Starting phenix.real_space_refine on Fri Jun 27 23:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpk_44780/06_2025/9bpk_44780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpk_44780/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpk_44780/06_2025/9bpk_44780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpk_44780/06_2025/9bpk_44780.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpk_44780/06_2025/9bpk_44780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpk_44780/06_2025/9bpk_44780.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.81, per 1000 atoms: 0.54 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: 8.21 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 2.46 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: 11.01 Time building geometry restraints manager: 9.95 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: 0.01 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: 1.400 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: 1.270 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 68.420 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.015 TRP N 93 HIS 0.014 0.003 HIS M 151 PHE 0.102 0.022 PHE U 41 TYR 0.145 0.028 TYR W 32 ARG 0.019 0.002 ARG M 172 Details of bonding type rmsd hydrogen bonds : bond 0.09911 ( 2688) hydrogen bonds : angle 5.49395 ( 8064) covalent geometry : bond 0.01137 (33816) covalent geometry : angle 1.77967 (45480) *********************** 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 : 4.021 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: 0.7419 (m-10) 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: 0.5820 (mm-30) REVERT: N 43 ARG cc_start: 0.7437 (mtp180) cc_final: 0.6885 (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: 0.7278 (m-10) REVERT: T 79 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7141 (mmp80) REVERT: X 15 ASP cc_start: 0.5622 (p0) cc_final: 0.5340 (p0) 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: 1.9097 time to fit residues: 2405.6239 Evaluate side-chains 577 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 549 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain C residue 15 ASP 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 344 optimal weight: 0.9990 chunk 309 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 370 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080464 restraints weight = 54694.931| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.42 r_work: 0.3134 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2951 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= 0.154 Angle : 0.597 6.794 45480 Z= 0.312 Chirality : 0.036 0.119 4872 Planarity : 0.004 0.034 5952 Dihedral : 5.358 92.614 4577 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.20 % Favored : 98.60 % Rotamer: Outliers : 3.42 % Allowed : 11.67 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.13), residues: 4080 helix: 2.58 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -1.21 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.006 0.001 HIS O 128 PHE 0.015 0.002 PHE O 39 TYR 0.030 0.002 TYR D 66 ARG 0.008 0.001 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 2688) hydrogen bonds : angle 3.75914 ( 8064) covalent geometry : bond 0.00343 (33816) covalent geometry : angle 0.59662 (45480) *********************** 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 999 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 880 time to evaluate : 3.940 Fit side-chains REVERT: A 49 GLU cc_start: 0.8109 (tp30) cc_final: 0.7875 (tp30) REVERT: A 61 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 107 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8329 (tp30) REVERT: A 125 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8602 (p) REVERT: B 22 SER cc_start: 0.9229 (m) cc_final: 0.8969 (p) REVERT: B 49 GLU cc_start: 0.8130 (tp30) cc_final: 0.7776 (tm-30) REVERT: B 61 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8157 (mm-30) REVERT: B 125 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8591 (p) REVERT: C 22 SER cc_start: 0.9241 (m) cc_final: 0.9015 (p) REVERT: C 42 ASP cc_start: 0.8369 (t0) cc_final: 0.8158 (t0) REVERT: C 49 GLU cc_start: 0.8087 (tp30) cc_final: 0.7726 (tm-30) REVERT: C 61 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8050 (mm-30) REVERT: C 84 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: D 61 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8118 (mm-30) REVERT: D 71 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8799 (ttmm) REVERT: E 15 ASP cc_start: 0.8666 (p0) cc_final: 0.8420 (p0) REVERT: E 42 ASP cc_start: 0.8291 (t0) cc_final: 0.7701 (t0) REVERT: F 49 GLU cc_start: 0.8098 (tp30) cc_final: 0.7716 (tm-30) REVERT: F 61 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8115 (mm-30) REVERT: F 125 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8587 (p) REVERT: G 22 SER cc_start: 0.9233 (m) cc_final: 0.8990 (p) REVERT: G 42 ASP cc_start: 0.8435 (t70) cc_final: 0.7570 (t0) REVERT: G 49 GLU cc_start: 0.8130 (tp30) cc_final: 0.7773 (tm-30) REVERT: G 61 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8176 (mm-30) REVERT: G 125 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8615 (p) REVERT: G 176 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7672 (ptmm) REVERT: H 15 ASP cc_start: 0.8658 (p0) cc_final: 0.8315 (p0) REVERT: H 61 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7954 (mm-30) REVERT: H 104 MET cc_start: 0.9107 (ttp) cc_final: 0.8889 (ttp) REVERT: I 49 GLU cc_start: 0.8125 (tp30) cc_final: 0.7789 (tm-30) REVERT: I 61 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8164 (mm-30) REVERT: I 68 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8612 (mtm-85) REVERT: I 125 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8565 (p) REVERT: J 49 GLU cc_start: 0.8071 (tp30) cc_final: 0.7712 (tm-30) REVERT: J 61 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: J 68 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8605 (mtm-85) REVERT: J 176 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8150 (pttm) REVERT: K 49 GLU cc_start: 0.8131 (tp30) cc_final: 0.7773 (tm-30) REVERT: K 61 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8183 (mm-30) REVERT: K 125 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8583 (p) REVERT: L 45 ASP cc_start: 0.8947 (p0) cc_final: 0.8747 (p0) REVERT: L 49 GLU cc_start: 0.8102 (tp30) cc_final: 0.7751 (tm-30) REVERT: L 71 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8826 (ttmm) REVERT: L 112 GLN cc_start: 0.9039 (tp40) cc_final: 0.8838 (tp40) REVERT: L 172 ARG cc_start: 0.8922 (mmp-170) cc_final: 0.8720 (mmm160) REVERT: M 61 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8145 (mm-30) REVERT: N 49 GLU cc_start: 0.8099 (tp30) cc_final: 0.7779 (tm-30) REVERT: N 61 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8029 (mm-30) REVERT: N 71 LYS cc_start: 0.9153 (ttpt) cc_final: 0.8818 (ttmm) REVERT: N 125 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8627 (p) REVERT: O 15 ASP cc_start: 0.8605 (p0) cc_final: 0.8399 (p0) REVERT: O 125 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8571 (p) REVERT: P 61 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8183 (mm-30) REVERT: P 64 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8442 (mm-30) REVERT: P 68 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8568 (mtm-85) REVERT: P 125 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8579 (p) REVERT: P 172 ARG cc_start: 0.8976 (mmp-170) cc_final: 0.8763 (mmm160) REVERT: Q 49 GLU cc_start: 0.8092 (tp30) cc_final: 0.7741 (tm-30) REVERT: Q 61 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8105 (mm-30) REVERT: Q 107 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: Q 124 ARG cc_start: 0.8984 (mmt-90) cc_final: 0.8728 (mmt-90) REVERT: Q 125 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8572 (p) REVERT: R 49 GLU cc_start: 0.8121 (tp30) cc_final: 0.7786 (tm-30) REVERT: R 61 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: R 140 GLU cc_start: 0.8414 (tt0) cc_final: 0.8211 (mp0) REVERT: S 61 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8004 (mm-30) REVERT: S 125 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8612 (p) REVERT: T 42 ASP cc_start: 0.8337 (t0) cc_final: 0.7741 (t0) REVERT: U 42 ASP cc_start: 0.8350 (t0) cc_final: 0.7748 (t0) REVERT: U 49 GLU cc_start: 0.8195 (tp30) cc_final: 0.7884 (tm-30) REVERT: U 61 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8078 (mm-30) REVERT: U 125 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8579 (p) REVERT: V 43 ARG cc_start: 0.8848 (mtm180) cc_final: 0.8629 (mtm180) REVERT: V 61 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8102 (mm-30) REVERT: V 112 GLN cc_start: 0.9040 (tp40) cc_final: 0.8828 (tp40) REVERT: W 22 SER cc_start: 0.9216 (m) cc_final: 0.9003 (p) REVERT: W 49 GLU cc_start: 0.8143 (tp30) cc_final: 0.7935 (tp30) REVERT: W 68 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8688 (mtm-85) REVERT: W 112 GLN cc_start: 0.8965 (tp40) cc_final: 0.8733 (tp40) REVERT: W 125 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8617 (p) REVERT: X 15 ASP cc_start: 0.8742 (p0) cc_final: 0.8436 (p0) REVERT: X 49 GLU cc_start: 0.8182 (tp30) cc_final: 0.7806 (tm-30) REVERT: X 61 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8042 (mm-30) outliers start: 119 outliers final: 28 residues processed: 925 average time/residue: 1.6201 time to fit residues: 1750.8190 Evaluate side-chains 704 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 656 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 84 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 G residue 176 LYS Chi-restraints excluded: chain I residue 15 ASP Chi-restraints excluded: chain I residue 125 THR 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 N residue 98 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 15 ASP Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 125 THR 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 193 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 349 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 301 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 112 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 73 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN H 112 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 R 112 GLN S 29 GLN T 29 GLN T 112 GLN U 29 GLN V 29 GLN V 136 HIS W 29 GLN X 29 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079012 restraints weight = 55141.232| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.43 r_work: 0.3092 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33816 Z= 0.158 Angle : 0.548 7.959 45480 Z= 0.284 Chirality : 0.036 0.118 4872 Planarity : 0.004 0.036 5952 Dihedral : 4.694 65.259 4557 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.05 % Favored : 98.77 % Rotamer: Outliers : 2.21 % Allowed : 16.84 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.13), residues: 4080 helix: 2.83 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.006 0.001 HIS L 128 PHE 0.015 0.002 PHE P 41 TYR 0.025 0.002 TYR C 66 ARG 0.008 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 2688) hydrogen bonds : angle 3.64928 ( 8064) covalent geometry : bond 0.00351 (33816) covalent geometry : angle 0.54780 (45480) *********************** 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 831 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 754 time to evaluate : 4.016 Fit side-chains REVERT: A 42 ASP cc_start: 0.8338 (t0) cc_final: 0.7625 (t0) REVERT: A 49 GLU cc_start: 0.8222 (tp30) cc_final: 0.7957 (tp30) REVERT: A 61 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 124 ARG cc_start: 0.8952 (mmt-90) cc_final: 0.8731 (mmt-90) REVERT: A 125 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 22 SER cc_start: 0.9204 (m) cc_final: 0.8987 (p) REVERT: B 42 ASP cc_start: 0.8263 (t70) cc_final: 0.7421 (t0) REVERT: B 49 GLU cc_start: 0.8063 (tp30) cc_final: 0.7675 (tm-30) REVERT: B 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8107 (mm-30) REVERT: C 22 SER cc_start: 0.9223 (m) cc_final: 0.8993 (p) REVERT: C 42 ASP cc_start: 0.8325 (t0) cc_final: 0.7989 (t0) REVERT: C 49 GLU cc_start: 0.8016 (tp30) cc_final: 0.7665 (tm-30) REVERT: C 61 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 84 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: C 148 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.9013 (mtp) REVERT: D 61 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8120 (mm-30) REVERT: D 71 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8811 (ttmm) REVERT: D 84 ASP cc_start: 0.8800 (m-30) cc_final: 0.8570 (m-30) REVERT: D 125 THR cc_start: 0.8833 (m) cc_final: 0.8376 (p) REVERT: E 22 SER cc_start: 0.9208 (m) cc_final: 0.8988 (p) REVERT: E 42 ASP cc_start: 0.8304 (t0) cc_final: 0.7520 (t0) REVERT: F 42 ASP cc_start: 0.8303 (t0) cc_final: 0.7625 (t0) REVERT: F 49 GLU cc_start: 0.8120 (tp30) cc_final: 0.7756 (tm-30) REVERT: F 61 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 125 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8542 (p) REVERT: G 22 SER cc_start: 0.9238 (m) cc_final: 0.9010 (p) REVERT: G 49 GLU cc_start: 0.8046 (tp30) cc_final: 0.7704 (tm-30) REVERT: G 61 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8098 (mm-30) REVERT: G 125 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8542 (p) REVERT: G 140 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: H 42 ASP cc_start: 0.8248 (t0) cc_final: 0.7566 (t0) REVERT: H 61 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7963 (mm-30) REVERT: H 148 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8713 (mpp) REVERT: I 42 ASP cc_start: 0.8333 (t0) cc_final: 0.7626 (t0) REVERT: I 49 GLU cc_start: 0.8113 (tp30) cc_final: 0.7714 (tm-30) REVERT: I 61 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8087 (mm-30) REVERT: I 125 THR cc_start: 0.9065 (m) cc_final: 0.8539 (p) REVERT: J 49 GLU cc_start: 0.8058 (tp30) cc_final: 0.7684 (tm-30) REVERT: J 61 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8007 (mm-30) REVERT: J 176 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8139 (pttm) REVERT: K 42 ASP cc_start: 0.8271 (t0) cc_final: 0.7559 (t0) REVERT: K 49 GLU cc_start: 0.8074 (tp30) cc_final: 0.7710 (tm-30) REVERT: K 61 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8083 (mm-30) REVERT: K 84 ASP cc_start: 0.8739 (m-30) cc_final: 0.8515 (m-30) REVERT: K 125 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8542 (p) REVERT: L 42 ASP cc_start: 0.8316 (t0) cc_final: 0.7639 (t0) REVERT: L 49 GLU cc_start: 0.8120 (tp30) cc_final: 0.7742 (tm-30) REVERT: L 71 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8791 (ttmm) REVERT: M 42 ASP cc_start: 0.8284 (t0) cc_final: 0.7583 (t0) REVERT: M 61 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8044 (mm-30) REVERT: N 49 GLU cc_start: 0.8167 (tp30) cc_final: 0.7812 (tm-30) REVERT: N 61 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8033 (mm-30) REVERT: N 71 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8780 (ttmm) REVERT: N 125 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8597 (p) REVERT: O 42 ASP cc_start: 0.8336 (t0) cc_final: 0.7616 (t0) REVERT: O 49 GLU cc_start: 0.8123 (tp30) cc_final: 0.7773 (tm-30) REVERT: O 125 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8536 (p) REVERT: P 42 ASP cc_start: 0.8336 (t0) cc_final: 0.7625 (t0) REVERT: P 49 GLU cc_start: 0.8197 (tp30) cc_final: 0.7861 (tm-30) REVERT: P 61 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8090 (mm-30) REVERT: P 68 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8588 (mtm-85) REVERT: P 125 THR cc_start: 0.9017 (m) cc_final: 0.8508 (p) REVERT: Q 34 TYR cc_start: 0.9346 (m-10) cc_final: 0.9119 (m-10) REVERT: Q 49 GLU cc_start: 0.8075 (tp30) cc_final: 0.7693 (tm-30) REVERT: Q 61 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8095 (mm-30) REVERT: Q 107 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: Q 125 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8548 (p) REVERT: R 42 ASP cc_start: 0.8288 (t70) cc_final: 0.7412 (t0) REVERT: R 49 GLU cc_start: 0.8088 (tp30) cc_final: 0.7737 (tm-30) REVERT: R 61 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: R 84 ASP cc_start: 0.8765 (m-30) cc_final: 0.8489 (m-30) REVERT: S 42 ASP cc_start: 0.8330 (t0) cc_final: 0.7633 (t0) REVERT: S 61 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7952 (mm-30) REVERT: S 125 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8546 (p) REVERT: T 42 ASP cc_start: 0.8339 (t0) cc_final: 0.7571 (t0) REVERT: T 49 GLU cc_start: 0.8087 (tp30) cc_final: 0.7742 (tm-30) REVERT: T 61 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8251 (mm-30) REVERT: T 172 ARG cc_start: 0.9026 (mmp-170) cc_final: 0.8807 (mmm160) REVERT: T 176 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7965 (pptt) REVERT: U 42 ASP cc_start: 0.8376 (t0) cc_final: 0.7603 (t0) REVERT: U 49 GLU cc_start: 0.8154 (tp30) cc_final: 0.7786 (tm-30) REVERT: U 61 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8135 (mm-30) REVERT: U 125 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8510 (p) REVERT: V 49 GLU cc_start: 0.8102 (tp30) cc_final: 0.7748 (tm-30) REVERT: V 61 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8006 (mm-30) REVERT: W 22 SER cc_start: 0.9225 (m) cc_final: 0.9000 (p) REVERT: W 49 GLU cc_start: 0.8095 (tp30) cc_final: 0.7888 (tp30) REVERT: W 125 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8525 (p) REVERT: X 15 ASP cc_start: 0.8698 (p0) cc_final: 0.8359 (p0) REVERT: X 42 ASP cc_start: 0.8285 (t0) cc_final: 0.7560 (t0) REVERT: X 49 GLU cc_start: 0.8083 (tp30) cc_final: 0.7730 (tm-30) REVERT: X 61 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: X 124 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8359 (mmt-90) REVERT: X 125 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8527 (p) outliers start: 77 outliers final: 9 residues processed: 787 average time/residue: 1.6577 time to fit residues: 1533.7506 Evaluate side-chains 630 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 600 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 15 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 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 F residue 125 THR 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 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 Q residue 107 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 402 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 M 29 GLN M 75 GLN N 29 GLN O 29 GLN P 29 GLN Q 29 GLN R 29 GLN S 29 GLN T 29 GLN U 29 GLN V 29 GLN V 112 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079224 restraints weight = 55087.401| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.43 r_work: 0.3099 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33816 Z= 0.148 Angle : 0.526 11.040 45480 Z= 0.272 Chirality : 0.035 0.163 4872 Planarity : 0.003 0.038 5952 Dihedral : 4.471 73.407 4527 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.13 % Favored : 98.70 % Rotamer: Outliers : 2.18 % Allowed : 18.74 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.13), residues: 4080 helix: 2.92 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 93 HIS 0.005 0.001 HIS L 128 PHE 0.013 0.002 PHE K 41 TYR 0.026 0.002 TYR Q 66 ARG 0.008 0.001 ARG U 56 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 2688) hydrogen bonds : angle 3.61336 ( 8064) covalent geometry : bond 0.00325 (33816) covalent geometry : angle 0.52626 (45480) *********************** 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 755 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 679 time to evaluate : 4.013 Fit side-chains REVERT: A 42 ASP cc_start: 0.8415 (t0) cc_final: 0.7635 (t0) REVERT: A 49 GLU cc_start: 0.8165 (tp30) cc_final: 0.7934 (tp30) REVERT: A 57 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 61 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 125 THR cc_start: 0.8993 (m) cc_final: 0.8485 (p) REVERT: B 22 SER cc_start: 0.9212 (m) cc_final: 0.8980 (p) REVERT: B 42 ASP cc_start: 0.8327 (t70) cc_final: 0.7409 (t0) REVERT: B 49 GLU cc_start: 0.8048 (tp30) cc_final: 0.7681 (tm-30) REVERT: B 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 107 GLU cc_start: 0.8970 (tp30) cc_final: 0.8761 (mm-30) REVERT: C 22 SER cc_start: 0.9229 (m) cc_final: 0.8997 (p) REVERT: C 42 ASP cc_start: 0.8377 (t0) cc_final: 0.7586 (t0) REVERT: C 49 GLU cc_start: 0.8071 (tp30) cc_final: 0.7678 (tm-30) REVERT: C 61 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7997 (mm-30) REVERT: C 148 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.9019 (mtp) REVERT: D 42 ASP cc_start: 0.8297 (t70) cc_final: 0.8015 (t0) REVERT: D 61 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8127 (mm-30) REVERT: D 71 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8810 (ttmm) REVERT: D 125 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8294 (p) REVERT: E 15 ASP cc_start: 0.8629 (p0) cc_final: 0.8151 (p0) REVERT: E 22 SER cc_start: 0.9212 (m) cc_final: 0.8987 (p) REVERT: E 42 ASP cc_start: 0.8347 (t0) cc_final: 0.7990 (t0) REVERT: E 124 ARG cc_start: 0.8695 (mmt-90) cc_final: 0.8330 (mmt-90) REVERT: E 148 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8820 (mtm) REVERT: F 42 ASP cc_start: 0.8330 (t0) cc_final: 0.7592 (t0) REVERT: F 49 GLU cc_start: 0.8168 (tp30) cc_final: 0.7913 (tp30) REVERT: F 61 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8060 (mm-30) REVERT: F 91 ASP cc_start: 0.8470 (p0) cc_final: 0.7957 (m-30) REVERT: F 125 THR cc_start: 0.8994 (m) cc_final: 0.8492 (p) REVERT: G 22 SER cc_start: 0.9242 (m) cc_final: 0.9001 (p) REVERT: G 49 GLU cc_start: 0.8027 (tp30) cc_final: 0.7670 (tm-30) REVERT: G 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8075 (mm-30) REVERT: G 125 THR cc_start: 0.9041 (m) cc_final: 0.8490 (p) REVERT: G 139 ASP cc_start: 0.8628 (t70) cc_final: 0.8297 (p0) REVERT: G 140 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: H 42 ASP cc_start: 0.8315 (t0) cc_final: 0.7554 (t0) REVERT: H 49 GLU cc_start: 0.8121 (tp30) cc_final: 0.7764 (tm-30) REVERT: H 61 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8011 (mm-30) REVERT: H 148 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: I 42 ASP cc_start: 0.8387 (t0) cc_final: 0.8119 (t0) REVERT: I 49 GLU cc_start: 0.8076 (tp30) cc_final: 0.7726 (tm-30) REVERT: I 61 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8080 (mm-30) REVERT: I 125 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8482 (p) REVERT: J 42 ASP cc_start: 0.8317 (t0) cc_final: 0.8081 (t0) REVERT: J 49 GLU cc_start: 0.8041 (tp30) cc_final: 0.7681 (tm-30) REVERT: J 61 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: J 176 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8159 (pttm) REVERT: K 42 ASP cc_start: 0.8348 (t0) cc_final: 0.7572 (t0) REVERT: K 49 GLU cc_start: 0.8086 (tp30) cc_final: 0.7690 (tm-30) REVERT: K 61 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8066 (mm-30) REVERT: K 125 THR cc_start: 0.9040 (m) cc_final: 0.8484 (p) REVERT: L 42 ASP cc_start: 0.8294 (t0) cc_final: 0.7678 (t0) REVERT: L 49 GLU cc_start: 0.8090 (tp30) cc_final: 0.7770 (tm-30) REVERT: L 71 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8784 (ttmm) REVERT: M 42 ASP cc_start: 0.8388 (t0) cc_final: 0.7655 (t0) REVERT: M 61 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8048 (mm-30) REVERT: N 49 GLU cc_start: 0.8144 (tp30) cc_final: 0.7792 (tm-30) REVERT: N 61 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8039 (mm-30) REVERT: N 71 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8769 (ttmm) REVERT: N 125 THR cc_start: 0.8991 (m) cc_final: 0.8525 (p) REVERT: O 10 GLN cc_start: 0.8940 (tt0) cc_final: 0.8738 (tt0) REVERT: O 15 ASP cc_start: 0.8790 (p0) cc_final: 0.8349 (p0) REVERT: O 42 ASP cc_start: 0.8328 (t0) cc_final: 0.8084 (t0) REVERT: O 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7830 (tm-30) REVERT: O 124 ARG cc_start: 0.8750 (mmt-90) cc_final: 0.8245 (mmt-90) REVERT: O 125 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8456 (p) REVERT: P 49 GLU cc_start: 0.8264 (tp30) cc_final: 0.8018 (tp30) REVERT: P 61 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8078 (mm-30) REVERT: P 68 ARG cc_start: 0.8812 (mtm110) cc_final: 0.8602 (mtm-85) REVERT: P 125 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8467 (p) REVERT: Q 49 GLU cc_start: 0.8082 (tp30) cc_final: 0.7711 (tm-30) REVERT: Q 61 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8112 (mm-30) REVERT: Q 125 THR cc_start: 0.9039 (m) cc_final: 0.8507 (p) REVERT: R 42 ASP cc_start: 0.8349 (t70) cc_final: 0.7428 (t0) REVERT: R 49 GLU cc_start: 0.8090 (tp30) cc_final: 0.7721 (tm-30) REVERT: R 61 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: S 42 ASP cc_start: 0.8399 (t0) cc_final: 0.7682 (t0) REVERT: S 61 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7955 (mm-30) REVERT: S 125 THR cc_start: 0.9045 (m) cc_final: 0.8497 (p) REVERT: S 148 MET cc_start: 0.9011 (mtp) cc_final: 0.8794 (mtm) REVERT: T 42 ASP cc_start: 0.8402 (t0) cc_final: 0.7560 (t0) REVERT: T 49 GLU cc_start: 0.8159 (tp30) cc_final: 0.7763 (tm-30) REVERT: T 61 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8258 (mm-30) REVERT: T 176 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7955 (pptt) REVERT: U 42 ASP cc_start: 0.8402 (t0) cc_final: 0.7553 (t0) REVERT: U 49 GLU cc_start: 0.8188 (tp30) cc_final: 0.7926 (tp30) REVERT: U 61 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8118 (mm-30) REVERT: U 124 ARG cc_start: 0.8870 (mmt-90) cc_final: 0.8658 (mmt-90) REVERT: U 125 THR cc_start: 0.9045 (m) cc_final: 0.8617 (p) REVERT: V 49 GLU cc_start: 0.8142 (tp30) cc_final: 0.7769 (tm-30) REVERT: V 61 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7966 (mm-30) REVERT: V 148 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8799 (mpp) REVERT: W 22 SER cc_start: 0.9216 (m) cc_final: 0.9000 (p) REVERT: W 42 ASP cc_start: 0.8362 (t70) cc_final: 0.8036 (t0) REVERT: W 49 GLU cc_start: 0.8123 (tp30) cc_final: 0.7874 (tp30) REVERT: W 125 THR cc_start: 0.8959 (m) cc_final: 0.8481 (p) REVERT: X 42 ASP cc_start: 0.8351 (t0) cc_final: 0.7550 (t0) REVERT: X 49 GLU cc_start: 0.8073 (tp30) cc_final: 0.7706 (tm-30) REVERT: X 61 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: X 124 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8542 (mmt-90) REVERT: X 125 THR cc_start: 0.8984 (m) cc_final: 0.8457 (p) outliers start: 76 outliers final: 17 residues processed: 708 average time/residue: 1.7018 time to fit residues: 1405.1220 Evaluate side-chains 640 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 609 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 81 LEU 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 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 L residue 98 ASP Chi-restraints excluded: chain M residue 98 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 125 THR Chi-restraints excluded: chain Q residue 98 ASP 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 V residue 98 ASP Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 268 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 336 optimal weight: 0.8980 chunk 385 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 F 75 GLN H 29 GLN I 29 GLN K 29 GLN L 29 GLN L 136 HIS M 11 ASN M 29 GLN N 29 GLN O 29 GLN P 29 GLN Q 29 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079443 restraints weight = 55052.959| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.50 r_work: 0.3085 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33816 Z= 0.132 Angle : 0.510 10.039 45480 Z= 0.263 Chirality : 0.035 0.142 4872 Planarity : 0.004 0.041 5952 Dihedral : 4.285 65.562 4524 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.10 % Favored : 98.75 % Rotamer: Outliers : 1.72 % Allowed : 20.46 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.13), residues: 4080 helix: 3.00 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 93 HIS 0.005 0.001 HIS L 128 PHE 0.012 0.002 PHE F 39 TYR 0.025 0.002 TYR N 66 ARG 0.009 0.001 ARG G 56 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 2688) hydrogen bonds : angle 3.56564 ( 8064) covalent geometry : bond 0.00289 (33816) covalent geometry : angle 0.50987 (45480) *********************** 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 741 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 681 time to evaluate : 4.285 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8448 (t0) cc_final: 0.8109 (t0) REVERT: A 49 GLU cc_start: 0.8120 (tp30) cc_final: 0.7920 (tp30) REVERT: A 57 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 61 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 71 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8831 (ttmm) REVERT: A 125 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 22 SER cc_start: 0.9234 (m) cc_final: 0.8957 (p) REVERT: B 42 ASP cc_start: 0.8366 (t70) cc_final: 0.7969 (t0) REVERT: B 49 GLU cc_start: 0.8095 (tp30) cc_final: 0.7716 (tm-30) REVERT: B 61 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 124 ARG cc_start: 0.8915 (mmt-90) cc_final: 0.8693 (mmt-90) REVERT: B 125 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8560 (p) REVERT: B 167 GLU cc_start: 0.8383 (tt0) cc_final: 0.8167 (tt0) REVERT: C 22 SER cc_start: 0.9220 (m) cc_final: 0.8979 (p) REVERT: C 42 ASP cc_start: 0.8383 (t0) cc_final: 0.7596 (t0) REVERT: C 49 GLU cc_start: 0.8107 (tp30) cc_final: 0.7711 (tm-30) REVERT: C 61 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 148 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9055 (mtp) REVERT: D 42 ASP cc_start: 0.8352 (t70) cc_final: 0.8035 (t0) REVERT: D 61 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8154 (mm-30) REVERT: D 71 LYS cc_start: 0.9141 (ttpt) cc_final: 0.8827 (ttmm) REVERT: D 125 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8202 (p) REVERT: D 167 GLU cc_start: 0.8432 (tt0) cc_final: 0.8215 (tt0) REVERT: E 22 SER cc_start: 0.9200 (m) cc_final: 0.8981 (p) REVERT: E 42 ASP cc_start: 0.8369 (t0) cc_final: 0.7929 (t0) REVERT: E 148 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8823 (mtm) REVERT: F 42 ASP cc_start: 0.8431 (t0) cc_final: 0.7656 (t0) REVERT: F 49 GLU cc_start: 0.8187 (tp30) cc_final: 0.7907 (tp30) REVERT: F 61 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8147 (mm-30) REVERT: F 91 ASP cc_start: 0.8553 (p0) cc_final: 0.8101 (m-30) REVERT: F 125 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8459 (p) REVERT: G 22 SER cc_start: 0.9225 (m) cc_final: 0.8933 (p) REVERT: G 42 ASP cc_start: 0.8332 (t70) cc_final: 0.8093 (t0) REVERT: G 49 GLU cc_start: 0.8088 (tp30) cc_final: 0.7704 (tm-30) REVERT: G 61 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8139 (mm-30) REVERT: G 124 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8670 (mmt-90) REVERT: G 125 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8568 (p) REVERT: G 139 ASP cc_start: 0.8579 (t70) cc_final: 0.8228 (p0) REVERT: G 140 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: H 42 ASP cc_start: 0.8393 (t0) cc_final: 0.7604 (t0) REVERT: H 49 GLU cc_start: 0.8127 (tp30) cc_final: 0.7787 (tm-30) REVERT: H 61 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8072 (mm-30) REVERT: H 148 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8850 (mmm) REVERT: I 42 ASP cc_start: 0.8364 (t0) cc_final: 0.8059 (t0) REVERT: I 49 GLU cc_start: 0.8139 (tp30) cc_final: 0.7748 (tm-30) REVERT: I 61 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8118 (mm-30) REVERT: I 125 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8604 (p) REVERT: J 49 GLU cc_start: 0.8109 (tp30) cc_final: 0.7726 (tm-30) REVERT: J 61 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: J 176 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8134 (pttm) REVERT: K 42 ASP cc_start: 0.8423 (t0) cc_final: 0.7589 (t0) REVERT: K 49 GLU cc_start: 0.8144 (tp30) cc_final: 0.7733 (tm-30) REVERT: K 61 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8136 (mm-30) REVERT: K 125 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8564 (p) REVERT: L 42 ASP cc_start: 0.8348 (t0) cc_final: 0.7600 (t0) REVERT: L 49 GLU cc_start: 0.8105 (tp30) cc_final: 0.7759 (tm-30) REVERT: L 71 LYS cc_start: 0.9137 (ttpt) cc_final: 0.8812 (ttmm) REVERT: M 42 ASP cc_start: 0.8425 (t0) cc_final: 0.8018 (t0) REVERT: M 49 GLU cc_start: 0.8127 (tp30) cc_final: 0.7703 (tm-30) REVERT: M 61 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8132 (mm-30) REVERT: N 15 ASP cc_start: 0.8622 (p0) cc_final: 0.8226 (p0) REVERT: N 49 GLU cc_start: 0.8190 (tp30) cc_final: 0.7813 (tm-30) REVERT: N 61 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8119 (mm-30) REVERT: N 125 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8467 (p) REVERT: O 42 ASP cc_start: 0.8432 (t0) cc_final: 0.8136 (t0) REVERT: O 49 GLU cc_start: 0.8133 (tp30) cc_final: 0.7755 (tm-30) REVERT: O 124 ARG cc_start: 0.8735 (mmt-90) cc_final: 0.8438 (mmt-90) REVERT: O 125 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8434 (p) REVERT: P 42 ASP cc_start: 0.8379 (t0) cc_final: 0.8157 (t0) REVERT: P 49 GLU cc_start: 0.8261 (tp30) cc_final: 0.7886 (tm-30) REVERT: P 61 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8097 (mm-30) REVERT: P 125 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8452 (p) REVERT: Q 49 GLU cc_start: 0.8118 (tp30) cc_final: 0.7721 (tm-30) REVERT: Q 61 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8168 (mm-30) REVERT: Q 125 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8481 (p) REVERT: R 42 ASP cc_start: 0.8386 (t70) cc_final: 0.8012 (t0) REVERT: R 49 GLU cc_start: 0.8140 (tp30) cc_final: 0.7753 (tm-30) REVERT: R 61 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: S 42 ASP cc_start: 0.8416 (t0) cc_final: 0.7585 (t0) REVERT: S 61 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8047 (mm-30) REVERT: S 125 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8458 (p) REVERT: T 42 ASP cc_start: 0.8439 (t0) cc_final: 0.7613 (t0) REVERT: T 49 GLU cc_start: 0.8128 (tp30) cc_final: 0.7747 (tm-30) REVERT: T 61 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8277 (mm-30) REVERT: T 79 ARG cc_start: 0.8155 (mmp80) cc_final: 0.7909 (mmt-90) REVERT: T 176 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (pptt) REVERT: U 42 ASP cc_start: 0.8426 (t0) cc_final: 0.7559 (t0) REVERT: U 49 GLU cc_start: 0.8212 (tp30) cc_final: 0.7842 (tm-30) REVERT: U 61 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8151 (mm-30) REVERT: U 124 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8643 (mmt-90) REVERT: U 125 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8574 (p) REVERT: V 42 ASP cc_start: 0.8395 (t70) cc_final: 0.8121 (t0) REVERT: V 49 GLU cc_start: 0.8174 (tp30) cc_final: 0.7782 (tm-30) REVERT: V 61 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8093 (mm-30) REVERT: V 148 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8795 (mpp) REVERT: W 22 SER cc_start: 0.9235 (m) cc_final: 0.9035 (p) REVERT: W 42 ASP cc_start: 0.8360 (t70) cc_final: 0.8026 (t0) REVERT: W 49 GLU cc_start: 0.8152 (tp30) cc_final: 0.7758 (tm-30) REVERT: W 124 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.8116 (mmt-90) REVERT: W 125 THR cc_start: 0.8954 (m) cc_final: 0.8460 (p) REVERT: X 42 ASP cc_start: 0.8396 (t0) cc_final: 0.8060 (t0) REVERT: X 49 GLU cc_start: 0.8159 (tp30) cc_final: 0.7766 (tm-30) REVERT: X 61 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: X 125 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8454 (p) outliers start: 60 outliers final: 13 residues processed: 705 average time/residue: 1.7211 time to fit residues: 1412.2333 Evaluate side-chains 668 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 631 time to evaluate : 4.067 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 4 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 368 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 362 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 75 GLN H 29 GLN I 29 GLN N 136 HIS O 29 GLN P 29 GLN Q 29 GLN Q 136 HIS T 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078945 restraints weight = 55089.543| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.49 r_work: 0.3065 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33816 Z= 0.144 Angle : 0.511 9.537 45480 Z= 0.263 Chirality : 0.035 0.135 4872 Planarity : 0.004 0.037 5952 Dihedral : 4.289 67.157 4524 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.15 % Favored : 98.75 % Rotamer: Outliers : 1.87 % Allowed : 21.24 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.13), residues: 4080 helix: 3.06 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.89 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 93 HIS 0.004 0.001 HIS C 128 PHE 0.013 0.002 PHE F 39 TYR 0.027 0.002 TYR N 66 ARG 0.010 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 2688) hydrogen bonds : angle 3.57058 ( 8064) covalent geometry : bond 0.00315 (33816) covalent geometry : angle 0.51104 (45480) *********************** 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 750 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 685 time to evaluate : 3.737 Fit side-chains REVERT: A 15 ASP cc_start: 0.8412 (p0) cc_final: 0.7634 (p0) REVERT: A 42 ASP cc_start: 0.8466 (t0) cc_final: 0.7592 (t0) REVERT: A 57 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8348 (mm-30) REVERT: A 61 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 71 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8783 (ttmm) REVERT: A 125 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 22 SER cc_start: 0.9206 (m) cc_final: 0.8912 (p) REVERT: B 42 ASP cc_start: 0.8329 (t70) cc_final: 0.7873 (t0) REVERT: B 49 GLU cc_start: 0.8158 (tp30) cc_final: 0.7772 (tm-30) REVERT: B 61 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 107 GLU cc_start: 0.8973 (tp30) cc_final: 0.8763 (mm-30) REVERT: B 124 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8709 (mmt-90) REVERT: B 125 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8525 (p) REVERT: C 22 SER cc_start: 0.9211 (m) cc_final: 0.8955 (p) REVERT: C 42 ASP cc_start: 0.8416 (t0) cc_final: 0.7625 (t0) REVERT: C 49 GLU cc_start: 0.8146 (tp30) cc_final: 0.7738 (tm-30) REVERT: C 61 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8106 (mm-30) REVERT: C 148 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9050 (mtp) REVERT: D 42 ASP cc_start: 0.8404 (t70) cc_final: 0.7496 (t0) REVERT: D 61 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8068 (mm-30) REVERT: D 71 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8787 (ttmm) REVERT: D 125 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8234 (p) REVERT: D 167 GLU cc_start: 0.8432 (tt0) cc_final: 0.8188 (tt0) REVERT: E 22 SER cc_start: 0.9197 (m) cc_final: 0.8966 (p) REVERT: E 42 ASP cc_start: 0.8345 (t0) cc_final: 0.7875 (t0) REVERT: E 148 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8848 (mtm) REVERT: F 42 ASP cc_start: 0.8461 (t0) cc_final: 0.7733 (t0) REVERT: F 49 GLU cc_start: 0.8231 (tp30) cc_final: 0.7943 (tp30) REVERT: F 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8122 (mm-30) REVERT: F 91 ASP cc_start: 0.8566 (p0) cc_final: 0.8141 (m-30) REVERT: F 125 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8458 (p) REVERT: G 22 SER cc_start: 0.9203 (m) cc_final: 0.8897 (p) REVERT: G 42 ASP cc_start: 0.8365 (t70) cc_final: 0.8049 (t0) REVERT: G 49 GLU cc_start: 0.8102 (tp30) cc_final: 0.7698 (tm-30) REVERT: G 60 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: G 61 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8292 (mm-30) REVERT: G 125 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8536 (p) REVERT: G 139 ASP cc_start: 0.8537 (t70) cc_final: 0.8234 (p0) REVERT: G 140 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: H 15 ASP cc_start: 0.8831 (p0) cc_final: 0.8499 (p0) REVERT: H 42 ASP cc_start: 0.8405 (t0) cc_final: 0.7617 (t0) REVERT: H 49 GLU cc_start: 0.8199 (tp30) cc_final: 0.7902 (tm-30) REVERT: H 61 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8064 (mm-30) REVERT: H 124 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8310 (mmt-90) REVERT: H 148 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8837 (mmm) REVERT: I 42 ASP cc_start: 0.8435 (t0) cc_final: 0.8038 (t0) REVERT: I 49 GLU cc_start: 0.8161 (tp30) cc_final: 0.7741 (tm-30) REVERT: I 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8069 (mm-30) REVERT: I 125 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8580 (p) REVERT: J 49 GLU cc_start: 0.8135 (tp30) cc_final: 0.7777 (tm-30) REVERT: J 61 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: J 176 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7975 (pttm) REVERT: K 42 ASP cc_start: 0.8407 (t0) cc_final: 0.7590 (t0) REVERT: K 49 GLU cc_start: 0.8215 (tp30) cc_final: 0.7843 (tm-30) REVERT: K 61 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8071 (mm-30) REVERT: K 125 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8547 (p) REVERT: L 42 ASP cc_start: 0.8333 (t0) cc_final: 0.7560 (t0) REVERT: L 49 GLU cc_start: 0.8132 (tp30) cc_final: 0.7738 (tm-30) REVERT: L 71 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8783 (ttmm) REVERT: M 42 ASP cc_start: 0.8442 (t0) cc_final: 0.7579 (t0) REVERT: M 49 GLU cc_start: 0.8207 (tp30) cc_final: 0.7821 (tm-30) REVERT: M 61 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8106 (mm-30) REVERT: N 49 GLU cc_start: 0.8226 (tp30) cc_final: 0.7842 (tm-30) REVERT: N 61 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8033 (mm-30) REVERT: N 125 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8482 (p) REVERT: O 42 ASP cc_start: 0.8379 (t0) cc_final: 0.7531 (t0) REVERT: O 49 GLU cc_start: 0.8202 (tp30) cc_final: 0.7866 (tm-30) REVERT: O 124 ARG cc_start: 0.8784 (mmt-90) cc_final: 0.8471 (mmt-90) REVERT: O 125 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8463 (p) REVERT: P 49 GLU cc_start: 0.8246 (tp30) cc_final: 0.7970 (tp30) REVERT: P 61 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8080 (mm-30) REVERT: P 124 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8681 (mmt-90) REVERT: P 125 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8484 (p) REVERT: Q 49 GLU cc_start: 0.8133 (tp30) cc_final: 0.7741 (tm-30) REVERT: Q 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8172 (mm-30) REVERT: Q 125 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8596 (p) REVERT: R 42 ASP cc_start: 0.8389 (t70) cc_final: 0.7467 (t0) REVERT: R 49 GLU cc_start: 0.8162 (tp30) cc_final: 0.7776 (tm-30) REVERT: R 61 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: S 42 ASP cc_start: 0.8392 (t0) cc_final: 0.7982 (t0) REVERT: S 61 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8049 (mm-30) REVERT: S 125 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8559 (p) REVERT: T 42 ASP cc_start: 0.8448 (t0) cc_final: 0.7595 (t0) REVERT: T 49 GLU cc_start: 0.8131 (tp30) cc_final: 0.7734 (tm-30) REVERT: T 61 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8271 (mm-30) REVERT: T 176 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7784 (pptt) REVERT: U 42 ASP cc_start: 0.8420 (t0) cc_final: 0.7542 (t0) REVERT: U 49 GLU cc_start: 0.8214 (tp30) cc_final: 0.7920 (tp30) REVERT: U 61 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8127 (mm-30) REVERT: U 125 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8597 (p) REVERT: V 42 ASP cc_start: 0.8362 (t70) cc_final: 0.8007 (t0) REVERT: V 49 GLU cc_start: 0.8189 (tp30) cc_final: 0.7771 (tm-30) REVERT: V 61 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7992 (mm-30) REVERT: V 148 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8790 (mpp) REVERT: W 22 SER cc_start: 0.9202 (m) cc_final: 0.8977 (p) REVERT: W 42 ASP cc_start: 0.8339 (t70) cc_final: 0.7455 (t0) REVERT: W 49 GLU cc_start: 0.8185 (tp30) cc_final: 0.7791 (tm-30) REVERT: W 125 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8460 (p) REVERT: X 42 ASP cc_start: 0.8413 (t0) cc_final: 0.7990 (t0) REVERT: X 49 GLU cc_start: 0.8182 (tp30) cc_final: 0.7768 (tm-30) REVERT: X 61 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: X 124 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.8434 (mmt-90) REVERT: X 125 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8449 (p) outliers start: 65 outliers final: 10 residues processed: 709 average time/residue: 1.6961 time to fit residues: 1402.8732 Evaluate side-chains 670 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 634 time to evaluate : 3.600 ------------------------------------------------------------------------------- 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 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 L 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 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 98 ASP Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain V residue 98 ASP Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W 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 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 283 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 398 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 381 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 29 GLN G 29 GLN H 29 GLN I 29 GLN O 29 GLN P 29 GLN Q 29 GLN S 136 HIS V 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 = 0.3445 r_free = 0.3445 target = 0.089611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077234 restraints weight = 54870.767| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.46 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33816 Z= 0.193 Angle : 0.539 8.989 45480 Z= 0.277 Chirality : 0.037 0.128 4872 Planarity : 0.004 0.041 5952 Dihedral : 4.244 66.059 4522 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.08 % Favored : 98.82 % Rotamer: Outliers : 1.81 % Allowed : 21.98 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.13), residues: 4080 helix: 2.93 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.81 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 93 HIS 0.004 0.001 HIS K 128 PHE 0.016 0.002 PHE F 39 TYR 0.027 0.002 TYR N 66 ARG 0.009 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 2688) hydrogen bonds : angle 3.66183 ( 8064) covalent geometry : bond 0.00421 (33816) covalent geometry : angle 0.53929 (45480) *********************** 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 722 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 659 time to evaluate : 3.727 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8457 (t0) cc_final: 0.7603 (t0) REVERT: A 57 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8356 (mm-30) REVERT: A 61 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 71 LYS cc_start: 0.9053 (ttpt) cc_final: 0.8765 (ttmm) REVERT: A 125 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8542 (p) REVERT: B 22 SER cc_start: 0.9208 (m) cc_final: 0.8912 (p) REVERT: B 42 ASP cc_start: 0.8371 (t70) cc_final: 0.7461 (t0) REVERT: B 49 GLU cc_start: 0.8222 (tp30) cc_final: 0.7917 (tp30) REVERT: B 61 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 22 SER cc_start: 0.9199 (m) cc_final: 0.8944 (p) REVERT: C 42 ASP cc_start: 0.8409 (t0) cc_final: 0.7731 (t0) REVERT: C 49 GLU cc_start: 0.8206 (tp30) cc_final: 0.7903 (tp30) REVERT: C 61 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8149 (mm-30) REVERT: C 148 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.9023 (mtp) REVERT: D 42 ASP cc_start: 0.8364 (t70) cc_final: 0.7479 (t0) REVERT: D 49 GLU cc_start: 0.8696 (tt0) cc_final: 0.8434 (tp30) REVERT: D 61 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8083 (mm-30) REVERT: D 71 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8790 (ttmm) REVERT: D 125 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8372 (p) REVERT: E 22 SER cc_start: 0.9206 (m) cc_final: 0.8957 (p) REVERT: E 42 ASP cc_start: 0.8383 (t0) cc_final: 0.7517 (t0) REVERT: E 148 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8986 (mtp) REVERT: F 42 ASP cc_start: 0.8465 (t0) cc_final: 0.7681 (t0) REVERT: F 49 GLU cc_start: 0.8235 (tp30) cc_final: 0.7927 (tp30) REVERT: F 61 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8149 (mm-30) REVERT: F 125 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8516 (p) REVERT: G 42 ASP cc_start: 0.8345 (t70) cc_final: 0.7434 (t0) REVERT: G 49 GLU cc_start: 0.8191 (tp30) cc_final: 0.7908 (tp30) REVERT: G 60 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: G 61 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8216 (mm-30) REVERT: G 139 ASP cc_start: 0.8634 (t70) cc_final: 0.8267 (p0) REVERT: G 140 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: H 42 ASP cc_start: 0.8433 (t0) cc_final: 0.7645 (t0) REVERT: H 49 GLU cc_start: 0.8195 (tp30) cc_final: 0.7925 (tp30) REVERT: H 61 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 104 MET cc_start: 0.9035 (tpp) cc_final: 0.8828 (ttp) REVERT: H 124 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.8494 (mmt-90) REVERT: H 148 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8663 (mpp) REVERT: I 42 ASP cc_start: 0.8425 (t0) cc_final: 0.7572 (t0) REVERT: I 49 GLU cc_start: 0.8213 (tp30) cc_final: 0.7935 (tp30) REVERT: I 61 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8066 (mm-30) REVERT: J 49 GLU cc_start: 0.8226 (tp30) cc_final: 0.7940 (tp30) REVERT: J 61 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: J 176 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (pttm) REVERT: K 42 ASP cc_start: 0.8375 (t0) cc_final: 0.7562 (t0) REVERT: K 49 GLU cc_start: 0.8241 (tp30) cc_final: 0.7933 (tp30) REVERT: K 61 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8079 (mm-30) REVERT: L 42 ASP cc_start: 0.8374 (t0) cc_final: 0.7617 (t0) REVERT: L 49 GLU cc_start: 0.8214 (tp30) cc_final: 0.7947 (tp30) REVERT: L 71 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8796 (ttmm) REVERT: L 104 MET cc_start: 0.8969 (ttp) cc_final: 0.8759 (ttp) REVERT: L 167 GLU cc_start: 0.8363 (tt0) cc_final: 0.8150 (tt0) REVERT: M 42 ASP cc_start: 0.8428 (t0) cc_final: 0.8006 (t0) REVERT: M 49 GLU cc_start: 0.8275 (tp30) cc_final: 0.8001 (tp30) REVERT: M 61 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8107 (mm-30) REVERT: N 15 ASP cc_start: 0.8779 (p0) cc_final: 0.8565 (p0) REVERT: N 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7968 (tp30) REVERT: N 61 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8081 (mm-30) REVERT: N 71 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8742 (ttmm) REVERT: N 125 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8540 (p) REVERT: O 42 ASP cc_start: 0.8423 (t0) cc_final: 0.7571 (t0) REVERT: O 49 GLU cc_start: 0.8259 (tp30) cc_final: 0.7973 (tp30) REVERT: O 124 ARG cc_start: 0.8927 (mmt-90) cc_final: 0.8579 (mmt-90) REVERT: O 125 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8498 (p) REVERT: P 49 GLU cc_start: 0.8253 (tp30) cc_final: 0.7978 (tp30) REVERT: P 61 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8123 (mm-30) REVERT: P 125 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8552 (p) REVERT: P 148 MET cc_start: 0.9029 (mtp) cc_final: 0.8829 (mtm) REVERT: Q 42 ASP cc_start: 0.8362 (t70) cc_final: 0.7570 (t0) REVERT: Q 49 GLU cc_start: 0.8245 (tp30) cc_final: 0.7926 (tp30) REVERT: Q 61 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8151 (mm-30) REVERT: R 42 ASP cc_start: 0.8430 (t70) cc_final: 0.7526 (t0) REVERT: R 49 GLU cc_start: 0.8180 (tp30) cc_final: 0.7915 (tp30) REVERT: R 61 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: S 42 ASP cc_start: 0.8413 (t0) cc_final: 0.7635 (t0) REVERT: S 57 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8322 (mm-30) REVERT: S 61 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8150 (mm-30) REVERT: T 42 ASP cc_start: 0.8429 (t0) cc_final: 0.7577 (t0) REVERT: T 49 GLU cc_start: 0.8157 (tp30) cc_final: 0.7863 (tp30) REVERT: T 61 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8260 (mm-30) REVERT: T 176 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7677 (pptt) REVERT: U 42 ASP cc_start: 0.8447 (t0) cc_final: 0.7620 (t0) REVERT: U 49 GLU cc_start: 0.8213 (tp30) cc_final: 0.7930 (tp30) REVERT: U 61 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8121 (mm-30) REVERT: V 42 ASP cc_start: 0.8350 (t70) cc_final: 0.8015 (t0) REVERT: V 49 GLU cc_start: 0.8239 (tp30) cc_final: 0.7940 (tp30) REVERT: V 61 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8010 (mm-30) REVERT: V 148 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8747 (mpp) REVERT: W 22 SER cc_start: 0.9207 (m) cc_final: 0.8976 (p) REVERT: W 42 ASP cc_start: 0.8388 (t70) cc_final: 0.7484 (t0) REVERT: W 49 GLU cc_start: 0.8242 (tp30) cc_final: 0.7964 (tp30) REVERT: W 125 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8513 (p) REVERT: X 42 ASP cc_start: 0.8365 (t0) cc_final: 0.7474 (t0) REVERT: X 49 GLU cc_start: 0.8216 (tp30) cc_final: 0.7923 (tp30) REVERT: X 61 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: X 124 ARG cc_start: 0.8831 (mmt-90) cc_final: 0.8510 (mmt-90) REVERT: X 125 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8504 (p) outliers start: 63 outliers final: 23 residues processed: 685 average time/residue: 1.9347 time to fit residues: 1576.2806 Evaluate side-chains 640 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 598 time to evaluate : 3.989 ------------------------------------------------------------------------------- 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 60 GLU 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 125 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 98 ASP 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 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 98 ASP 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 R residue 98 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 125 THR Chi-restraints excluded: chain V residue 98 ASP Chi-restraints excluded: chain V residue 148 MET Chi-restraints excluded: chain W 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 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 19 optimal weight: 0.9990 chunk 301 optimal weight: 0.9980 chunk 364 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 D 29 GLN F 29 GLN F 75 GLN G 29 GLN H 29 GLN I 29 GLN M 11 ASN O 11 ASN O 29 GLN P 29 GLN Q 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079704 restraints weight = 54915.821| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.49 r_work: 0.3081 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33816 Z= 0.131 Angle : 0.511 9.237 45480 Z= 0.265 Chirality : 0.035 0.124 4872 Planarity : 0.004 0.047 5952 Dihedral : 4.100 60.264 4522 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.20 % Favored : 98.73 % Rotamer: Outliers : 1.52 % Allowed : 22.33 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.13), residues: 4080 helix: 3.05 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.80 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 93 HIS 0.005 0.001 HIS L 128 PHE 0.012 0.002 PHE F 39 TYR 0.025 0.002 TYR N 66 ARG 0.012 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 2688) hydrogen bonds : angle 3.56169 ( 8064) covalent geometry : bond 0.00287 (33816) covalent geometry : angle 0.51139 (45480) *********************** 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 716 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 663 time to evaluate : 4.681 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8408 (t0) cc_final: 0.8051 (t0) REVERT: A 57 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8298 (mm-30) REVERT: A 61 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 71 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8725 (ttmm) REVERT: A 125 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 22 SER cc_start: 0.9203 (m) cc_final: 0.8910 (p) REVERT: B 42 ASP cc_start: 0.8312 (t70) cc_final: 0.7796 (t0) REVERT: B 49 GLU cc_start: 0.8157 (tp30) cc_final: 0.7783 (tm-30) REVERT: B 61 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 125 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8517 (p) REVERT: C 22 SER cc_start: 0.9211 (m) cc_final: 0.8922 (p) REVERT: C 42 ASP cc_start: 0.8348 (t0) cc_final: 0.7622 (t0) REVERT: C 49 GLU cc_start: 0.8152 (tp30) cc_final: 0.7753 (tm-30) REVERT: C 61 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8122 (mm-30) REVERT: C 148 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9036 (mtp) REVERT: D 42 ASP cc_start: 0.8334 (t70) cc_final: 0.7905 (t0) REVERT: D 49 GLU cc_start: 0.8657 (tt0) cc_final: 0.8311 (tp30) REVERT: D 61 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8084 (mm-30) REVERT: D 71 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8728 (ttmm) REVERT: D 125 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8208 (p) REVERT: E 22 SER cc_start: 0.9179 (m) cc_final: 0.8941 (p) REVERT: E 42 ASP cc_start: 0.8309 (t0) cc_final: 0.7798 (t0) REVERT: E 148 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8790 (mtm) REVERT: F 42 ASP cc_start: 0.8403 (t0) cc_final: 0.7666 (t0) REVERT: F 49 GLU cc_start: 0.8217 (tp30) cc_final: 0.7920 (tp30) REVERT: F 61 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8161 (mm-30) REVERT: F 125 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8392 (p) REVERT: G 42 ASP cc_start: 0.8277 (t70) cc_final: 0.7865 (t0) REVERT: G 49 GLU cc_start: 0.8167 (tp30) cc_final: 0.7798 (tm-30) REVERT: G 60 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: G 61 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8202 (mm-30) REVERT: G 125 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8509 (p) REVERT: G 139 ASP cc_start: 0.8525 (t70) cc_final: 0.8213 (p0) REVERT: H 15 ASP cc_start: 0.8832 (p0) cc_final: 0.8437 (p0) REVERT: H 42 ASP cc_start: 0.8380 (t0) cc_final: 0.7524 (t0) REVERT: H 49 GLU cc_start: 0.8151 (tp30) cc_final: 0.7886 (tp30) REVERT: H 61 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8078 (mm-30) REVERT: H 124 ARG cc_start: 0.8513 (mmt-90) cc_final: 0.8263 (mmt-90) REVERT: H 148 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8734 (mpp) REVERT: I 42 ASP cc_start: 0.8361 (t0) cc_final: 0.7940 (t0) REVERT: I 49 GLU cc_start: 0.8159 (tp30) cc_final: 0.7869 (tp30) REVERT: I 61 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8110 (mm-30) REVERT: I 125 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8542 (p) REVERT: J 49 GLU cc_start: 0.8139 (tp30) cc_final: 0.7793 (tm-30) REVERT: J 61 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: J 176 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7814 (pttm) REVERT: K 42 ASP cc_start: 0.8359 (t0) cc_final: 0.7980 (t0) REVERT: K 49 GLU cc_start: 0.8211 (tp30) cc_final: 0.7899 (tp30) REVERT: K 61 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8059 (mm-30) REVERT: K 125 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8516 (p) REVERT: L 42 ASP cc_start: 0.8362 (t0) cc_final: 0.7947 (t0) REVERT: L 49 GLU cc_start: 0.8169 (tp30) cc_final: 0.7774 (tm-30) REVERT: L 71 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8761 (ttmm) REVERT: L 167 GLU cc_start: 0.8273 (tt0) cc_final: 0.8045 (tt0) REVERT: M 42 ASP cc_start: 0.8338 (t0) cc_final: 0.7895 (t0) REVERT: M 49 GLU cc_start: 0.8237 (tp30) cc_final: 0.7887 (tm-30) REVERT: M 61 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8143 (mm-30) REVERT: N 49 GLU cc_start: 0.8190 (tp30) cc_final: 0.7806 (tm-30) REVERT: N 61 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8050 (mm-30) REVERT: N 125 THR cc_start: 0.8922 (m) cc_final: 0.8470 (p) REVERT: O 42 ASP cc_start: 0.8376 (t0) cc_final: 0.8019 (t0) REVERT: O 49 GLU cc_start: 0.8226 (tp30) cc_final: 0.7865 (tm-30) REVERT: O 124 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.8441 (mmt-90) REVERT: O 125 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8401 (p) REVERT: P 49 GLU cc_start: 0.8217 (tp30) cc_final: 0.7948 (tp30) REVERT: P 61 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8091 (mm-30) REVERT: P 125 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8563 (p) REVERT: Q 42 ASP cc_start: 0.8348 (t70) cc_final: 0.8010 (t0) REVERT: Q 49 GLU cc_start: 0.8177 (tp30) cc_final: 0.7823 (tm-30) REVERT: Q 61 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8173 (mm-30) REVERT: R 42 ASP cc_start: 0.8363 (t70) cc_final: 0.7891 (t0) REVERT: R 49 GLU cc_start: 0.8156 (tp30) cc_final: 0.7779 (tm-30) REVERT: R 61 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: S 42 ASP cc_start: 0.8344 (t0) cc_final: 0.7928 (t0) REVERT: S 57 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8188 (mm-30) REVERT: S 61 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8010 (mm-30) REVERT: T 42 ASP cc_start: 0.8358 (t0) cc_final: 0.7864 (t0) REVERT: T 49 GLU cc_start: 0.8140 (tp30) cc_final: 0.7845 (tp30) REVERT: T 61 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8249 (mm-30) REVERT: T 176 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7771 (pptt) REVERT: U 42 ASP cc_start: 0.8369 (t0) cc_final: 0.7510 (t0) REVERT: U 49 GLU cc_start: 0.8178 (tp30) cc_final: 0.7900 (tp30) REVERT: U 61 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8146 (mm-30) REVERT: U 125 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8569 (p) REVERT: V 42 ASP cc_start: 0.8306 (t70) cc_final: 0.7917 (t0) REVERT: V 49 GLU cc_start: 0.8187 (tp30) cc_final: 0.7845 (tm-30) REVERT: V 61 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8045 (mm-30) REVERT: W 22 SER cc_start: 0.9210 (m) cc_final: 0.8994 (p) REVERT: W 42 ASP cc_start: 0.8350 (t70) cc_final: 0.7906 (t0) REVERT: W 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7917 (tp30) REVERT: W 125 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8419 (p) REVERT: X 42 ASP cc_start: 0.8320 (t0) cc_final: 0.7874 (t0) REVERT: X 49 GLU cc_start: 0.8202 (tp30) cc_final: 0.7904 (tp30) REVERT: X 61 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: X 124 ARG cc_start: 0.8736 (mmt-90) cc_final: 0.8381 (mmt-90) REVERT: X 125 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8408 (p) outliers start: 53 outliers final: 14 residues processed: 690 average time/residue: 2.0244 time to fit residues: 1631.6839 Evaluate side-chains 662 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 627 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 GLU Chi-restraints excluded: chain G residue 72 MET 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 98 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain L residue 98 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 125 THR 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 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain V residue 98 ASP Chi-restraints excluded: chain W 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 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 156 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 267 optimal weight: 0.0070 chunk 243 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 G 29 GLN H 29 GLN I 29 GLN O 29 GLN Q 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080354 restraints weight = 54803.785| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.50 r_work: 0.3099 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33816 Z= 0.122 Angle : 0.514 9.147 45480 Z= 0.266 Chirality : 0.035 0.123 4872 Planarity : 0.003 0.052 5952 Dihedral : 4.076 67.374 4522 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.20 % Favored : 98.73 % Rotamer: Outliers : 1.21 % Allowed : 23.62 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.13), residues: 4080 helix: 3.11 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.75 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 93 HIS 0.005 0.001 HIS L 128 PHE 0.012 0.002 PHE F 39 TYR 0.027 0.002 TYR Q 66 ARG 0.012 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 2688) hydrogen bonds : angle 3.53511 ( 8064) covalent geometry : bond 0.00269 (33816) covalent geometry : angle 0.51353 (45480) *********************** 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 717 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 675 time to evaluate : 4.208 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8442 (t0) cc_final: 0.8046 (t0) REVERT: A 57 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 61 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 71 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8729 (ttmm) REVERT: A 124 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7761 (mtp85) REVERT: A 125 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8442 (p) REVERT: B 22 SER cc_start: 0.9212 (m) cc_final: 0.8920 (p) REVERT: B 42 ASP cc_start: 0.8314 (t70) cc_final: 0.7799 (t0) REVERT: B 49 GLU cc_start: 0.8154 (tp30) cc_final: 0.7795 (tm-30) REVERT: B 61 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8052 (mm-30) REVERT: B 125 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8447 (p) REVERT: C 22 SER cc_start: 0.9209 (m) cc_final: 0.8954 (p) REVERT: C 42 ASP cc_start: 0.8309 (t0) cc_final: 0.7881 (t0) REVERT: C 49 GLU cc_start: 0.8118 (tp30) cc_final: 0.7708 (tm-30) REVERT: C 61 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8181 (mm-30) REVERT: C 148 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9054 (mtp) REVERT: D 42 ASP cc_start: 0.8319 (t70) cc_final: 0.7882 (t0) REVERT: D 49 GLU cc_start: 0.8651 (tt0) cc_final: 0.8313 (tp30) REVERT: D 61 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8044 (mm-30) REVERT: D 71 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8759 (ttmm) REVERT: D 125 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8132 (p) REVERT: E 22 SER cc_start: 0.9169 (m) cc_final: 0.8945 (p) REVERT: E 42 ASP cc_start: 0.8288 (t0) cc_final: 0.7796 (t0) REVERT: E 43 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8374 (mtm180) REVERT: F 42 ASP cc_start: 0.8415 (t0) cc_final: 0.7622 (t0) REVERT: F 49 GLU cc_start: 0.8204 (tp30) cc_final: 0.7925 (tp30) REVERT: F 61 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8162 (mm-30) REVERT: F 124 ARG cc_start: 0.8769 (mmt-90) cc_final: 0.8435 (mmt-90) REVERT: F 125 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8508 (p) REVERT: G 42 ASP cc_start: 0.8269 (t70) cc_final: 0.7869 (t0) REVERT: G 49 GLU cc_start: 0.8119 (tp30) cc_final: 0.7753 (tm-30) REVERT: G 60 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: G 61 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8214 (mm-30) REVERT: G 125 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8484 (p) REVERT: G 135 THR cc_start: 0.9106 (m) cc_final: 0.8825 (t) REVERT: G 139 ASP cc_start: 0.8509 (t70) cc_final: 0.8197 (p0) REVERT: H 42 ASP cc_start: 0.8385 (t0) cc_final: 0.7566 (t0) REVERT: H 49 GLU cc_start: 0.8095 (tp30) cc_final: 0.7832 (tp30) REVERT: H 61 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8091 (mm-30) REVERT: H 104 MET cc_start: 0.9033 (tpp) cc_final: 0.8798 (ttp) REVERT: H 148 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8775 (mpp) REVERT: I 42 ASP cc_start: 0.8380 (t0) cc_final: 0.7958 (t0) REVERT: I 49 GLU cc_start: 0.8138 (tp30) cc_final: 0.7684 (tm-30) REVERT: I 61 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8083 (mm-30) REVERT: I 125 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8510 (p) REVERT: J 49 GLU cc_start: 0.8153 (tp30) cc_final: 0.7783 (tm-30) REVERT: J 61 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: J 176 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7764 (pttm) REVERT: K 42 ASP cc_start: 0.8382 (t0) cc_final: 0.7546 (t0) REVERT: K 49 GLU cc_start: 0.8198 (tp30) cc_final: 0.7884 (tp30) REVERT: K 61 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8040 (mm-30) REVERT: K 125 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8499 (p) REVERT: L 42 ASP cc_start: 0.8334 (t0) cc_final: 0.7490 (t0) REVERT: L 49 GLU cc_start: 0.8129 (tp30) cc_final: 0.7729 (tm-30) REVERT: L 71 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8753 (ttmm) REVERT: L 167 GLU cc_start: 0.8234 (tt0) cc_final: 0.8033 (tt0) REVERT: M 42 ASP cc_start: 0.8392 (t0) cc_final: 0.8008 (t0) REVERT: M 49 GLU cc_start: 0.8245 (tp30) cc_final: 0.7885 (tm-30) REVERT: M 61 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8159 (mm-30) REVERT: N 49 GLU cc_start: 0.8172 (tp30) cc_final: 0.7788 (tm-30) REVERT: N 61 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8052 (mm-30) REVERT: N 125 THR cc_start: 0.8903 (m) cc_final: 0.8461 (p) REVERT: N 139 ASP cc_start: 0.8617 (t0) cc_final: 0.8194 (p0) REVERT: O 42 ASP cc_start: 0.8376 (t0) cc_final: 0.8011 (t0) REVERT: O 49 GLU cc_start: 0.8223 (tp30) cc_final: 0.7871 (tm-30) REVERT: O 124 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.8410 (mmt-90) REVERT: O 125 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8486 (p) REVERT: P 49 GLU cc_start: 0.8199 (tp30) cc_final: 0.7952 (tp30) REVERT: P 61 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8079 (mm-30) REVERT: P 125 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8543 (p) REVERT: Q 42 ASP cc_start: 0.8341 (t70) cc_final: 0.8021 (t0) REVERT: Q 49 GLU cc_start: 0.8164 (tp30) cc_final: 0.7794 (tm-30) REVERT: Q 61 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8175 (mm-30) REVERT: Q 125 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8504 (p) REVERT: Q 139 ASP cc_start: 0.8552 (t0) cc_final: 0.7949 (p0) REVERT: R 42 ASP cc_start: 0.8392 (t70) cc_final: 0.7922 (t0) REVERT: R 49 GLU cc_start: 0.8154 (tp30) cc_final: 0.7784 (tm-30) REVERT: R 61 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: S 42 ASP cc_start: 0.8388 (t0) cc_final: 0.7960 (t0) REVERT: S 57 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8336 (mm-30) REVERT: S 61 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8163 (mm-30) REVERT: S 125 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8511 (p) REVERT: T 42 ASP cc_start: 0.8355 (t0) cc_final: 0.7884 (t0) REVERT: T 49 GLU cc_start: 0.8124 (tp30) cc_final: 0.7714 (tm-30) REVERT: T 61 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8211 (mm-30) REVERT: T 176 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7770 (pptt) REVERT: U 42 ASP cc_start: 0.8364 (t0) cc_final: 0.7889 (t0) REVERT: U 49 GLU cc_start: 0.8173 (tp30) cc_final: 0.7913 (tp30) REVERT: U 61 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8170 (mm-30) REVERT: U 125 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8548 (p) REVERT: V 42 ASP cc_start: 0.8306 (t70) cc_final: 0.7931 (t0) REVERT: V 49 GLU cc_start: 0.8196 (tp30) cc_final: 0.7821 (tm-30) REVERT: V 61 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8089 (mm-30) REVERT: V 148 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8784 (mpp) REVERT: W 15 ASP cc_start: 0.8442 (p0) cc_final: 0.8034 (p0) REVERT: W 22 SER cc_start: 0.9211 (m) cc_final: 0.9007 (p) REVERT: W 42 ASP cc_start: 0.8337 (t70) cc_final: 0.7890 (t0) REVERT: W 49 GLU cc_start: 0.8155 (tp30) cc_final: 0.7746 (tm-30) REVERT: W 125 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8376 (p) REVERT: X 42 ASP cc_start: 0.8351 (t0) cc_final: 0.7907 (t0) REVERT: X 49 GLU cc_start: 0.8196 (tp30) cc_final: 0.7776 (tm-30) REVERT: X 61 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7984 (mm-30) REVERT: X 124 ARG cc_start: 0.8650 (mmt-90) cc_final: 0.8355 (mmt-90) REVERT: X 125 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8390 (p) outliers start: 42 outliers final: 7 residues processed: 691 average time/residue: 1.6895 time to fit residues: 1365.2229 Evaluate side-chains 700 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 670 time to evaluate : 3.802 ------------------------------------------------------------------------------- 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 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 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 125 THR 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 98 ASP 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 176 LYS Chi-restraints excluded: chain U residue 98 ASP 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 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 378 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 399 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 306 optimal weight: 0.0370 chunk 236 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN E 29 GLN F 29 GLN G 29 GLN H 29 GLN I 29 GLN L 29 GLN M 11 ASN M 29 GLN Q 29 GLN W 29 GLN X 29 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078700 restraints weight = 54764.139| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.51 r_work: 0.3059 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33816 Z= 0.158 Angle : 0.533 8.875 45480 Z= 0.276 Chirality : 0.036 0.127 4872 Planarity : 0.004 0.047 5952 Dihedral : 4.190 77.134 4522 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.13 % Favored : 98.80 % Rotamer: Outliers : 1.09 % Allowed : 24.37 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.13), residues: 4080 helix: 3.02 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 93 HIS 0.004 0.001 HIS C 128 PHE 0.015 0.002 PHE F 39 TYR 0.028 0.002 TYR Q 66 ARG 0.011 0.001 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 2688) hydrogen bonds : angle 3.59882 ( 8064) covalent geometry : bond 0.00349 (33816) covalent geometry : angle 0.53348 (45480) ********************** 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 693 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 655 time to evaluate : 3.999 Fit side-chains REVERT: A 42 ASP cc_start: 0.8482 (t0) cc_final: 0.7616 (t0) REVERT: A 57 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8262 (mm-30) REVERT: A 61 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 71 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8733 (ttmm) REVERT: A 124 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7841 (mtp85) REVERT: A 125 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 22 SER cc_start: 0.9205 (m) cc_final: 0.8911 (p) REVERT: B 42 ASP cc_start: 0.8373 (t70) cc_final: 0.7914 (t0) REVERT: B 49 GLU cc_start: 0.8209 (tp30) cc_final: 0.7847 (tm-30) REVERT: B 61 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8057 (mm-30) REVERT: C 22 SER cc_start: 0.9192 (m) cc_final: 0.8942 (p) REVERT: C 42 ASP cc_start: 0.8353 (t0) cc_final: 0.7650 (t0) REVERT: C 49 GLU cc_start: 0.8213 (tp30) cc_final: 0.7793 (tm-30) REVERT: C 61 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8129 (mm-30) REVERT: C 84 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7218 (t0) REVERT: C 148 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9059 (mtp) REVERT: D 42 ASP cc_start: 0.8381 (t70) cc_final: 0.7539 (t0) REVERT: D 49 GLU cc_start: 0.8673 (tt0) cc_final: 0.8332 (tp30) REVERT: D 61 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8093 (mm-30) REVERT: D 71 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8783 (ttmm) REVERT: D 125 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8254 (p) REVERT: E 22 SER cc_start: 0.9192 (m) cc_final: 0.8958 (p) REVERT: E 42 ASP cc_start: 0.8353 (t0) cc_final: 0.7851 (t0) REVERT: F 42 ASP cc_start: 0.8471 (t0) cc_final: 0.7691 (t0) REVERT: F 49 GLU cc_start: 0.8208 (tp30) cc_final: 0.7930 (tp30) REVERT: F 61 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8145 (mm-30) REVERT: F 125 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8429 (p) REVERT: G 42 ASP cc_start: 0.8329 (t70) cc_final: 0.7934 (t0) REVERT: G 49 GLU cc_start: 0.8187 (tp30) cc_final: 0.7832 (tm-30) REVERT: G 60 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: G 61 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8297 (mm-30) REVERT: G 125 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8529 (p) REVERT: G 139 ASP cc_start: 0.8511 (t70) cc_final: 0.8211 (p0) REVERT: H 15 ASP cc_start: 0.8849 (p0) cc_final: 0.8613 (p0) REVERT: H 42 ASP cc_start: 0.8434 (t0) cc_final: 0.7627 (t0) REVERT: H 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7908 (tp30) REVERT: H 61 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8087 (mm-30) REVERT: H 104 MET cc_start: 0.9067 (tpp) cc_final: 0.8823 (ttp) REVERT: H 148 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8726 (mpp) REVERT: I 42 ASP cc_start: 0.8436 (t0) cc_final: 0.7590 (t0) REVERT: I 49 GLU cc_start: 0.8170 (tp30) cc_final: 0.7912 (tp30) REVERT: I 61 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8089 (mm-30) REVERT: I 125 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8548 (p) REVERT: J 49 GLU cc_start: 0.8206 (tp30) cc_final: 0.7872 (tm-30) REVERT: J 61 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: J 176 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7725 (pttm) REVERT: K 42 ASP cc_start: 0.8400 (t0) cc_final: 0.7581 (t0) REVERT: K 49 GLU cc_start: 0.8244 (tp30) cc_final: 0.7939 (tp30) REVERT: K 61 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8063 (mm-30) REVERT: K 125 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8535 (p) REVERT: L 42 ASP cc_start: 0.8358 (t0) cc_final: 0.7605 (t0) REVERT: L 49 GLU cc_start: 0.8163 (tp30) cc_final: 0.7757 (tm-30) REVERT: L 71 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8804 (ttmm) REVERT: M 42 ASP cc_start: 0.8375 (t0) cc_final: 0.7944 (t0) REVERT: M 49 GLU cc_start: 0.8250 (tp30) cc_final: 0.7912 (tm-30) REVERT: M 61 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8144 (mm-30) REVERT: N 49 GLU cc_start: 0.8217 (tp30) cc_final: 0.7839 (tm-30) REVERT: N 61 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8054 (mm-30) REVERT: N 124 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8177 (ptp-110) REVERT: N 125 THR cc_start: 0.8907 (m) cc_final: 0.8452 (p) REVERT: O 15 ASP cc_start: 0.8806 (p0) cc_final: 0.8289 (p0) REVERT: O 42 ASP cc_start: 0.8414 (t0) cc_final: 0.7529 (t0) REVERT: O 49 GLU cc_start: 0.8258 (tp30) cc_final: 0.7908 (tm-30) REVERT: O 124 ARG cc_start: 0.8848 (mmt-90) cc_final: 0.8338 (mmt-90) REVERT: O 125 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8544 (p) REVERT: P 49 GLU cc_start: 0.8218 (tp30) cc_final: 0.7954 (tp30) REVERT: P 61 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8160 (mm-30) REVERT: P 125 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8475 (p) REVERT: Q 42 ASP cc_start: 0.8402 (t70) cc_final: 0.7563 (t0) REVERT: Q 49 GLU cc_start: 0.8245 (tp30) cc_final: 0.7883 (tm-30) REVERT: Q 61 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8183 (mm-30) REVERT: R 42 ASP cc_start: 0.8428 (t70) cc_final: 0.7498 (t0) REVERT: R 49 GLU cc_start: 0.8192 (tp30) cc_final: 0.7815 (tm-30) REVERT: R 61 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: S 42 ASP cc_start: 0.8431 (t0) cc_final: 0.7621 (t0) REVERT: S 57 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8359 (mm-30) REVERT: S 61 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8177 (mm-30) REVERT: T 42 ASP cc_start: 0.8404 (t0) cc_final: 0.7569 (t0) REVERT: T 49 GLU cc_start: 0.8179 (tp30) cc_final: 0.7875 (tp30) REVERT: T 61 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8257 (mm-30) REVERT: T 176 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7707 (pptt) REVERT: U 42 ASP cc_start: 0.8418 (t0) cc_final: 0.7563 (t0) REVERT: U 49 GLU cc_start: 0.8216 (tp30) cc_final: 0.7923 (tp30) REVERT: U 61 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8153 (mm-30) REVERT: U 125 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8567 (p) REVERT: V 42 ASP cc_start: 0.8331 (t70) cc_final: 0.7953 (t0) REVERT: V 49 GLU cc_start: 0.8220 (tp30) cc_final: 0.7876 (tm-30) REVERT: V 61 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8147 (mm-30) REVERT: W 22 SER cc_start: 0.9209 (m) cc_final: 0.8979 (p) REVERT: W 42 ASP cc_start: 0.8404 (t70) cc_final: 0.7527 (t0) REVERT: W 49 GLU cc_start: 0.8230 (tp30) cc_final: 0.7971 (tp30) REVERT: W 125 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8540 (p) REVERT: X 42 ASP cc_start: 0.8346 (t0) cc_final: 0.7906 (t0) REVERT: X 49 GLU cc_start: 0.8209 (tp30) cc_final: 0.7796 (tm-30) REVERT: X 61 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7988 (mm-30) REVERT: X 124 ARG cc_start: 0.8770 (mmt-90) cc_final: 0.8441 (mmt-90) REVERT: X 125 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8431 (p) outliers start: 38 outliers final: 11 residues processed: 669 average time/residue: 1.5475 time to fit residues: 1219.2740 Evaluate side-chains 675 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 644 time to evaluate : 3.773 ------------------------------------------------------------------------------- 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 84 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 125 THR 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 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 125 THR 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 98 ASP 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 176 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain W 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 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 345 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 288 optimal weight: 0.5980 chunk 383 optimal weight: 0.7980 chunk 294 optimal weight: 0.7980 chunk 349 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN E 29 GLN F 29 GLN G 29 GLN H 29 GLN I 53 HIS L 29 GLN M 11 ASN Q 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 = 0.3508 r_free = 0.3508 target = 0.092838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080374 restraints weight = 54832.547| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.51 r_work: 0.3099 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33816 Z= 0.123 Angle : 0.519 9.066 45480 Z= 0.269 Chirality : 0.035 0.141 4872 Planarity : 0.003 0.045 5952 Dihedral : 4.129 76.631 4522 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.30 % Favored : 98.68 % Rotamer: Outliers : 1.06 % Allowed : 24.34 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.13), residues: 4080 helix: 3.09 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.72 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 93 HIS 0.005 0.001 HIS L 128 PHE 0.011 0.002 PHE F 39 TYR 0.026 0.002 TYR Q 66 ARG 0.011 0.001 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 2688) hydrogen bonds : angle 3.53567 ( 8064) covalent geometry : bond 0.00271 (33816) covalent geometry : angle 0.51881 (45480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38243.53 seconds wall clock time: 664 minutes 4.49 seconds (39844.49 seconds total)