0) cc_final: 0.8347 (p0) REVERT: O 42 ASP cc_start: 0.8387 (t0) cc_final: 0.7634 (t0) REVERT: O 49 GLU cc_start: 0.8179 (tp30) cc_final: 0.7829 (tm-30) REVERT: O 124 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8355 (mmt-90) REVERT: O 125 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8536 (p) REVERT: P 42 ASP cc_start: 0.8395 (t0) cc_final: 0.7716 (t0) REVERT: P 49 GLU cc_start: 0.8220 (tp30) cc_final: 0.7969 (tp30) REVERT: P 61 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8188 (mm-30) REVERT: P 68 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8569 (mtm-85) REVERT: P 125 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8574 (p) REVERT: Q 49 GLU cc_start: 0.8151 (tp30) cc_final: 0.7778 (tm-30) REVERT: Q 61 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8168 (mm-30) REVERT: Q 125 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8571 (p) REVERT: R 42 ASP cc_start: 0.8406 (t70) cc_final: 0.7558 (t0) REVERT: R 61 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: S 42 ASP cc_start: 0.8487 (t0) cc_final: 0.7697 (t0) REVERT: S 61 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8002 (mm-30) REVERT: S 125 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8554 (p) REVERT: T 42 ASP cc_start: 0.8458 (t0) cc_final: 0.7655 (t0) REVERT: T 49 GLU cc_start: 0.8192 (tp30) cc_final: 0.7922 (tp30) REVERT: T 61 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8307 (mm-30) REVERT: T 176 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7783 (pptt) REVERT: U 42 ASP cc_start: 0.8432 (t0) cc_final: 0.7609 (t0) REVERT: U 49 GLU cc_start: 0.8195 (tp30) cc_final: 0.7933 (tp30) REVERT: U 61 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8185 (mm-30) REVERT: U 125 THR cc_start: 0.9097 (m) cc_final: 0.8562 (p) REVERT: V 42 ASP cc_start: 0.8433 (t70) cc_final: 0.7573 (t0) REVERT: V 49 GLU cc_start: 0.8147 (tp30) cc_final: 0.7899 (tp30) REVERT: V 61 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8027 (mm-30) REVERT: V 148 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8837 (mpp) REVERT: W 22 SER cc_start: 0.9218 (m) cc_final: 0.8986 (p) REVERT: W 42 ASP cc_start: 0.8409 (t70) cc_final: 0.8115 (t0) REVERT: W 125 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8547 (p) REVERT: X 42 ASP cc_start: 0.8429 (t0) cc_final: 0.7653 (t0) REVERT: X 49 GLU cc_start: 0.8138 (tp30) cc_final: 0.7901 (tp30) REVERT: X 61 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7989 (mm-30) outliers start: 88 outliers final: 17 residues processed: 698 average time/residue: 0.7017 time to fit residues: 573.2311 Evaluate side-chains 645 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 607 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 98 ASP Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 346 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 350 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 29 GLN D 29 GLN E 29 GLN F 29 GLN H 29 GLN I 29 GLN K 29 GLN L 29 GLN L 136 HIS M 29 GLN N 29 GLN O 29 GLN P 29 GLN Q 29 GLN S 29 GLN T 29 GLN U 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079423 restraints weight = 55216.778| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.50 r_work: 0.3082 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33816 Z= 0.133 Angle : 0.509 9.999 45480 Z= 0.262 Chirality : 0.035 0.140 4872 Planarity : 0.003 0.036 5952 Dihedral : 4.260 62.068 4524 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.13 % Favored : 98.73 % Rotamer: Outliers : 1.87 % Allowed : 19.80 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.13), residues: 4080 helix: 2.98 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.80 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 63 TYR 0.027 0.002 TYR Q 66 PHE 0.012 0.002 PHE F 39 TRP 0.004 0.001 TRP O 93 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00292 (33816) covalent geometry : angle 0.50925 (45480) hydrogen bonds : bond 0.03298 ( 2688) hydrogen bonds : angle 3.57849 ( 8064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 698 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8463 (t0) cc_final: 0.8134 (t0) REVERT: A 49 GLU cc_start: 0.8176 (tp30) cc_final: 0.7946 (tp30) REVERT: A 57 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 61 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 71 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8779 (ttmm) REVERT: A 125 THR cc_start: 0.9010 (m) cc_final: 0.8497 (p) REVERT: B 22 SER cc_start: 0.9225 (m) cc_final: 0.8953 (p) REVERT: B 42 ASP cc_start: 0.8336 (t70) cc_final: 0.7928 (t0) REVERT: B 49 GLU cc_start: 0.8097 (tp30) cc_final: 0.7732 (tm-30) REVERT: B 61 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8140 (mm-30) REVERT: C 22 SER cc_start: 0.9222 (m) cc_final: 0.8994 (p) REVERT: C 42 ASP cc_start: 0.8371 (t0) cc_final: 0.7586 (t0) REVERT: C 49 GLU cc_start: 0.8139 (tp30) cc_final: 0.7754 (tm-30) REVERT: C 61 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8090 (mm-30) REVERT: C 148 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.9030 (mtp) REVERT: D 42 ASP cc_start: 0.8329 (t70) cc_final: 0.8015 (t0) REVERT: D 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 71 LYS cc_start: 0.9143 (ttpt) cc_final: 0.8831 (ttmm) REVERT: D 125 THR cc_start: 0.8749 (m) cc_final: 0.8232 (p) REVERT: E 22 SER cc_start: 0.9196 (m) cc_final: 0.8984 (p) REVERT: E 42 ASP cc_start: 0.8340 (t0) cc_final: 0.7921 (t0) REVERT: E 148 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.9023 (mtp) REVERT: F 42 ASP cc_start: 0.8433 (t0) cc_final: 0.7669 (t0) REVERT: F 49 GLU cc_start: 0.8192 (tp30) cc_final: 0.7911 (tp30) REVERT: F 61 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8157 (mm-30) REVERT: F 91 ASP cc_start: 0.8627 (p0) cc_final: 0.8258 (m-30) REVERT: F 125 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8464 (p) REVERT: G 22 SER cc_start: 0.9231 (m) cc_final: 0.8940 (p) REVERT: G 42 ASP cc_start: 0.8352 (t70) cc_final: 0.8104 (t0) REVERT: G 49 GLU cc_start: 0.8097 (tp30) cc_final: 0.7720 (tm-30) REVERT: G 61 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8152 (mm-30) REVERT: G 125 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8555 (p) REVERT: G 139 ASP cc_start: 0.8648 (t0) cc_final: 0.8336 (p0) REVERT: G 140 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: H 42 ASP cc_start: 0.8387 (t0) cc_final: 0.7578 (t0) REVERT: H 49 GLU cc_start: 0.8181 (tp30) cc_final: 0.7862 (tm-30) REVERT: H 61 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8107 (mm-30) REVERT: H 148 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8735 (mpp) REVERT: I 42 ASP cc_start: 0.8429 (t0) cc_final: 0.8082 (t0) REVERT: I 49 GLU cc_start: 0.8194 (tp30) cc_final: 0.7798 (tm-30) REVERT: I 61 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8131 (mm-30) REVERT: I 125 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8583 (p) REVERT: J 22 SER cc_start: 0.9202 (m) cc_final: 0.9001 (p) REVERT: J 42 ASP cc_start: 0.8400 (t0) cc_final: 0.8048 (t0) REVERT: J 49 GLU cc_start: 0.8090 (tp30) cc_final: 0.7710 (tm-30) REVERT: J 61 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: J 176 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8130 (pttm) REVERT: K 42 ASP cc_start: 0.8427 (t0) cc_final: 0.7594 (t0) REVERT: K 49 GLU cc_start: 0.8188 (tp30) cc_final: 0.7792 (tm-30) REVERT: K 61 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8152 (mm-30) REVERT: K 125 THR cc_start: 0.9004 (m) cc_final: 0.8577 (p) REVERT: L 42 ASP cc_start: 0.8400 (t0) cc_final: 0.7645 (t0) REVERT: L 49 GLU cc_start: 0.8159 (tp30) cc_final: 0.7784 (tm-30) REVERT: L 61 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8204 (mm-30) REVERT: L 71 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8812 (ttmm) REVERT: L 167 GLU cc_start: 0.8308 (tt0) cc_final: 0.8106 (tt0) REVERT: M 42 ASP cc_start: 0.8427 (t0) cc_final: 0.8052 (t0) REVERT: M 61 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8151 (mm-30) REVERT: M 63 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8171 (ttp80) REVERT: N 49 GLU cc_start: 0.8211 (tp30) cc_final: 0.7855 (tm-30) REVERT: N 61 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8115 (mm-30) REVERT: N 125 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8499 (p) REVERT: O 42 ASP cc_start: 0.8416 (t0) cc_final: 0.8062 (t0) REVERT: O 49 GLU cc_start: 0.8201 (tp30) cc_final: 0.7829 (tm-30) REVERT: O 124 ARG cc_start: 0.8760 (mmt-90) cc_final: 0.8450 (mmt-90) REVERT: O 125 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8422 (p) REVERT: P 42 ASP cc_start: 0.8376 (t0) cc_final: 0.8080 (t0) REVERT: P 49 GLU cc_start: 0.8225 (tp30) cc_final: 0.7961 (tp30) REVERT: P 61 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8129 (mm-30) REVERT: P 125 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8443 (p) REVERT: Q 42 ASP cc_start: 0.8333 (t70) cc_final: 0.8074 (t0) REVERT: Q 49 GLU cc_start: 0.8117 (tp30) cc_final: 0.7731 (tm-30) REVERT: Q 61 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8176 (mm-30) REVERT: Q 125 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8488 (p) REVERT: R 42 ASP cc_start: 0.8340 (t70) cc_final: 0.8021 (t0) REVERT: R 61 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: S 42 ASP cc_start: 0.8379 (t0) cc_final: 0.8031 (t0) REVERT: S 61 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8061 (mm-30) REVERT: S 125 THR cc_start: 0.9019 (m) cc_final: 0.8466 (p) REVERT: T 42 ASP cc_start: 0.8437 (t0) cc_final: 0.7599 (t0) REVERT: T 49 GLU cc_start: 0.8150 (tp30) cc_final: 0.7762 (tm-30) REVERT: T 61 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8303 (mm-30) REVERT: T 176 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7851 (pptt) REVERT: U 42 ASP cc_start: 0.8421 (t0) cc_final: 0.7565 (t0) REVERT: U 49 GLU cc_start: 0.8196 (tp30) cc_final: 0.7924 (tp30) REVERT: U 61 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8180 (mm-30) REVERT: U 125 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8575 (p) REVERT: V 42 ASP cc_start: 0.8362 (t70) cc_final: 0.7945 (t0) REVERT: V 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7772 (tm-30) REVERT: V 61 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8025 (mm-30) REVERT: W 22 SER cc_start: 0.9212 (m) cc_final: 0.8992 (p) REVERT: W 42 ASP cc_start: 0.8320 (t70) cc_final: 0.7917 (t0) REVERT: W 49 GLU cc_start: 0.8136 (tp30) cc_final: 0.7773 (tm-30) REVERT: W 125 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8466 (p) REVERT: X 42 ASP cc_start: 0.8386 (t0) cc_final: 0.8055 (t0) REVERT: X 49 GLU cc_start: 0.8190 (tp30) cc_final: 0.7788 (tm-30) REVERT: X 61 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: X 124 ARG cc_start: 0.8887 (mmt-90) cc_final: 0.8575 (mmt-90) REVERT: X 125 THR cc_start: 0.8996 (m) cc_final: 0.8558 (p) outliers start: 65 outliers final: 18 residues processed: 731 average time/residue: 0.7308 time to fit residues: 621.8433 Evaluate side-chains 662 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 626 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain V residue 98 ASP Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 371 optimal weight: 0.8980 chunk 306 optimal weight: 0.0050 chunk 176 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 151 optimal weight: 0.0980 chunk 325 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 29 GLN D 29 GLN D 112 GLN E 29 GLN H 29 GLN I 29 GLN K 29 GLN M 29 GLN N 136 HIS O 29 GLN P 29 GLN Q 29 GLN Q 136 HIS R 29 GLN S 29 GLN T 29 GLN U 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.078360 restraints weight = 54974.955| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.51 r_work: 0.3048 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33816 Z= 0.157 Angle : 0.520 9.387 45480 Z= 0.268 Chirality : 0.036 0.133 4872 Planarity : 0.004 0.038 5952 Dihedral : 4.344 70.718 4524 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.15 % Favored : 98.75 % Rotamer: Outliers : 1.75 % Allowed : 21.09 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.13), residues: 4080 helix: 2.95 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.74 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 63 TYR 0.026 0.002 TYR G 66 PHE 0.015 0.002 PHE F 39 TRP 0.006 0.001 TRP I 93 HIS 0.005 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00344 (33816) covalent geometry : angle 0.52014 (45480) hydrogen bonds : bond 0.03491 ( 2688) hydrogen bonds : angle 3.59944 ( 8064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 672 time to evaluate : 1.164 Fit side-chains REVERT: A 42 ASP cc_start: 0.8452 (t0) cc_final: 0.8103 (t0) REVERT: A 49 GLU cc_start: 0.8150 (tp30) cc_final: 0.7931 (tp30) REVERT: A 57 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 61 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 71 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8798 (ttmm) REVERT: A 125 THR cc_start: 0.9049 (m) cc_final: 0.8519 (p) REVERT: B 22 SER cc_start: 0.9222 (m) cc_final: 0.8936 (p) REVERT: B 42 ASP cc_start: 0.8304 (t70) cc_final: 0.7890 (t0) REVERT: B 49 GLU cc_start: 0.8174 (tp30) cc_final: 0.7788 (tm-30) REVERT: B 61 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 22 SER cc_start: 0.9187 (m) cc_final: 0.8942 (p) REVERT: C 42 ASP cc_start: 0.8400 (t0) cc_final: 0.7641 (t0) REVERT: C 49 GLU cc_start: 0.8161 (tp30) cc_final: 0.7757 (tm-30) REVERT: C 61 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8104 (mm-30) REVERT: C 84 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7182 (t0) REVERT: C 148 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9048 (mtp) REVERT: D 42 ASP cc_start: 0.8393 (t70) cc_final: 0.8044 (t0) REVERT: D 61 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8094 (mm-30) REVERT: D 71 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8797 (ttmm) REVERT: D 125 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8312 (p) REVERT: E 22 SER cc_start: 0.9193 (m) cc_final: 0.8955 (p) REVERT: E 42 ASP cc_start: 0.8328 (t0) cc_final: 0.7879 (t0) REVERT: E 148 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.9022 (mtp) REVERT: F 42 ASP cc_start: 0.8437 (t0) cc_final: 0.7718 (t0) REVERT: F 49 GLU cc_start: 0.8224 (tp30) cc_final: 0.7931 (tp30) REVERT: F 61 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8088 (mm-30) REVERT: F 125 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8468 (p) REVERT: G 22 SER cc_start: 0.9200 (m) cc_final: 0.8902 (p) REVERT: G 49 GLU cc_start: 0.8152 (tp30) cc_final: 0.7756 (tm-30) REVERT: G 60 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: G 61 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8200 (mm-30) REVERT: G 125 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8546 (p) REVERT: G 139 ASP cc_start: 0.8664 (t0) cc_final: 0.8292 (p0) REVERT: G 140 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: H 42 ASP cc_start: 0.8432 (t0) cc_final: 0.7639 (t0) REVERT: H 49 GLU cc_start: 0.8203 (tp30) cc_final: 0.7927 (tp30) REVERT: H 61 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8065 (mm-30) REVERT: H 148 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8701 (mpp) REVERT: I 42 ASP cc_start: 0.8437 (t0) cc_final: 0.7593 (t0) REVERT: I 49 GLU cc_start: 0.8246 (tp30) cc_final: 0.7955 (tp30) REVERT: I 61 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8095 (mm-30) REVERT: I 125 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8589 (p) REVERT: J 22 SER cc_start: 0.9182 (m) cc_final: 0.8956 (p) REVERT: J 42 ASP cc_start: 0.8441 (t0) cc_final: 0.8042 (t0) REVERT: J 49 GLU cc_start: 0.8206 (tp30) cc_final: 0.7852 (tm-30) REVERT: J 61 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: J 176 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8002 (pttm) REVERT: K 42 ASP cc_start: 0.8352 (t0) cc_final: 0.7552 (t0) REVERT: K 49 GLU cc_start: 0.8217 (tp30) cc_final: 0.7921 (tp30) REVERT: K 61 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8127 (mm-30) REVERT: K 125 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8567 (p) REVERT: L 42 ASP cc_start: 0.8385 (t0) cc_final: 0.7702 (t0) REVERT: L 49 GLU cc_start: 0.8211 (tp30) cc_final: 0.7816 (tm-30) REVERT: L 61 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8171 (mm-30) REVERT: L 71 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8802 (ttmm) REVERT: M 42 ASP cc_start: 0.8414 (t0) cc_final: 0.8024 (t0) REVERT: M 61 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8089 (mm-30) REVERT: M 63 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8173 (ttp80) REVERT: N 49 GLU cc_start: 0.8231 (tp30) cc_final: 0.7855 (tm-30) REVERT: N 61 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8095 (mm-30) REVERT: N 125 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8493 (p) REVERT: O 42 ASP cc_start: 0.8397 (t0) cc_final: 0.7530 (t0) REVERT: O 49 GLU cc_start: 0.8247 (tp30) cc_final: 0.7909 (tm-30) REVERT: O 124 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8510 (mmt-90) REVERT: O 125 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8458 (p) REVERT: P 42 ASP cc_start: 0.8401 (t0) cc_final: 0.7579 (t0) REVERT: P 49 GLU cc_start: 0.8246 (tp30) cc_final: 0.7969 (tp30) REVERT: P 61 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8118 (mm-30) REVERT: P 125 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8507 (p) REVERT: Q 42 ASP cc_start: 0.8389 (t70) cc_final: 0.8102 (t0) REVERT: Q 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7773 (tm-30) REVERT: Q 61 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8130 (mm-30) REVERT: Q 125 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8505 (p) REVERT: R 42 ASP cc_start: 0.8353 (t70) cc_final: 0.7509 (t0) REVERT: R 61 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: S 42 ASP cc_start: 0.8412 (t0) cc_final: 0.7569 (t0) REVERT: S 61 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8065 (mm-30) REVERT: S 125 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8603 (p) REVERT: T 42 ASP cc_start: 0.8425 (t0) cc_final: 0.7566 (t0) REVERT: T 49 GLU cc_start: 0.8164 (tp30) cc_final: 0.7763 (tm-30) REVERT: T 61 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8255 (mm-30) REVERT: T 176 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7794 (pptt) REVERT: U 42 ASP cc_start: 0.8424 (t0) cc_final: 0.7593 (t0) REVERT: U 49 GLU cc_start: 0.8203 (tp30) cc_final: 0.7916 (tp30) REVERT: U 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8137 (mm-30) REVERT: U 104 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8538 (tpt) REVERT: U 125 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8584 (p) REVERT: U 148 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: V 42 ASP cc_start: 0.8378 (t70) cc_final: 0.7982 (t0) REVERT: V 49 GLU cc_start: 0.8221 (tp30) cc_final: 0.7981 (tp30) REVERT: V 61 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8011 (mm-30) REVERT: V 148 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8810 (mpp) REVERT: W 22 SER cc_start: 0.9210 (m) cc_final: 0.8966 (p) REVERT: W 42 ASP cc_start: 0.8299 (t70) cc_final: 0.7884 (t0) REVERT: W 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7850 (tm-30) REVERT: W 125 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8473 (p) REVERT: X 42 ASP cc_start: 0.8380 (t0) cc_final: 0.7949 (t0) REVERT: X 49 GLU cc_start: 0.8192 (tp30) cc_final: 0.7777 (tm-30) REVERT: X 61 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: X 125 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8574 (p) outliers start: 61 outliers final: 14 residues processed: 690 average time/residue: 0.7035 time to fit residues: 569.6437 Evaluate side-chains 650 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 609 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 104 MET Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain U residue 148 MET Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 275 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 329 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 364 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 29 GLN D 29 GLN F 75 GLN H 29 GLN I 29 GLN K 29 GLN O 29 GLN P 29 GLN Q 29 GLN T 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078978 restraints weight = 54766.037| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.51 r_work: 0.3061 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33816 Z= 0.146 Angle : 0.517 9.226 45480 Z= 0.267 Chirality : 0.035 0.123 4872 Planarity : 0.004 0.040 5952 Dihedral : 4.303 68.944 4524 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.73 % Rotamer: Outliers : 1.90 % Allowed : 21.84 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.13), residues: 4080 helix: 3.02 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.82 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 63 TYR 0.025 0.002 TYR G 66 PHE 0.013 0.002 PHE F 39 TRP 0.005 0.001 TRP I 93 HIS 0.004 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00320 (33816) covalent geometry : angle 0.51738 (45480) hydrogen bonds : bond 0.03383 ( 2688) hydrogen bonds : angle 3.57528 ( 8064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 654 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8468 (t0) cc_final: 0.8108 (t0) REVERT: A 49 GLU cc_start: 0.8156 (tp30) cc_final: 0.7936 (tp30) REVERT: A 57 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 61 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8184 (mm-30) REVERT: A 71 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8732 (ttmm) REVERT: A 125 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 22 SER cc_start: 0.9214 (m) cc_final: 0.8927 (p) REVERT: B 42 ASP cc_start: 0.8341 (t70) cc_final: 0.7886 (t0) REVERT: B 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7806 (tm-30) REVERT: B 61 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 125 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8537 (p) REVERT: C 22 SER cc_start: 0.9203 (m) cc_final: 0.8949 (p) REVERT: C 42 ASP cc_start: 0.8395 (t0) cc_final: 0.7667 (t0) REVERT: C 49 GLU cc_start: 0.8162 (tp30) cc_final: 0.7762 (tm-30) REVERT: C 61 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8139 (mm-30) REVERT: C 84 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7253 (t0) REVERT: C 148 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.9041 (mtp) REVERT: D 42 ASP cc_start: 0.8381 (t70) cc_final: 0.8008 (t0) REVERT: D 61 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8076 (mm-30) REVERT: D 71 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8779 (ttmm) REVERT: D 125 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8243 (p) REVERT: E 22 SER cc_start: 0.9201 (m) cc_final: 0.8970 (p) REVERT: E 42 ASP cc_start: 0.8322 (t0) cc_final: 0.7871 (t0) REVERT: E 43 ARG cc_start: 0.8665 (mtm180) cc_final: 0.8345 (mtm180) REVERT: E 148 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.9021 (mtp) REVERT: F 42 ASP cc_start: 0.8448 (t0) cc_final: 0.7683 (t0) REVERT: F 49 GLU cc_start: 0.8200 (tp30) cc_final: 0.7913 (tp30) REVERT: F 61 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8131 (mm-30) REVERT: F 125 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8442 (p) REVERT: G 22 SER cc_start: 0.9210 (m) cc_final: 0.8900 (p) REVERT: G 42 ASP cc_start: 0.8354 (t70) cc_final: 0.8124 (t0) REVERT: G 49 GLU cc_start: 0.8152 (tp30) cc_final: 0.7763 (tm-30) REVERT: G 60 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: G 61 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8200 (mm-30) REVERT: G 125 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8524 (p) REVERT: G 139 ASP cc_start: 0.8628 (t0) cc_final: 0.8299 (p0) REVERT: G 140 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: H 42 ASP cc_start: 0.8397 (t0) cc_final: 0.7587 (t0) REVERT: H 49 GLU cc_start: 0.8194 (tp30) cc_final: 0.7927 (tp30) REVERT: H 61 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8100 (mm-30) REVERT: H 148 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8704 (mpp) REVERT: I 42 ASP cc_start: 0.8406 (t0) cc_final: 0.7994 (t0) REVERT: I 49 GLU cc_start: 0.8199 (tp30) cc_final: 0.7912 (tp30) REVERT: I 61 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8085 (mm-30) REVERT: I 84 ASP cc_start: 0.8828 (m-30) cc_final: 0.8626 (m-30) REVERT: I 125 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8565 (p) REVERT: J 22 SER cc_start: 0.9182 (m) cc_final: 0.8960 (p) REVERT: J 42 ASP cc_start: 0.8411 (t0) cc_final: 0.8026 (t0) REVERT: J 49 GLU cc_start: 0.8183 (tp30) cc_final: 0.7841 (tm-30) REVERT: J 61 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: J 176 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7761 (pttm) REVERT: K 42 ASP cc_start: 0.8418 (t0) cc_final: 0.7575 (t0) REVERT: K 49 GLU cc_start: 0.8189 (tp30) cc_final: 0.7900 (tp30) REVERT: K 61 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8104 (mm-30) REVERT: K 104 MET cc_start: 0.8887 (ttp) cc_final: 0.8653 (ttp) REVERT: K 125 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8552 (p) REVERT: L 42 ASP cc_start: 0.8321 (t0) cc_final: 0.7552 (t0) REVERT: L 49 GLU cc_start: 0.8160 (tp30) cc_final: 0.7752 (tm-30) REVERT: L 61 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8176 (mm-30) REVERT: L 71 LYS cc_start: 0.9103 (ttpt) cc_final: 0.8798 (ttmm) REVERT: L 167 GLU cc_start: 0.8297 (tt0) cc_final: 0.8084 (tt0) REVERT: M 42 ASP cc_start: 0.8405 (t0) cc_final: 0.8018 (t0) REVERT: M 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8103 (mm-30) REVERT: M 63 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8178 (ttp80) REVERT: N 49 GLU cc_start: 0.8213 (tp30) cc_final: 0.7835 (tm-30) REVERT: N 61 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8092 (mm-30) REVERT: N 68 ARG cc_start: 0.8720 (ptp90) cc_final: 0.8484 (ptp90) REVERT: N 125 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8575 (p) REVERT: O 42 ASP cc_start: 0.8371 (t0) cc_final: 0.8021 (t0) REVERT: O 49 GLU cc_start: 0.8228 (tp30) cc_final: 0.7892 (tm-30) REVERT: O 124 ARG cc_start: 0.8839 (mmt-90) cc_final: 0.8521 (mmt-90) REVERT: O 125 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8413 (p) REVERT: P 42 ASP cc_start: 0.8453 (t0) cc_final: 0.8078 (t0) REVERT: P 49 GLU cc_start: 0.8241 (tp30) cc_final: 0.7962 (tp30) REVERT: P 61 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8168 (mm-30) REVERT: P 125 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8476 (p) REVERT: Q 42 ASP cc_start: 0.8372 (t70) cc_final: 0.8013 (t0) REVERT: Q 49 GLU cc_start: 0.8184 (tp30) cc_final: 0.7841 (tm-30) REVERT: Q 61 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8132 (mm-30) REVERT: Q 68 ARG cc_start: 0.8677 (ptp90) cc_final: 0.8449 (ptp90) REVERT: Q 125 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8573 (p) REVERT: R 42 ASP cc_start: 0.8359 (t70) cc_final: 0.8012 (t0) REVERT: R 61 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: S 42 ASP cc_start: 0.8363 (t0) cc_final: 0.7967 (t0) REVERT: S 57 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8249 (mm-30) REVERT: S 61 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8066 (mm-30) REVERT: S 125 THR cc_start: 0.8966 (m) cc_final: 0.8564 (p) REVERT: T 42 ASP cc_start: 0.8393 (t0) cc_final: 0.7557 (t0) REVERT: T 49 GLU cc_start: 0.8146 (tp30) cc_final: 0.7862 (tp30) REVERT: T 61 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8247 (mm-30) REVERT: T 176 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7823 (pptt) REVERT: U 42 ASP cc_start: 0.8392 (t0) cc_final: 0.7550 (t0) REVERT: U 49 GLU cc_start: 0.8216 (tp30) cc_final: 0.7925 (tp30) REVERT: U 61 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8163 (mm-30) REVERT: U 104 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8483 (tpt) REVERT: U 125 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8583 (p) REVERT: U 148 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8758 (mpp) REVERT: V 42 ASP cc_start: 0.8412 (t70) cc_final: 0.7984 (t0) REVERT: V 49 GLU cc_start: 0.8194 (tp30) cc_final: 0.7848 (tm-30) REVERT: V 61 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8034 (mm-30) REVERT: V 148 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8769 (mpp) REVERT: W 22 SER cc_start: 0.9211 (m) cc_final: 0.8968 (p) REVERT: W 42 ASP cc_start: 0.8356 (t70) cc_final: 0.7916 (t0) REVERT: W 49 GLU cc_start: 0.8202 (tp30) cc_final: 0.7834 (tm-30) REVERT: W 125 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8564 (p) REVERT: X 42 ASP cc_start: 0.8323 (t0) cc_final: 0.7919 (t0) REVERT: X 49 GLU cc_start: 0.8196 (tp30) cc_final: 0.7963 (tp30) REVERT: X 61 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: X 124 ARG cc_start: 0.8818 (mmt-90) cc_final: 0.8515 (mmt-90) REVERT: X 125 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8402 (p) outliers start: 66 outliers final: 16 residues processed: 683 average time/residue: 0.7267 time to fit residues: 578.5003 Evaluate side-chains 648 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 604 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 104 MET Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain U residue 148 MET Chi-restraints excluded: chain V residue 98 ASP Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 373 optimal weight: 0.7980 chunk 357 optimal weight: 6.9990 chunk 291 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 29 GLN D 136 HIS F 29 GLN F 75 GLN H 29 GLN I 29 GLN K 29 GLN O 11 ASN O 29 GLN Q 29 GLN T 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078909 restraints weight = 54439.972| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.50 r_work: 0.3058 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33816 Z= 0.149 Angle : 0.517 9.004 45480 Z= 0.268 Chirality : 0.035 0.118 4872 Planarity : 0.004 0.046 5952 Dihedral : 4.270 64.645 4524 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.20 % Favored : 98.73 % Rotamer: Outliers : 1.61 % Allowed : 22.41 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.13), residues: 4080 helix: 3.00 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.77 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 63 TYR 0.023 0.002 TYR Q 66 PHE 0.014 0.002 PHE F 39 TRP 0.003 0.001 TRP B 93 HIS 0.004 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00328 (33816) covalent geometry : angle 0.51750 (45480) hydrogen bonds : bond 0.03407 ( 2688) hydrogen bonds : angle 3.58601 ( 8064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 654 time to evaluate : 1.101 Fit side-chains REVERT: A 42 ASP cc_start: 0.8465 (t0) cc_final: 0.7596 (t0) REVERT: A 49 GLU cc_start: 0.8179 (tp30) cc_final: 0.7934 (tp30) REVERT: A 57 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 61 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 71 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8746 (ttmm) REVERT: A 125 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 22 SER cc_start: 0.9214 (m) cc_final: 0.8926 (p) REVERT: B 42 ASP cc_start: 0.8328 (t70) cc_final: 0.7892 (t0) REVERT: B 49 GLU cc_start: 0.8169 (tp30) cc_final: 0.7839 (tm-30) REVERT: B 61 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 22 SER cc_start: 0.9190 (m) cc_final: 0.8944 (p) REVERT: C 42 ASP cc_start: 0.8378 (t0) cc_final: 0.7670 (t0) REVERT: C 49 GLU cc_start: 0.8215 (tp30) cc_final: 0.7811 (tm-30) REVERT: C 61 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8127 (mm-30) REVERT: C 84 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7220 (t0) REVERT: C 148 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.9041 (mtp) REVERT: D 42 ASP cc_start: 0.8349 (t70) cc_final: 0.7943 (t0) REVERT: D 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8058 (mm-30) REVERT: D 71 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8795 (ttmm) REVERT: D 125 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8255 (p) REVERT: E 22 SER cc_start: 0.9198 (m) cc_final: 0.8967 (p) REVERT: E 42 ASP cc_start: 0.8335 (t0) cc_final: 0.7851 (t0) REVERT: E 148 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.9028 (mtp) REVERT: F 34 TYR cc_start: 0.9348 (m-10) cc_final: 0.9142 (m-10) REVERT: F 42 ASP cc_start: 0.8478 (t0) cc_final: 0.7718 (t0) REVERT: F 49 GLU cc_start: 0.8230 (tp30) cc_final: 0.7942 (tp30) REVERT: F 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8118 (mm-30) REVERT: F 125 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8464 (p) REVERT: G 42 ASP cc_start: 0.8373 (t70) cc_final: 0.8108 (t0) REVERT: G 49 GLU cc_start: 0.8182 (tp30) cc_final: 0.7832 (tm-30) REVERT: G 60 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: G 61 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8220 (mm-30) REVERT: G 125 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8522 (p) REVERT: G 139 ASP cc_start: 0.8581 (t0) cc_final: 0.8279 (p0) REVERT: G 140 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: H 42 ASP cc_start: 0.8409 (t0) cc_final: 0.7601 (t0) REVERT: H 49 GLU cc_start: 0.8195 (tp30) cc_final: 0.7929 (tp30) REVERT: H 61 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8056 (mm-30) REVERT: H 148 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8722 (mpp) REVERT: I 42 ASP cc_start: 0.8408 (t0) cc_final: 0.7987 (t0) REVERT: I 49 GLU cc_start: 0.8225 (tp30) cc_final: 0.7937 (tp30) REVERT: I 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8071 (mm-30) REVERT: I 125 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8570 (p) REVERT: J 22 SER cc_start: 0.9184 (m) cc_final: 0.8958 (p) REVERT: J 42 ASP cc_start: 0.8396 (t0) cc_final: 0.8009 (t0) REVERT: J 49 GLU cc_start: 0.8206 (tp30) cc_final: 0.7860 (tm-30) REVERT: J 61 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: J 176 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (pttm) REVERT: K 42 ASP cc_start: 0.8370 (t0) cc_final: 0.7559 (t0) REVERT: K 49 GLU cc_start: 0.8212 (tp30) cc_final: 0.7909 (tp30) REVERT: K 61 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8088 (mm-30) REVERT: K 125 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8536 (p) REVERT: L 42 ASP cc_start: 0.8361 (t0) cc_final: 0.7622 (t0) REVERT: L 49 GLU cc_start: 0.8159 (tp30) cc_final: 0.7753 (tm-30) REVERT: L 61 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8226 (mm-30) REVERT: L 71 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8803 (ttmm) REVERT: L 167 GLU cc_start: 0.8273 (tt0) cc_final: 0.8043 (tt0) REVERT: M 42 ASP cc_start: 0.8427 (t0) cc_final: 0.7993 (t0) REVERT: M 61 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8079 (mm-30) REVERT: M 63 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8170 (ttp80) REVERT: N 61 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8099 (mm-30) REVERT: O 42 ASP cc_start: 0.8390 (t0) cc_final: 0.7516 (t0) REVERT: O 49 GLU cc_start: 0.8249 (tp30) cc_final: 0.7915 (tm-30) REVERT: O 124 ARG cc_start: 0.8843 (mmt-90) cc_final: 0.8497 (mmt-90) REVERT: O 125 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8525 (p) REVERT: P 42 ASP cc_start: 0.8443 (t0) cc_final: 0.7551 (t0) REVERT: P 49 GLU cc_start: 0.8233 (tp30) cc_final: 0.7956 (tp30) REVERT: P 61 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8111 (mm-30) REVERT: P 125 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8443 (p) REVERT: Q 42 ASP cc_start: 0.8378 (t70) cc_final: 0.8019 (t0) REVERT: Q 49 GLU cc_start: 0.8200 (tp30) cc_final: 0.7847 (tm-30) REVERT: Q 61 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8136 (mm-30) REVERT: Q 68 ARG cc_start: 0.8671 (ptp90) cc_final: 0.8459 (ptp90) REVERT: R 42 ASP cc_start: 0.8353 (t70) cc_final: 0.7981 (t0) REVERT: R 61 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: S 42 ASP cc_start: 0.8347 (t0) cc_final: 0.7892 (t0) REVERT: S 57 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8179 (mm-30) REVERT: S 61 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8021 (mm-30) REVERT: T 42 ASP cc_start: 0.8387 (t0) cc_final: 0.7549 (t0) REVERT: T 49 GLU cc_start: 0.8147 (tp30) cc_final: 0.7857 (tp30) REVERT: T 61 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8267 (mm-30) REVERT: T 176 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7767 (pptt) REVERT: U 42 ASP cc_start: 0.8390 (t0) cc_final: 0.7551 (t0) REVERT: U 49 GLU cc_start: 0.8210 (tp30) cc_final: 0.7923 (tp30) REVERT: U 61 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8174 (mm-30) REVERT: U 104 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8497 (tpt) REVERT: U 148 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8745 (mpp) REVERT: V 42 ASP cc_start: 0.8400 (t70) cc_final: 0.7963 (t0) REVERT: V 61 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8081 (mm-30) REVERT: V 148 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8788 (mpp) REVERT: W 22 SER cc_start: 0.9211 (m) cc_final: 0.8965 (p) REVERT: W 42 ASP cc_start: 0.8347 (t70) cc_final: 0.7909 (t0) REVERT: W 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7903 (tp30) REVERT: W 107 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8376 (mm-30) REVERT: W 125 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8573 (p) REVERT: X 42 ASP cc_start: 0.8317 (t0) cc_final: 0.7914 (t0) REVERT: X 49 GLU cc_start: 0.8173 (tp30) cc_final: 0.7938 (tp30) REVERT: X 61 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7991 (mm-30) REVERT: X 124 ARG cc_start: 0.8851 (mmt-90) cc_final: 0.8477 (mmt-90) REVERT: X 125 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8452 (p) outliers start: 56 outliers final: 17 residues processed: 676 average time/residue: 0.7023 time to fit residues: 554.5603 Evaluate side-chains 650 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 609 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 104 MET Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain U residue 148 MET Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 331 optimal weight: 6.9990 chunk 386 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 360 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 332 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 396 optimal weight: 0.6980 chunk 238 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 29 GLN D 11 ASN F 75 GLN G 29 GLN H 29 GLN I 29 GLN K 29 GLN L 29 GLN O 29 GLN Q 29 GLN T 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079962 restraints weight = 54533.742| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.45 r_work: 0.3090 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33816 Z= 0.129 Angle : 0.516 9.050 45480 Z= 0.267 Chirality : 0.035 0.116 4872 Planarity : 0.003 0.052 5952 Dihedral : 4.194 63.118 4524 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.18 % Favored : 98.75 % Rotamer: Outliers : 1.35 % Allowed : 23.68 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.13), residues: 4080 helix: 3.07 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.75 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.023 0.002 TYR Q 66 PHE 0.013 0.002 PHE F 39 TRP 0.004 0.001 TRP A 93 HIS 0.005 0.001 HIS N 128 Details of bonding type rmsd covalent geometry : bond 0.00284 (33816) covalent geometry : angle 0.51607 (45480) hydrogen bonds : bond 0.03212 ( 2688) hydrogen bonds : angle 3.53576 ( 8064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 651 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8425 (t0) cc_final: 0.8018 (t0) REVERT: A 57 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 61 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 71 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8708 (ttmm) REVERT: A 125 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 22 SER cc_start: 0.9210 (m) cc_final: 0.8915 (p) REVERT: B 42 ASP cc_start: 0.8322 (t70) cc_final: 0.7842 (t0) REVERT: B 49 GLU cc_start: 0.8156 (tp30) cc_final: 0.7786 (tm-30) REVERT: B 61 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 125 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8503 (p) REVERT: C 22 SER cc_start: 0.9200 (m) cc_final: 0.8908 (p) REVERT: C 42 ASP cc_start: 0.8348 (t0) cc_final: 0.7638 (t0) REVERT: C 49 GLU cc_start: 0.8152 (tp30) cc_final: 0.7727 (tm-30) REVERT: C 61 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 148 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.9022 (mtp) REVERT: D 42 ASP cc_start: 0.8367 (t70) cc_final: 0.7962 (t0) REVERT: D 61 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8074 (mm-30) REVERT: D 71 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8757 (ttmm) REVERT: D 125 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8150 (p) REVERT: E 22 SER cc_start: 0.9183 (m) cc_final: 0.8955 (p) REVERT: E 42 ASP cc_start: 0.8276 (t0) cc_final: 0.7782 (t0) REVERT: E 148 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.9017 (mtp) REVERT: F 42 ASP cc_start: 0.8392 (t0) cc_final: 0.7615 (t0) REVERT: F 49 GLU cc_start: 0.8203 (tp30) cc_final: 0.7916 (tp30) REVERT: F 61 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8134 (mm-30) REVERT: F 125 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8477 (p) REVERT: G 22 SER cc_start: 0.9197 (m) cc_final: 0.8903 (p) REVERT: G 42 ASP cc_start: 0.8342 (t70) cc_final: 0.8061 (t0) REVERT: G 49 GLU cc_start: 0.8158 (tp30) cc_final: 0.7787 (tm-30) REVERT: G 60 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: G 61 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8247 (mm-30) REVERT: G 125 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8498 (p) REVERT: G 139 ASP cc_start: 0.8581 (t0) cc_final: 0.8237 (p0) REVERT: H 42 ASP cc_start: 0.8381 (t0) cc_final: 0.7551 (t0) REVERT: H 49 GLU cc_start: 0.8129 (tp30) cc_final: 0.7872 (tp30) REVERT: H 61 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8078 (mm-30) REVERT: H 148 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8741 (mpp) REVERT: I 42 ASP cc_start: 0.8360 (t0) cc_final: 0.7912 (t0) REVERT: I 49 GLU cc_start: 0.8186 (tp30) cc_final: 0.7892 (tp30) REVERT: I 61 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8053 (mm-30) REVERT: I 125 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8543 (p) REVERT: J 22 SER cc_start: 0.9159 (m) cc_final: 0.8938 (p) REVERT: J 42 ASP cc_start: 0.8400 (t0) cc_final: 0.7950 (t0) REVERT: J 49 GLU cc_start: 0.8137 (tp30) cc_final: 0.7780 (tm-30) REVERT: J 61 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: J 63 ARG cc_start: 0.8378 (ttm-80) cc_final: 0.8092 (ttp80) REVERT: J 176 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7755 (pttm) REVERT: K 42 ASP cc_start: 0.8341 (t0) cc_final: 0.7965 (t0) REVERT: K 49 GLU cc_start: 0.8214 (tp30) cc_final: 0.7918 (tp30) REVERT: K 61 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8071 (mm-30) REVERT: K 125 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8499 (p) REVERT: L 42 ASP cc_start: 0.8305 (t0) cc_final: 0.7568 (t0) REVERT: L 49 GLU cc_start: 0.8112 (tp30) cc_final: 0.7660 (tm-30) REVERT: L 61 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8193 (mm-30) REVERT: L 71 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8744 (ttmm) REVERT: L 167 GLU cc_start: 0.8226 (tt0) cc_final: 0.8009 (tt0) REVERT: M 42 ASP cc_start: 0.8375 (t0) cc_final: 0.7947 (t0) REVERT: M 61 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8123 (mm-30) REVERT: M 63 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8151 (ttp80) REVERT: N 61 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8074 (mm-30) REVERT: N 125 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8530 (p) REVERT: O 42 ASP cc_start: 0.8343 (t0) cc_final: 0.7942 (t0) REVERT: O 49 GLU cc_start: 0.8197 (tp30) cc_final: 0.7860 (tm-30) REVERT: O 124 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8410 (mmt-90) REVERT: O 125 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8484 (p) REVERT: P 42 ASP cc_start: 0.8416 (t0) cc_final: 0.7984 (t0) REVERT: P 49 GLU cc_start: 0.8194 (tp30) cc_final: 0.7910 (tp30) REVERT: P 61 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8121 (mm-30) REVERT: P 125 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8429 (p) REVERT: Q 42 ASP cc_start: 0.8348 (t70) cc_final: 0.7983 (t0) REVERT: Q 49 GLU cc_start: 0.8139 (tp30) cc_final: 0.7788 (tm-30) REVERT: Q 61 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8123 (mm-30) REVERT: Q 68 ARG cc_start: 0.8652 (ptp90) cc_final: 0.8447 (ptp90) REVERT: Q 125 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8534 (p) REVERT: R 42 ASP cc_start: 0.8305 (t70) cc_final: 0.7928 (t0) REVERT: R 49 GLU cc_start: 0.8141 (tp30) cc_final: 0.7795 (tm-30) REVERT: R 61 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: S 42 ASP cc_start: 0.8332 (t0) cc_final: 0.7926 (t0) REVERT: S 57 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8310 (mm-30) REVERT: S 61 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8133 (mm-30) REVERT: S 125 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8531 (p) REVERT: T 42 ASP cc_start: 0.8344 (t0) cc_final: 0.7869 (t0) REVERT: T 49 GLU cc_start: 0.8129 (tp30) cc_final: 0.7723 (tm-30) REVERT: T 61 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8199 (mm-30) REVERT: T 176 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7762 (pptt) REVERT: U 42 ASP cc_start: 0.8358 (t0) cc_final: 0.7492 (t0) REVERT: U 49 GLU cc_start: 0.8203 (tp30) cc_final: 0.7907 (tp30) REVERT: U 61 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8154 (mm-30) REVERT: U 125 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8547 (p) REVERT: V 42 ASP cc_start: 0.8342 (t70) cc_final: 0.7910 (t0) REVERT: V 61 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8128 (mm-30) REVERT: V 148 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8791 (mpp) REVERT: W 22 SER cc_start: 0.9191 (m) cc_final: 0.8941 (p) REVERT: W 42 ASP cc_start: 0.8301 (t70) cc_final: 0.7857 (t0) REVERT: W 49 GLU cc_start: 0.8215 (tp30) cc_final: 0.7837 (tm-30) REVERT: W 125 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8533 (p) REVERT: X 42 ASP cc_start: 0.8309 (t0) cc_final: 0.7841 (t0) REVERT: X 49 GLU cc_start: 0.8175 (tp30) cc_final: 0.7753 (tm-30) REVERT: X 61 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: X 124 ARG cc_start: 0.8776 (mmt-90) cc_final: 0.8463 (mmt-90) REVERT: X 125 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8376 (p) outliers start: 47 outliers final: 7 residues processed: 669 average time/residue: 0.7518 time to fit residues: 583.4081 Evaluate side-chains 667 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 635 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 221 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 199 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN E 29 GLN G 29 GLN H 29 GLN K 29 GLN L 29 GLN M 29 GLN N 29 GLN O 29 GLN Q 29 GLN T 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079512 restraints weight = 54799.086| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.51 r_work: 0.3074 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33816 Z= 0.140 Angle : 0.526 9.013 45480 Z= 0.272 Chirality : 0.035 0.137 4872 Planarity : 0.003 0.043 5952 Dihedral : 4.250 67.027 4524 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % Rotamer: Outliers : 1.03 % Allowed : 24.28 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.13), residues: 4080 helix: 3.05 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.72 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 63 TYR 0.024 0.002 TYR E 66 PHE 0.013 0.002 PHE F 39 TRP 0.003 0.001 TRP U 93 HIS 0.004 0.001 HIS N 128 Details of bonding type rmsd covalent geometry : bond 0.00311 (33816) covalent geometry : angle 0.52643 (45480) hydrogen bonds : bond 0.03313 ( 2688) hydrogen bonds : angle 3.54515 ( 8064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 651 time to evaluate : 1.392 Fit side-chains REVERT: A 42 ASP cc_start: 0.8475 (t0) cc_final: 0.8085 (t0) REVERT: A 57 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 61 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 71 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8721 (ttmm) REVERT: A 125 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8446 (p) REVERT: B 22 SER cc_start: 0.9214 (m) cc_final: 0.8923 (p) REVERT: B 42 ASP cc_start: 0.8322 (t70) cc_final: 0.7909 (t0) REVERT: B 49 GLU cc_start: 0.8192 (tp30) cc_final: 0.7841 (tm-30) REVERT: B 61 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8120 (mm-30) REVERT: C 22 SER cc_start: 0.9193 (m) cc_final: 0.8943 (p) REVERT: C 42 ASP cc_start: 0.8339 (t0) cc_final: 0.7628 (t0) REVERT: C 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7739 (tm-30) REVERT: C 61 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8118 (mm-30) REVERT: D 42 ASP cc_start: 0.8377 (t70) cc_final: 0.7905 (t0) REVERT: D 49 GLU cc_start: 0.8168 (tp30) cc_final: 0.7863 (tm-30) REVERT: D 61 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8087 (mm-30) REVERT: D 71 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8762 (ttmm) REVERT: D 125 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8224 (p) REVERT: E 22 SER cc_start: 0.9193 (m) cc_final: 0.8961 (p) REVERT: E 42 ASP cc_start: 0.8320 (t0) cc_final: 0.7830 (t0) REVERT: E 148 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.9014 (mtp) REVERT: F 42 ASP cc_start: 0.8439 (t0) cc_final: 0.7724 (t0) REVERT: F 49 GLU cc_start: 0.8172 (tp30) cc_final: 0.7903 (tp30) REVERT: F 61 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8141 (mm-30) REVERT: F 125 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8534 (p) REVERT: G 22 SER cc_start: 0.9204 (m) cc_final: 0.8899 (p) REVERT: G 42 ASP cc_start: 0.8383 (t70) cc_final: 0.8109 (t0) REVERT: G 49 GLU cc_start: 0.8199 (tp30) cc_final: 0.7843 (tm-30) REVERT: G 60 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: G 61 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8281 (mm-30) REVERT: G 139 ASP cc_start: 0.8576 (t0) cc_final: 0.8246 (p0) REVERT: H 42 ASP cc_start: 0.8411 (t0) cc_final: 0.7605 (t0) REVERT: H 49 GLU cc_start: 0.8140 (tp30) cc_final: 0.7887 (tp30) REVERT: H 61 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8093 (mm-30) REVERT: H 148 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8734 (mpp) REVERT: I 42 ASP cc_start: 0.8419 (t0) cc_final: 0.7962 (t0) REVERT: I 49 GLU cc_start: 0.8196 (tp30) cc_final: 0.7898 (tp30) REVERT: I 61 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8078 (mm-30) REVERT: I 125 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8547 (p) REVERT: J 22 SER cc_start: 0.9183 (m) cc_final: 0.8958 (p) REVERT: J 42 ASP cc_start: 0.8419 (t0) cc_final: 0.8001 (t0) REVERT: J 49 GLU cc_start: 0.8135 (tp30) cc_final: 0.7789 (tm-30) REVERT: J 61 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: J 63 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8105 (ttp80) REVERT: J 104 MET cc_start: 0.8838 (tpp) cc_final: 0.8619 (tpp) REVERT: K 42 ASP cc_start: 0.8382 (t0) cc_final: 0.7556 (t0) REVERT: K 49 GLU cc_start: 0.8220 (tp30) cc_final: 0.7920 (tp30) REVERT: K 61 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8074 (mm-30) REVERT: K 125 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8512 (p) REVERT: L 42 ASP cc_start: 0.8373 (t0) cc_final: 0.7586 (t0) REVERT: L 49 GLU cc_start: 0.8141 (tp30) cc_final: 0.7689 (tm-30) REVERT: L 61 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8226 (mm-30) REVERT: L 71 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8760 (ttmm) REVERT: M 42 ASP cc_start: 0.8434 (t0) cc_final: 0.7981 (t0) REVERT: M 61 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8123 (mm-30) REVERT: M 63 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8168 (ttp80) REVERT: N 61 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8096 (mm-30) REVERT: O 42 ASP cc_start: 0.8355 (t0) cc_final: 0.7469 (t0) REVERT: O 49 GLU cc_start: 0.8237 (tp30) cc_final: 0.7892 (tm-30) REVERT: O 124 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8464 (mmt-90) REVERT: O 125 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8497 (p) REVERT: P 42 ASP cc_start: 0.8444 (t0) cc_final: 0.7536 (t0) REVERT: P 49 GLU cc_start: 0.8202 (tp30) cc_final: 0.7927 (tp30) REVERT: P 61 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8120 (mm-30) REVERT: P 124 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8543 (mmt-90) REVERT: P 125 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8428 (p) REVERT: Q 42 ASP cc_start: 0.8389 (t70) cc_final: 0.8053 (t0) REVERT: Q 49 GLU cc_start: 0.8198 (tp30) cc_final: 0.7844 (tm-30) REVERT: Q 61 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8127 (mm-30) REVERT: Q 68 ARG cc_start: 0.8667 (ptp90) cc_final: 0.8462 (ptp90) REVERT: R 42 ASP cc_start: 0.8360 (t70) cc_final: 0.8006 (t0) REVERT: R 49 GLU cc_start: 0.8133 (tp30) cc_final: 0.7793 (tm-30) REVERT: R 61 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: S 42 ASP cc_start: 0.8403 (t0) cc_final: 0.8004 (t0) REVERT: S 57 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8326 (mm-30) REVERT: S 61 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8155 (mm-30) REVERT: T 42 ASP cc_start: 0.8367 (t0) cc_final: 0.7889 (t0) REVERT: T 49 GLU cc_start: 0.8144 (tp30) cc_final: 0.7756 (tm-30) REVERT: T 60 GLU cc_start: 0.8464 (tp30) cc_final: 0.8048 (tm-30) REVERT: T 61 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8088 (mm-30) REVERT: T 176 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7646 (pptt) REVERT: U 42 ASP cc_start: 0.8391 (t0) cc_final: 0.7531 (t0) REVERT: U 49 GLU cc_start: 0.8213 (tp30) cc_final: 0.7927 (tp30) REVERT: U 61 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8180 (mm-30) REVERT: V 42 ASP cc_start: 0.8356 (t70) cc_final: 0.7927 (t0) REVERT: V 61 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8171 (mm-30) REVERT: W 22 SER cc_start: 0.9208 (m) cc_final: 0.8958 (p) REVERT: W 42 ASP cc_start: 0.8343 (t70) cc_final: 0.7896 (t0) REVERT: W 49 GLU cc_start: 0.8242 (tp30) cc_final: 0.7878 (tm-30) REVERT: W 125 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8530 (p) REVERT: X 42 ASP cc_start: 0.8352 (t0) cc_final: 0.7889 (t0) REVERT: X 49 GLU cc_start: 0.8193 (tp30) cc_final: 0.7774 (tm-30) REVERT: X 61 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: X 124 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.8485 (mmt-90) REVERT: X 125 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8391 (p) outliers start: 36 outliers final: 12 residues processed: 663 average time/residue: 0.7150 time to fit residues: 554.6648 Evaluate side-chains 646 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 618 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 98 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain T residue 98 ASP Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 383 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN E 29 GLN F 10 GLN H 29 GLN K 29 GLN L 29 GLN Q 29 GLN T 29 GLN U 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079317 restraints weight = 54572.074| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.47 r_work: 0.3074 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33816 Z= 0.145 Angle : 0.532 8.910 45480 Z= 0.274 Chirality : 0.036 0.127 4872 Planarity : 0.003 0.044 5952 Dihedral : 4.123 70.433 4518 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.27 % Favored : 98.70 % Rotamer: Outliers : 1.06 % Allowed : 24.54 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.13), residues: 4080 helix: 3.03 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.69 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 124 TYR 0.024 0.002 TYR E 66 PHE 0.014 0.002 PHE F 39 TRP 0.003 0.001 TRP A 93 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00321 (33816) covalent geometry : angle 0.53152 (45480) hydrogen bonds : bond 0.03343 ( 2688) hydrogen bonds : angle 3.55695 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15395.57 seconds wall clock time: 261 minutes 43.61 seconds (15703.61 seconds total)