Starting phenix.real_space_refine on Tue Aug 26 01:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpj_44779/08_2025/9bpj_44779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpj_44779/08_2025/9bpj_44779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bpj_44779/08_2025/9bpj_44779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpj_44779/08_2025/9bpj_44779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bpj_44779/08_2025/9bpj_44779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpj_44779/08_2025/9bpj_44779.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 242 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33192 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "D" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "J" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "N" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "P" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "R" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "T" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "V" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "X" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Time building chain proxies: 7.77, per 1000 atoms: 0.23 Number of scatterers: 33192 At special positions: 0 Unit cell: (135.96, 135.96, 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.508A pdb=" N ASP A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) 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 removed outlier: 3.677A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 removed outlier: 3.635A pdb=" N ASP B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) 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 removed outlier: 3.692A pdb=" N ASP C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) 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 159 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 42 removed outlier: 3.539A pdb=" N ASP D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'E' and resid 13 through 42 removed outlier: 3.557A pdb=" N ASP E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 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 42 removed outlier: 3.553A pdb=" N ASP F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) 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 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 removed outlier: 3.629A pdb=" N ASP G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) 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 163 through 174 Processing helix chain 'H' and resid 13 through 42 removed outlier: 3.614A pdb=" N ASP H 42 " --> pdb=" O GLY H 38 " (cutoff:3.500A) 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 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 41 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 163 through 175 Processing helix chain 'J' and resid 13 through 43 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 125 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 158 Processing helix chain 'J' and resid 163 through 174 removed outlier: 3.551A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 39 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 163 through 174 Processing helix chain 'L' and resid 13 through 43 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 163 through 174 removed outlier: 3.695A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 removed outlier: 3.584A pdb=" N ASP M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) 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 159 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'N' and resid 13 through 42 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 removed outlier: 3.510A pdb=" N ASP O 42 " --> pdb=" O GLY O 38 " (cutoff:3.500A) 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 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.629A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) 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 125 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 174 Processing helix chain 'Q' and resid 13 through 42 removed outlier: 3.639A pdb=" N ASP Q 42 " --> pdb=" O GLY Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 125 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 removed outlier: 3.532A pdb=" N ASP R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 removed outlier: 3.542A pdb=" N ASP S 42 " --> pdb=" O GLY S 38 " (cutoff:3.500A) 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 41 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 158 Processing helix chain 'T' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 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 159 Processing helix chain 'U' and resid 163 through 175 Processing helix chain 'V' and resid 13 through 39 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 162 through 174 Processing helix chain 'W' and resid 13 through 41 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 138 through 158 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.688A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 removed outlier: 3.593A pdb=" N ASP X 42 " --> pdb=" O GLY X 38 " (cutoff:3.500A) 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 2656 hydrogen bonds defined for protein. 7968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 3.95 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: 9327 1.33 - 1.45: 5638 1.45 - 1.57: 18635 1.57 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 33816 Sorted by residual: bond pdb=" CZ ARG J 157 " pdb=" NH2 ARG J 157 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" CZ ARG E 172 " pdb=" NH2 ARG E 172 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" CZ ARG C 172 " pdb=" NH2 ARG C 172 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.99e+00 bond pdb=" CZ ARG B 157 " pdb=" NH2 ARG B 157 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.73e+00 bond pdb=" CZ ARG H 76 " pdb=" NH2 ARG H 76 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.73e+00 ... (remaining 33811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 34867 2.05 - 4.09: 9502 4.09 - 6.14: 1026 6.14 - 8.19: 81 8.19 - 10.23: 4 Bond angle restraints: 45480 Sorted by residual: angle pdb=" CD ARG S 63 " pdb=" NE ARG S 63 " pdb=" CZ ARG S 63 " ideal model delta sigma weight residual 124.40 134.63 -10.23 1.40e+00 5.10e-01 5.34e+01 angle pdb=" CA ASP S 131 " pdb=" CB ASP S 131 " pdb=" CG ASP S 131 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.00e+00 1.00e+00 3.47e+01 angle pdb=" CA ASP X 15 " pdb=" CB ASP X 15 " pdb=" CG ASP X 15 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CB HIS I 53 " pdb=" CG HIS I 53 " pdb=" CD2 HIS I 53 " ideal model delta sigma weight residual 131.20 124.41 6.79 1.30e+00 5.92e-01 2.73e+01 angle pdb=" CB HIS V 53 " pdb=" CG HIS V 53 " pdb=" CD2 HIS V 53 " ideal model delta sigma weight residual 131.20 124.47 6.73 1.30e+00 5.92e-01 2.68e+01 ... (remaining 45475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 18472 17.99 - 35.97: 1464 35.97 - 53.96: 326 53.96 - 71.94: 122 71.94 - 89.93: 40 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 -138.14 15.54 0 2.50e+00 1.60e-01 3.86e+01 dihedral pdb=" CA SER L 5 " pdb=" C SER L 5 " pdb=" N SER L 6 " pdb=" CA SER L 6 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE B 82 " pdb=" C PHE B 82 " pdb=" N GLN B 83 " pdb=" CA GLN B 83 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 20421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3762 0.115 - 0.231: 1006 0.231 - 0.346: 88 0.346 - 0.461: 14 0.461 - 0.577: 2 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 1.93 0.58 2.00e-01 2.50e+01 8.31e+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 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA HIS S 136 " pdb=" N HIS S 136 " pdb=" C HIS S 136 " pdb=" CB HIS S 136 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 4869 not shown) Planarity restraints: 5952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 34 " -0.161 2.00e-02 2.50e+03 8.84e-02 1.56e+02 pdb=" CG TYR R 34 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR R 34 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TYR R 34 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR R 34 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR R 34 " 0.049 2.00e-02 2.50e+03 pdb=" CZ TYR R 34 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR R 34 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 34 " -0.152 2.00e-02 2.50e+03 8.80e-02 1.55e+02 pdb=" CG TYR S 34 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR S 34 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR S 34 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR S 34 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR S 34 " 0.062 2.00e-02 2.50e+03 pdb=" CZ TYR S 34 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR S 34 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 66 " -0.147 2.00e-02 2.50e+03 8.08e-02 1.31e+02 pdb=" CG TYR L 66 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR L 66 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR L 66 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR L 66 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR L 66 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR L 66 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR L 66 " -0.125 2.00e-02 2.50e+03 ... (remaining 5949 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 14720 2.96 - 3.44: 38103 3.44 - 3.93: 64052 3.93 - 4.41: 71915 4.41 - 4.90: 119203 Nonbonded interactions: 307993 Sorted by model distance: nonbonded pdb=" OH TYR O 27 " pdb=" OE2 GLU O 141 " model vdw 2.472 3.040 nonbonded pdb=" OH TYR L 27 " pdb=" OE2 GLU L 141 " model vdw 2.513 3.040 nonbonded pdb=" OH TYR U 27 " pdb=" OE2 GLU U 141 " model vdw 2.520 3.040 nonbonded pdb=" OH TYR M 27 " pdb=" OE2 GLU M 141 " model vdw 2.521 3.040 nonbonded pdb=" OH TYR N 27 " pdb=" OE2 GLU N 141 " model vdw 2.528 3.040 ... (remaining 307988 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.220 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.170 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:7.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 0.042 33816 Z= 0.699 Angle : 1.775 10.232 45480 Z= 1.202 Chirality : 0.097 0.577 4872 Planarity : 0.018 0.216 5952 Dihedral : 15.272 89.930 12744 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.69 % Allowed : 3.14 % Favored : 96.18 % Rotamer: Outliers : 2.84 % Allowed : 4.71 % Favored : 92.44 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 4080 helix: 0.41 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -2.29 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG R 63 TYR 0.161 0.027 TYR R 34 PHE 0.113 0.020 PHE X 41 TRP 0.052 0.012 TRP B 93 HIS 0.018 0.004 HIS Q 53 Details of bonding type rmsd covalent geometry : bond 0.01117 (33816) covalent geometry : angle 1.77475 (45480) hydrogen bonds : bond 0.10175 ( 2656) hydrogen bonds : angle 5.94390 ( 7968) *********************** 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 702 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 603 time to evaluate : 1.475 Fit side-chains REVERT: G 72 MET cc_start: 0.7236 (tmm) cc_final: 0.7017 (tmt) REVERT: I 162 GLU cc_start: 0.4599 (OUTLIER) cc_final: 0.4301 (pm20) REVERT: M 72 MET cc_start: 0.7030 (tmm) cc_final: 0.6387 (tmt) REVERT: S 72 MET cc_start: 0.7122 (tmm) cc_final: 0.6880 (tmt) REVERT: T 136 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7139 (p-80) REVERT: T 176 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6906 (ptmm) REVERT: X 162 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.3798 (pm20) outliers start: 99 outliers final: 9 residues processed: 689 average time/residue: 0.9068 time to fit residues: 721.6688 Evaluate side-chains 369 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 356 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 176 LYS Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 136 HIS C 136 HIS D 7 GLN D 75 GLN D 83 GLN E 11 ASN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 136 HIS F 29 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN H 11 ASN H 75 GLN I 136 HIS J 75 GLN J 136 HIS J 156 HIS L 29 GLN L 75 GLN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS M 11 ASN N 75 GLN P 29 GLN Q 29 GLN Q 75 GLN R 75 GLN R 136 HIS S 29 GLN S 74 ASN S 136 HIS U 11 ASN U 136 HIS W 53 HIS W 83 GLN X 136 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065623 restraints weight = 81795.857| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.22 r_work: 0.3104 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2301 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= 0.142 Angle : 0.592 8.065 45480 Z= 0.317 Chirality : 0.038 0.182 4872 Planarity : 0.004 0.045 5952 Dihedral : 5.168 49.660 4544 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.18 % Favored : 97.50 % Rotamer: Outliers : 2.21 % Allowed : 12.16 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.13), residues: 4080 helix: 2.30 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -2.26 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 68 TYR 0.033 0.002 TYR N 66 PHE 0.018 0.002 PHE H 132 TRP 0.007 0.001 TRP J 93 HIS 0.008 0.001 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00309 (33816) covalent geometry : angle 0.59194 (45480) hydrogen bonds : bond 0.04108 ( 2656) hydrogen bonds : angle 3.86286 ( 7968) *********************** 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 509 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 432 time to evaluate : 1.432 Fit side-chains REVERT: A 56 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6481 (tmt170) REVERT: A 124 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.8482 (mmt-90) REVERT: B 83 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7777 (mm-40) REVERT: C 124 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8645 (mmt-90) REVERT: C 136 HIS cc_start: 0.9012 (OUTLIER) cc_final: 0.8758 (p90) REVERT: C 148 MET cc_start: 0.8686 (mtp) cc_final: 0.8453 (ttp) REVERT: D 68 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7509 (mtm-85) REVERT: E 11 ASN cc_start: 0.8207 (m-40) cc_final: 0.7770 (t0) REVERT: E 27 TYR cc_start: 0.9032 (m-80) cc_final: 0.8728 (m-80) REVERT: E 83 GLN cc_start: 0.8535 (mm110) cc_final: 0.8298 (mm-40) REVERT: E 125 THR cc_start: 0.8859 (m) cc_final: 0.8099 (p) REVERT: E 136 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8617 (p90) REVERT: F 34 TYR cc_start: 0.8835 (m-10) cc_final: 0.8448 (m-10) REVERT: F 107 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: F 124 ARG cc_start: 0.8772 (mmt-90) cc_final: 0.8521 (mmt-90) REVERT: F 156 HIS cc_start: 0.8889 (t-90) cc_final: 0.8452 (t-90) REVERT: G 104 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: H 63 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7352 (ttm-80) REVERT: H 135 THR cc_start: 0.9107 (m) cc_final: 0.8873 (p) REVERT: H 148 MET cc_start: 0.8639 (tpp) cc_final: 0.8394 (mmm) REVERT: I 63 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7399 (ttm-80) REVERT: I 124 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8663 (mmt-90) REVERT: I 136 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8516 (p90) REVERT: K 34 TYR cc_start: 0.8824 (m-80) cc_final: 0.8476 (m-10) REVERT: K 124 ARG cc_start: 0.8880 (mmt-90) cc_final: 0.8626 (mmt-90) REVERT: M 68 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7324 (ttp-170) REVERT: N 27 TYR cc_start: 0.8767 (m-80) cc_final: 0.8525 (m-80) REVERT: N 112 GLN cc_start: 0.8220 (tp40) cc_final: 0.7957 (tp40) REVERT: N 124 ARG cc_start: 0.8782 (mmt-90) cc_final: 0.8511 (mmt-90) REVERT: N 135 THR cc_start: 0.8765 (m) cc_final: 0.8515 (p) REVERT: O 72 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8413 (tmm) REVERT: O 148 MET cc_start: 0.8598 (mmm) cc_final: 0.8240 (mtm) REVERT: P 72 MET cc_start: 0.8847 (tmm) cc_final: 0.8587 (tmt) REVERT: P 135 THR cc_start: 0.9011 (m) cc_final: 0.8790 (t) REVERT: Q 83 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8469 (mm-40) REVERT: Q 124 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8443 (tpp80) REVERT: R 7 GLN cc_start: 0.7574 (mt0) cc_final: 0.7139 (pt0) REVERT: R 63 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6949 (ttp80) REVERT: R 83 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8419 (mp10) REVERT: S 136 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8316 (p90) REVERT: T 112 GLN cc_start: 0.8382 (tp40) cc_final: 0.8158 (mm-40) REVERT: T 136 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8328 (p-80) REVERT: U 57 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7784 (mm-30) REVERT: U 135 THR cc_start: 0.8976 (m) cc_final: 0.8741 (p) REVERT: U 171 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: V 12 TYR cc_start: 0.8643 (t80) cc_final: 0.8256 (t80) REVERT: V 68 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7940 (ttp-170) REVERT: V 112 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7620 (tp40) REVERT: W 112 GLN cc_start: 0.8190 (tp40) cc_final: 0.7834 (tp-100) REVERT: W 124 ARG cc_start: 0.9065 (mmt-90) cc_final: 0.8856 (mmt-90) REVERT: X 112 GLN cc_start: 0.8044 (tp40) cc_final: 0.7767 (tp40) REVERT: X 125 THR cc_start: 0.9176 (t) cc_final: 0.8937 (p) REVERT: X 145 ILE cc_start: 0.8444 (mp) cc_final: 0.8223 (mp) REVERT: X 162 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6122 (pm20) REVERT: X 171 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7449 (tm-30) REVERT: X 174 THR cc_start: 0.8963 (m) cc_final: 0.8736 (p) outliers start: 77 outliers final: 23 residues processed: 488 average time/residue: 0.8158 time to fit residues: 467.6530 Evaluate side-chains 382 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 346 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 136 HIS Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain X residue 49 GLU Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 382 optimal weight: 0.2980 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 377 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 11 ASN B 136 HIS C 136 HIS ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS G 75 GLN H 83 GLN I 136 HIS J 75 GLN J 136 HIS L 136 HIS Q 75 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN S 136 HIS U 29 GLN X 136 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065261 restraints weight = 82259.713| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.23 r_work: 0.3092 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33816 Z= 0.147 Angle : 0.538 8.166 45480 Z= 0.285 Chirality : 0.037 0.160 4872 Planarity : 0.003 0.039 5952 Dihedral : 4.585 53.837 4521 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.96 % Favored : 97.77 % Rotamer: Outliers : 2.18 % Allowed : 14.77 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.13), residues: 4080 helix: 2.71 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 56 TYR 0.029 0.002 TYR P 66 PHE 0.025 0.002 PHE C 137 TRP 0.003 0.001 TRP P 93 HIS 0.008 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00323 (33816) covalent geometry : angle 0.53772 (45480) hydrogen bonds : bond 0.03669 ( 2656) hydrogen bonds : angle 3.66651 ( 7968) *********************** 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 460 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 384 time to evaluate : 1.245 Fit side-chains REVERT: A 56 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6479 (tmt170) REVERT: A 148 MET cc_start: 0.8297 (mmm) cc_final: 0.7996 (mtt) REVERT: B 83 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7749 (mm-40) REVERT: B 136 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.7889 (p-80) REVERT: C 72 MET cc_start: 0.8568 (tmm) cc_final: 0.8323 (tmt) REVERT: C 124 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8756 (mmt-90) REVERT: C 148 MET cc_start: 0.8623 (mtp) cc_final: 0.8405 (ttp) REVERT: C 172 ARG cc_start: 0.8396 (mmp-170) cc_final: 0.8156 (mmm160) REVERT: D 15 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8043 (p0) REVERT: D 64 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7915 (mm-30) REVERT: D 68 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7586 (mtm-85) REVERT: E 11 ASN cc_start: 0.8193 (m-40) cc_final: 0.7718 (t160) REVERT: E 27 TYR cc_start: 0.9015 (m-80) cc_final: 0.8747 (m-80) REVERT: E 83 GLN cc_start: 0.8708 (mm110) cc_final: 0.8426 (mm-40) REVERT: E 136 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (p90) REVERT: F 34 TYR cc_start: 0.8895 (m-10) cc_final: 0.8519 (m-10) REVERT: F 107 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: F 156 HIS cc_start: 0.8856 (t-90) cc_final: 0.8446 (t-90) REVERT: H 135 THR cc_start: 0.9091 (m) cc_final: 0.8827 (p) REVERT: H 148 MET cc_start: 0.8671 (tpp) cc_final: 0.8427 (mmm) REVERT: H 156 HIS cc_start: 0.8768 (t70) cc_final: 0.8369 (t-90) REVERT: I 63 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7424 (ttm-80) REVERT: I 124 ARG cc_start: 0.8910 (mmt-90) cc_final: 0.8704 (mmt-90) REVERT: J 136 HIS cc_start: 0.9050 (OUTLIER) cc_final: 0.8837 (p90) REVERT: K 34 TYR cc_start: 0.8854 (m-80) cc_final: 0.8532 (m-10) REVERT: K 124 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8670 (mmt-90) REVERT: L 27 TYR cc_start: 0.9033 (m-80) cc_final: 0.8794 (m-80) REVERT: L 136 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.8486 (p90) REVERT: M 68 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7364 (ttp-170) REVERT: N 27 TYR cc_start: 0.8787 (m-80) cc_final: 0.8538 (m-80) REVERT: N 135 THR cc_start: 0.8720 (m) cc_final: 0.8496 (p) REVERT: O 72 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8348 (tmm) REVERT: P 72 MET cc_start: 0.8831 (tmm) cc_final: 0.8526 (tmt) REVERT: P 124 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8327 (mtp85) REVERT: P 135 THR cc_start: 0.8994 (m) cc_final: 0.8794 (t) REVERT: Q 83 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8447 (mm-40) REVERT: Q 124 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8261 (tpp80) REVERT: R 7 GLN cc_start: 0.7734 (mt0) cc_final: 0.7351 (pt0) REVERT: R 83 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8389 (mp10) REVERT: S 11 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.7780 (t0) REVERT: T 112 GLN cc_start: 0.8344 (tp40) cc_final: 0.8060 (mm-40) REVERT: T 136 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7375 (p-80) REVERT: U 112 GLN cc_start: 0.8159 (tp40) cc_final: 0.7930 (tp40) REVERT: U 135 THR cc_start: 0.9031 (m) cc_final: 0.8792 (p) REVERT: U 171 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8625 (tm-30) REVERT: V 12 TYR cc_start: 0.8693 (t80) cc_final: 0.8147 (t80) REVERT: V 68 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7914 (ttp-170) REVERT: V 112 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7638 (tp40) REVERT: W 112 GLN cc_start: 0.8158 (tp40) cc_final: 0.7880 (tp40) REVERT: X 112 GLN cc_start: 0.8017 (tp40) cc_final: 0.7746 (tp40) REVERT: X 145 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8189 (mp) REVERT: X 162 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: X 171 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7537 (tm-30) outliers start: 76 outliers final: 24 residues processed: 433 average time/residue: 0.7946 time to fit residues: 404.7064 Evaluate side-chains 383 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 136 HIS Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 124 ARG Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 145 ILE Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 190 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS C 136 HIS D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS G 75 GLN H 11 ASN J 75 GLN J 83 GLN J 136 HIS L 136 HIS M 29 GLN P 83 GLN Q 75 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN U 83 GLN X 136 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.074701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065490 restraints weight = 81625.811| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.22 r_work: 0.3089 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2872 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= 0.137 Angle : 0.516 7.679 45480 Z= 0.273 Chirality : 0.036 0.146 4872 Planarity : 0.003 0.038 5952 Dihedral : 4.409 58.777 4521 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.11 % Favored : 97.72 % Rotamer: Outliers : 2.41 % Allowed : 16.12 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.13), residues: 4080 helix: 2.95 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.88 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 56 TYR 0.028 0.002 TYR P 66 PHE 0.017 0.002 PHE S 132 TRP 0.003 0.001 TRP H 93 HIS 0.013 0.001 HIS L 136 Details of bonding type rmsd covalent geometry : bond 0.00299 (33816) covalent geometry : angle 0.51590 (45480) hydrogen bonds : bond 0.03457 ( 2656) hydrogen bonds : angle 3.56433 ( 7968) *********************** 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 475 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 391 time to evaluate : 1.439 Fit side-chains REVERT: A 56 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6437 (tmt170) REVERT: A 148 MET cc_start: 0.8345 (mmm) cc_final: 0.8052 (mtt) REVERT: B 90 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8403 (mp0) REVERT: B 135 THR cc_start: 0.8876 (t) cc_final: 0.8668 (p) REVERT: D 64 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7877 (mm-30) REVERT: E 11 ASN cc_start: 0.8241 (m-40) cc_final: 0.7793 (t160) REVERT: E 27 TYR cc_start: 0.8974 (m-80) cc_final: 0.8711 (m-80) REVERT: E 56 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.8014 (mmm-85) REVERT: E 68 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7778 (ttp-170) REVERT: E 83 GLN cc_start: 0.8773 (mm110) cc_final: 0.8462 (mm-40) REVERT: E 136 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8317 (p90) REVERT: F 34 TYR cc_start: 0.8867 (m-10) cc_final: 0.8534 (m-10) REVERT: F 107 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: F 112 GLN cc_start: 0.7953 (tp40) cc_final: 0.7599 (tp40) REVERT: F 156 HIS cc_start: 0.8809 (t-90) cc_final: 0.8374 (t-170) REVERT: F 171 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 13 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7716 (p) REVERT: H 83 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8256 (mp10) REVERT: H 112 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: H 144 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8468 (tp) REVERT: H 156 HIS cc_start: 0.8755 (t70) cc_final: 0.8361 (t-90) REVERT: I 63 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7444 (ttm-80) REVERT: J 7 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: J 136 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8596 (p90) REVERT: K 34 TYR cc_start: 0.8875 (m-80) cc_final: 0.8486 (m-10) REVERT: L 27 TYR cc_start: 0.9031 (m-80) cc_final: 0.8801 (m-80) REVERT: M 63 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7288 (ttm-80) REVERT: M 68 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7589 (ttp-170) REVERT: N 27 TYR cc_start: 0.8790 (m-80) cc_final: 0.8582 (m-80) REVERT: N 124 ARG cc_start: 0.8717 (mmt-90) cc_final: 0.8475 (mmt-90) REVERT: N 135 THR cc_start: 0.8680 (m) cc_final: 0.8477 (p) REVERT: O 72 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8336 (tmm) REVERT: O 124 ARG cc_start: 0.8242 (mmt-90) cc_final: 0.8017 (mmt-90) REVERT: O 148 MET cc_start: 0.8536 (mtp) cc_final: 0.8275 (mtm) REVERT: P 16 VAL cc_start: 0.8380 (t) cc_final: 0.8149 (t) REVERT: Q 83 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8486 (mm-40) REVERT: Q 124 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8459 (tpp80) REVERT: R 7 GLN cc_start: 0.7735 (mt0) cc_final: 0.7353 (pt0) REVERT: R 60 GLU cc_start: 0.8324 (tp30) cc_final: 0.7854 (tm-30) REVERT: R 63 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7041 (ttm110) REVERT: R 83 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8440 (mp10) REVERT: S 11 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.7865 (t0) REVERT: T 11 ASN cc_start: 0.8491 (m-40) cc_final: 0.7831 (t0) REVERT: T 112 GLN cc_start: 0.8324 (tp40) cc_final: 0.8051 (mm-40) REVERT: T 136 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7551 (p-80) REVERT: U 112 GLN cc_start: 0.8181 (tp40) cc_final: 0.7940 (tp40) REVERT: U 135 THR cc_start: 0.9031 (m) cc_final: 0.8795 (p) REVERT: U 171 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: V 12 TYR cc_start: 0.8686 (t80) cc_final: 0.8145 (t80) REVERT: V 68 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7962 (ttp-170) REVERT: V 112 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7619 (tp40) REVERT: W 112 GLN cc_start: 0.8245 (tp40) cc_final: 0.7947 (tp40) REVERT: W 156 HIS cc_start: 0.8645 (t70) cc_final: 0.8379 (t70) REVERT: X 64 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8128 (mm-30) REVERT: X 112 GLN cc_start: 0.7994 (tp40) cc_final: 0.7723 (tp40) REVERT: X 136 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8615 (p90) REVERT: X 145 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8166 (mp) REVERT: X 162 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.6063 (pm20) REVERT: X 171 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7398 (tm-30) REVERT: X 174 THR cc_start: 0.8985 (m) cc_final: 0.8742 (p) outliers start: 84 outliers final: 32 residues processed: 446 average time/residue: 0.7890 time to fit residues: 414.8376 Evaluate side-chains 402 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 136 HIS Chi-restraints excluded: chain X residue 145 ILE Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 346 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 192 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS C 136 HIS D 74 ASN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS J 75 GLN J 136 HIS L 136 HIS M 7 GLN M 25 ASN M 29 GLN M 83 GLN P 136 HIS Q 75 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN T 156 HIS U 29 GLN X 136 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.075421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.066187 restraints weight = 81556.707| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.22 r_work: 0.3112 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33816 Z= 0.121 Angle : 0.506 8.248 45480 Z= 0.268 Chirality : 0.035 0.227 4872 Planarity : 0.003 0.046 5952 Dihedral : 4.288 54.674 4521 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 2.27 % Allowed : 17.82 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.13), residues: 4080 helix: 3.17 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -2.03 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 124 TYR 0.030 0.002 TYR P 66 PHE 0.019 0.002 PHE L 132 TRP 0.004 0.001 TRP X 93 HIS 0.014 0.001 HIS J 136 Details of bonding type rmsd covalent geometry : bond 0.00261 (33816) covalent geometry : angle 0.50620 (45480) hydrogen bonds : bond 0.03306 ( 2656) hydrogen bonds : angle 3.50856 ( 7968) *********************** 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 475 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 1.299 Fit side-chains REVERT: A 56 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6424 (tmt170) REVERT: A 148 MET cc_start: 0.8377 (mmm) cc_final: 0.8104 (mtt) REVERT: B 83 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7881 (mm-40) REVERT: C 34 TYR cc_start: 0.8892 (m-10) cc_final: 0.8669 (m-10) REVERT: C 72 MET cc_start: 0.8587 (tmm) cc_final: 0.8344 (tmt) REVERT: D 64 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7861 (mm-30) REVERT: D 68 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7691 (mtm-85) REVERT: E 11 ASN cc_start: 0.8165 (m-40) cc_final: 0.7735 (t160) REVERT: E 62 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7963 (mptt) REVERT: E 83 GLN cc_start: 0.8774 (mm110) cc_final: 0.8461 (mm-40) REVERT: E 136 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8264 (p90) REVERT: F 16 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (p) REVERT: F 112 GLN cc_start: 0.7974 (tp40) cc_final: 0.7650 (tp40) REVERT: F 124 ARG cc_start: 0.8671 (mmt-90) cc_final: 0.8434 (mmt-90) REVERT: F 156 HIS cc_start: 0.8754 (t-90) cc_final: 0.8321 (t-170) REVERT: F 171 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8059 (tm-30) REVERT: G 13 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7819 (p) REVERT: H 83 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8231 (mp10) REVERT: H 112 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: H 156 HIS cc_start: 0.8732 (t70) cc_final: 0.8350 (t-90) REVERT: I 63 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7458 (ttm-80) REVERT: J 7 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: K 34 TYR cc_start: 0.8927 (m-80) cc_final: 0.8525 (m-10) REVERT: K 104 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7457 (ttm) REVERT: K 162 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: L 27 TYR cc_start: 0.9058 (m-80) cc_final: 0.8834 (m-80) REVERT: L 104 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7742 (tpp) REVERT: M 63 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7264 (ttm-80) REVERT: M 68 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7740 (ttp-170) REVERT: N 27 TYR cc_start: 0.8814 (m-80) cc_final: 0.8586 (m-80) REVERT: N 124 ARG cc_start: 0.8742 (mmt-90) cc_final: 0.8532 (mmt-90) REVERT: O 72 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8340 (tmm) REVERT: O 104 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: Q 83 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8478 (mm-40) REVERT: R 7 GLN cc_start: 0.7708 (mt0) cc_final: 0.7380 (pt0) REVERT: R 60 GLU cc_start: 0.8322 (tp30) cc_final: 0.7936 (tm-30) REVERT: R 63 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7244 (ttp80) REVERT: R 83 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8377 (mp10) REVERT: S 11 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8003 (t0) REVERT: T 11 ASN cc_start: 0.8515 (m-40) cc_final: 0.7951 (t0) REVERT: T 104 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: T 112 GLN cc_start: 0.8320 (tp40) cc_final: 0.8046 (mm-40) REVERT: T 136 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7492 (p-80) REVERT: U 14 THR cc_start: 0.9260 (m) cc_final: 0.9022 (p) REVERT: U 57 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7821 (mm-30) REVERT: U 112 GLN cc_start: 0.8191 (tp40) cc_final: 0.7939 (tp40) REVERT: U 124 ARG cc_start: 0.8804 (mmt90) cc_final: 0.8554 (mmt-90) REVERT: U 135 THR cc_start: 0.9059 (m) cc_final: 0.8838 (p) REVERT: U 171 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: V 12 TYR cc_start: 0.8710 (t80) cc_final: 0.8167 (t80) REVERT: V 68 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7971 (ttp-170) REVERT: V 79 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6667 (mmp-170) REVERT: V 112 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7622 (tp40) REVERT: W 112 GLN cc_start: 0.8247 (tp40) cc_final: 0.7929 (tp40) REVERT: W 156 HIS cc_start: 0.8625 (t70) cc_final: 0.8209 (t70) REVERT: X 15 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8285 (p0) REVERT: X 64 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8108 (mm-30) REVERT: X 112 GLN cc_start: 0.8001 (tp40) cc_final: 0.7730 (tp40) REVERT: X 136 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.8325 (p90) REVERT: X 162 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: X 171 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7399 (tm-30) REVERT: X 174 THR cc_start: 0.8972 (m) cc_final: 0.8744 (p) outliers start: 79 outliers final: 27 residues processed: 446 average time/residue: 0.7597 time to fit residues: 398.1285 Evaluate side-chains 403 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 104 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 104 MET Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 136 HIS Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 371 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 136 HIS C 136 HIS D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN J 136 HIS J 156 HIS ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS M 29 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 83 GLN X 136 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.075518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066364 restraints weight = 81563.741| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.21 r_work: 0.3121 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33816 Z= 0.119 Angle : 0.507 10.431 45480 Z= 0.268 Chirality : 0.036 0.233 4872 Planarity : 0.003 0.042 5952 Dihedral : 4.215 51.373 4521 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 2.39 % Allowed : 18.51 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.13), residues: 4080 helix: 3.25 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.98 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 56 TYR 0.030 0.002 TYR P 66 PHE 0.018 0.002 PHE B 132 TRP 0.004 0.001 TRP B 93 HIS 0.009 0.001 HIS L 136 Details of bonding type rmsd covalent geometry : bond 0.00256 (33816) covalent geometry : angle 0.50712 (45480) hydrogen bonds : bond 0.03232 ( 2656) hydrogen bonds : angle 3.48413 ( 7968) *********************** 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 465 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 382 time to evaluate : 1.530 Fit side-chains REVERT: A 56 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6447 (tmt170) REVERT: A 148 MET cc_start: 0.8360 (mmm) cc_final: 0.8084 (mtt) REVERT: B 83 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7821 (mm-40) REVERT: B 136 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.8121 (p90) REVERT: C 124 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8485 (mmt-90) REVERT: D 64 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7832 (mm-30) REVERT: D 68 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7697 (mtm-85) REVERT: E 11 ASN cc_start: 0.8194 (m-40) cc_final: 0.7635 (t0) REVERT: E 83 GLN cc_start: 0.8801 (mm110) cc_final: 0.8405 (mm-40) REVERT: E 136 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8307 (p90) REVERT: F 16 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7918 (p) REVERT: F 112 GLN cc_start: 0.7948 (tp40) cc_final: 0.7659 (tp40) REVERT: F 124 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.8456 (mmt-90) REVERT: F 148 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8065 (ttm) REVERT: F 156 HIS cc_start: 0.8740 (t-90) cc_final: 0.8311 (t-170) REVERT: F 171 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7867 (tm-30) REVERT: G 7 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: H 83 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8286 (mt0) REVERT: H 112 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: H 156 HIS cc_start: 0.8754 (t70) cc_final: 0.8382 (t-90) REVERT: I 63 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7428 (ttm-80) REVERT: I 148 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7778 (mtm) REVERT: J 7 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: J 136 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8583 (p90) REVERT: K 34 TYR cc_start: 0.8944 (m-80) cc_final: 0.8608 (m-10) REVERT: K 104 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7506 (ttm) REVERT: L 75 GLN cc_start: 0.8685 (mt0) cc_final: 0.8438 (mt0) REVERT: M 68 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7799 (ttp-170) REVERT: M 135 THR cc_start: 0.8384 (m) cc_final: 0.8150 (p) REVERT: O 72 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8321 (tmm) REVERT: O 104 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7975 (ttm) REVERT: O 148 MET cc_start: 0.8548 (mtp) cc_final: 0.8147 (mtm) REVERT: P 7 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: P 124 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7937 (mtp85) REVERT: Q 83 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8365 (mm110) REVERT: R 7 GLN cc_start: 0.7700 (mt0) cc_final: 0.7391 (pt0) REVERT: R 11 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7882 (t0) REVERT: R 60 GLU cc_start: 0.8296 (tp30) cc_final: 0.7894 (tm-30) REVERT: R 63 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7227 (ttp80) REVERT: R 83 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8331 (mp10) REVERT: S 11 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8118 (t0) REVERT: S 61 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7977 (mm-30) REVERT: T 11 ASN cc_start: 0.8542 (m-40) cc_final: 0.7927 (t0) REVERT: T 112 GLN cc_start: 0.8283 (tp40) cc_final: 0.8006 (mm-40) REVERT: T 124 ARG cc_start: 0.8626 (ptp-110) cc_final: 0.8417 (ptp-110) REVERT: T 125 THR cc_start: 0.8950 (p) cc_final: 0.8205 (t) REVERT: T 132 PHE cc_start: 0.7820 (t80) cc_final: 0.7604 (t80) REVERT: T 136 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7172 (p-80) REVERT: U 57 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7714 (mm-30) REVERT: U 112 GLN cc_start: 0.8151 (tp40) cc_final: 0.7886 (tp40) REVERT: U 124 ARG cc_start: 0.8730 (mmt90) cc_final: 0.8493 (mmt-90) REVERT: U 135 THR cc_start: 0.9050 (m) cc_final: 0.8833 (p) REVERT: U 171 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: V 12 TYR cc_start: 0.8681 (t80) cc_final: 0.8106 (t80) REVERT: V 68 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8002 (ttp-170) REVERT: V 112 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7619 (tp40) REVERT: W 112 GLN cc_start: 0.8253 (tp40) cc_final: 0.7936 (tp40) REVERT: W 156 HIS cc_start: 0.8635 (t70) cc_final: 0.8216 (t70) REVERT: X 15 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8291 (p0) REVERT: X 64 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8100 (mm-30) REVERT: X 162 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6094 (pm20) REVERT: X 171 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7381 (tm-30) outliers start: 83 outliers final: 32 residues processed: 438 average time/residue: 0.7800 time to fit residues: 401.6172 Evaluate side-chains 401 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 63 ARG Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 275 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 364 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 74 ASN B 136 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 ASN J 75 GLN J 136 HIS L 136 HIS M 29 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 74 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065214 restraints weight = 81814.704| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.22 r_work: 0.3091 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33816 Z= 0.154 Angle : 0.524 9.379 45480 Z= 0.273 Chirality : 0.037 0.242 4872 Planarity : 0.004 0.042 5952 Dihedral : 4.232 49.794 4521 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 18.91 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.13), residues: 4080 helix: 3.21 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 63 TYR 0.030 0.002 TYR P 66 PHE 0.019 0.002 PHE E 137 TRP 0.003 0.001 TRP X 93 HIS 0.011 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00340 (33816) covalent geometry : angle 0.52449 (45480) hydrogen bonds : bond 0.03330 ( 2656) hydrogen bonds : angle 3.50182 ( 7968) *********************** 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 448 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 359 time to evaluate : 1.086 Fit side-chains REVERT: A 56 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6538 (tmt170) REVERT: A 148 MET cc_start: 0.8357 (mmm) cc_final: 0.8058 (mtt) REVERT: B 83 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7843 (mm-40) REVERT: B 136 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.7553 (p90) REVERT: C 72 MET cc_start: 0.8609 (tmm) cc_final: 0.8366 (tmt) REVERT: C 124 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8510 (mmt-90) REVERT: D 64 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7836 (mm-30) REVERT: D 68 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7670 (mtm-85) REVERT: E 11 ASN cc_start: 0.8177 (m-40) cc_final: 0.7620 (t0) REVERT: E 83 GLN cc_start: 0.8738 (mm110) cc_final: 0.8444 (mm-40) REVERT: E 136 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8128 (p90) REVERT: F 16 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7943 (p) REVERT: F 112 GLN cc_start: 0.7974 (tp40) cc_final: 0.7689 (tp40) REVERT: F 124 ARG cc_start: 0.8670 (mmt-90) cc_final: 0.8449 (mmt-90) REVERT: F 148 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7835 (ttp) REVERT: F 156 HIS cc_start: 0.8812 (t-90) cc_final: 0.8427 (t-90) REVERT: F 171 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8010 (tm-30) REVERT: G 7 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: G 15 ASP cc_start: 0.8793 (m-30) cc_final: 0.8526 (t0) REVERT: H 83 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8228 (mt0) REVERT: H 112 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: H 156 HIS cc_start: 0.8772 (t70) cc_final: 0.8391 (t-90) REVERT: I 63 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: I 148 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7752 (mtm) REVERT: J 7 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: K 34 TYR cc_start: 0.8936 (m-80) cc_final: 0.8546 (m-10) REVERT: K 104 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7474 (ttm) REVERT: L 75 GLN cc_start: 0.8701 (mt0) cc_final: 0.8481 (mt0) REVERT: M 68 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7797 (ttp-170) REVERT: M 135 THR cc_start: 0.8487 (m) cc_final: 0.8250 (p) REVERT: N 16 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8033 (p) REVERT: O 72 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: O 104 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8047 (ttp) REVERT: O 124 ARG cc_start: 0.8178 (mmt-90) cc_final: 0.7927 (mmt-90) REVERT: O 148 MET cc_start: 0.8525 (mtp) cc_final: 0.8153 (mtm) REVERT: P 7 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: Q 83 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8337 (mm110) REVERT: R 7 GLN cc_start: 0.7794 (mt0) cc_final: 0.7471 (pt0) REVERT: R 60 GLU cc_start: 0.8287 (tp30) cc_final: 0.7858 (tm-30) REVERT: R 83 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8327 (mp10) REVERT: S 11 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.7967 (t0) REVERT: S 61 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7996 (mm-30) REVERT: T 8 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8975 (pt) REVERT: T 11 ASN cc_start: 0.8538 (m-40) cc_final: 0.7974 (t0) REVERT: T 112 GLN cc_start: 0.8300 (tp40) cc_final: 0.8037 (mm-40) REVERT: T 124 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8362 (ptp-110) REVERT: T 136 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.6974 (p-80) REVERT: U 57 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7733 (mm-30) REVERT: U 112 GLN cc_start: 0.8156 (tp40) cc_final: 0.7885 (tp40) REVERT: U 135 THR cc_start: 0.9049 (m) cc_final: 0.8815 (p) REVERT: U 171 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: V 12 TYR cc_start: 0.8711 (t80) cc_final: 0.8165 (t80) REVERT: V 68 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7975 (ttp-170) REVERT: V 79 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6673 (mmp-170) REVERT: V 112 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7611 (tp40) REVERT: W 112 GLN cc_start: 0.8258 (tp40) cc_final: 0.7976 (tp40) REVERT: W 156 HIS cc_start: 0.8657 (t70) cc_final: 0.8226 (t70) REVERT: X 15 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8275 (p0) REVERT: X 64 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8071 (mm-30) REVERT: X 162 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6049 (pm20) REVERT: X 171 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7414 (tm-30) outliers start: 89 outliers final: 35 residues processed: 420 average time/residue: 0.7995 time to fit residues: 394.5704 Evaluate side-chains 394 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 335 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 373 optimal weight: 6.9990 chunk 357 optimal weight: 0.3980 chunk 291 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 136 HIS C 136 HIS E 136 HIS G 136 HIS G 151 HIS J 75 GLN ** J 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS L 136 HIS M 29 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 83 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063408 restraints weight = 80356.758| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.24 r_work: 0.3036 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33816 Z= 0.211 Angle : 0.570 12.050 45480 Z= 0.290 Chirality : 0.039 0.260 4872 Planarity : 0.004 0.045 5952 Dihedral : 4.366 49.564 4521 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 2.30 % Allowed : 19.40 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.13), residues: 4080 helix: 3.07 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.86 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 63 TYR 0.028 0.002 TYR P 66 PHE 0.024 0.002 PHE B 132 TRP 0.003 0.000 TRP R 93 HIS 0.011 0.001 HIS L 136 Details of bonding type rmsd covalent geometry : bond 0.00470 (33816) covalent geometry : angle 0.57019 (45480) hydrogen bonds : bond 0.03586 ( 2656) hydrogen bonds : angle 3.57178 ( 7968) *********************** 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 437 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 1.366 Fit side-chains REVERT: A 56 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6755 (tmt170) REVERT: A 148 MET cc_start: 0.8542 (mmm) cc_final: 0.8282 (mtt) REVERT: B 83 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7919 (mm-40) REVERT: C 34 TYR cc_start: 0.9028 (m-10) cc_final: 0.8824 (m-80) REVERT: C 72 MET cc_start: 0.8747 (tmm) cc_final: 0.8478 (tmt) REVERT: D 64 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8012 (mm-30) REVERT: D 68 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7875 (mtm-85) REVERT: E 11 ASN cc_start: 0.8208 (m-40) cc_final: 0.7805 (t0) REVERT: E 83 GLN cc_start: 0.8801 (mm110) cc_final: 0.8495 (mm-40) REVERT: E 136 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8385 (p90) REVERT: F 16 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (p) REVERT: F 112 GLN cc_start: 0.8288 (tp40) cc_final: 0.8066 (tp40) REVERT: F 124 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8548 (mmt-90) REVERT: F 148 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8178 (ttp) REVERT: F 156 HIS cc_start: 0.8874 (t-90) cc_final: 0.8496 (t-90) REVERT: F 171 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8096 (tm-30) REVERT: G 7 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: H 112 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: H 156 HIS cc_start: 0.8849 (t70) cc_final: 0.8482 (t-90) REVERT: I 63 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7741 (ttm-80) REVERT: I 125 THR cc_start: 0.8891 (p) cc_final: 0.8686 (p) REVERT: I 148 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8060 (mtm) REVERT: J 7 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: K 34 TYR cc_start: 0.9127 (m-80) cc_final: 0.8800 (m-10) REVERT: K 104 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7797 (ttm) REVERT: L 75 GLN cc_start: 0.8816 (mt0) cc_final: 0.8526 (mt0) REVERT: M 34 TYR cc_start: 0.9157 (m-10) cc_final: 0.8904 (m-10) REVERT: M 68 ARG cc_start: 0.8455 (tpp80) cc_final: 0.7988 (ttp-170) REVERT: O 72 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8600 (tmm) REVERT: O 104 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8297 (ttp) REVERT: O 148 MET cc_start: 0.8770 (mtp) cc_final: 0.8395 (mtm) REVERT: Q 83 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8468 (mm110) REVERT: R 7 GLN cc_start: 0.7987 (mt0) cc_final: 0.7639 (pt0) REVERT: R 60 GLU cc_start: 0.8395 (tp30) cc_final: 0.8121 (mm-30) REVERT: R 83 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8447 (mp10) REVERT: S 11 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.7902 (t0) REVERT: S 61 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8101 (mm-30) REVERT: T 8 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9107 (pt) REVERT: T 10 GLN cc_start: 0.8511 (tt0) cc_final: 0.8268 (tt0) REVERT: T 11 ASN cc_start: 0.8542 (m-40) cc_final: 0.8041 (t0) REVERT: T 104 MET cc_start: 0.8548 (tpp) cc_final: 0.8326 (ttm) REVERT: T 112 GLN cc_start: 0.8517 (tp40) cc_final: 0.8234 (mm-40) REVERT: T 136 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.8421 (p90) REVERT: U 112 GLN cc_start: 0.8367 (tp40) cc_final: 0.8070 (tp40) REVERT: U 171 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: V 12 TYR cc_start: 0.8806 (t80) cc_final: 0.8324 (t80) REVERT: V 68 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8171 (ttp-170) REVERT: V 79 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6942 (mmp-170) REVERT: V 112 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7840 (tp40) REVERT: W 112 GLN cc_start: 0.8481 (tp40) cc_final: 0.8187 (tp40) REVERT: W 156 HIS cc_start: 0.8705 (t70) cc_final: 0.8291 (t70) REVERT: X 64 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8205 (mm-30) REVERT: X 162 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5948 (pm20) REVERT: X 171 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7574 (tm-30) outliers start: 80 outliers final: 38 residues processed: 407 average time/residue: 0.7120 time to fit residues: 342.3289 Evaluate side-chains 394 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 331 optimal weight: 0.8980 chunk 386 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 360 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 332 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN J 75 GLN J 136 HIS ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS M 29 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.075756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.066428 restraints weight = 79761.742| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.27 r_work: 0.3108 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33816 Z= 0.110 Angle : 0.526 11.489 45480 Z= 0.273 Chirality : 0.035 0.230 4872 Planarity : 0.004 0.045 5952 Dihedral : 4.184 46.725 4521 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 1.81 % Allowed : 20.17 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.13), residues: 4080 helix: 3.24 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.81 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 63 TYR 0.029 0.002 TYR J 66 PHE 0.020 0.001 PHE B 132 TRP 0.005 0.001 TRP H 93 HIS 0.011 0.001 HIS L 136 Details of bonding type rmsd covalent geometry : bond 0.00235 (33816) covalent geometry : angle 0.52617 (45480) hydrogen bonds : bond 0.03160 ( 2656) hydrogen bonds : angle 3.49020 ( 7968) *********************** 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 440 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 377 time to evaluate : 1.788 Fit side-chains REVERT: A 124 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8103 (mtp85) REVERT: A 148 MET cc_start: 0.8527 (mmm) cc_final: 0.8297 (mtt) REVERT: B 75 GLN cc_start: 0.8877 (mt0) cc_final: 0.8648 (mt0) REVERT: B 83 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7821 (mm-40) REVERT: B 136 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.8333 (p90) REVERT: C 72 MET cc_start: 0.8732 (tmm) cc_final: 0.8473 (tmt) REVERT: C 124 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8370 (mtt-85) REVERT: D 64 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7976 (mm-30) REVERT: D 68 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7900 (mtm-85) REVERT: E 11 ASN cc_start: 0.8115 (m-40) cc_final: 0.7702 (t0) REVERT: E 83 GLN cc_start: 0.8816 (mm110) cc_final: 0.8519 (mm-40) REVERT: E 136 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8248 (p90) REVERT: F 16 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8161 (p) REVERT: F 112 GLN cc_start: 0.8230 (tp40) cc_final: 0.7862 (tp40) REVERT: F 124 ARG cc_start: 0.8720 (mmt-90) cc_final: 0.8509 (mmt-90) REVERT: F 156 HIS cc_start: 0.8766 (t-90) cc_final: 0.8425 (t-90) REVERT: F 171 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8172 (tm-30) REVERT: H 112 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: H 156 HIS cc_start: 0.8767 (t70) cc_final: 0.8421 (t-90) REVERT: I 63 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7728 (ttm-80) REVERT: I 125 THR cc_start: 0.8803 (p) cc_final: 0.8591 (p) REVERT: J 7 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: K 34 TYR cc_start: 0.9101 (m-80) cc_final: 0.8709 (m-10) REVERT: K 72 MET cc_start: 0.8479 (tmt) cc_final: 0.8245 (tmm) REVERT: M 68 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8024 (ttp-170) REVERT: M 135 THR cc_start: 0.8473 (m) cc_final: 0.8244 (p) REVERT: N 124 ARG cc_start: 0.8386 (mtt90) cc_final: 0.8140 (mtp85) REVERT: O 72 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8482 (tmm) REVERT: O 148 MET cc_start: 0.8755 (mtp) cc_final: 0.8404 (mtm) REVERT: P 124 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7861 (mtp85) REVERT: Q 83 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8468 (mm110) REVERT: Q 124 ARG cc_start: 0.8746 (tpp80) cc_final: 0.8506 (tpp80) REVERT: R 7 GLN cc_start: 0.7985 (mt0) cc_final: 0.7638 (pt0) REVERT: R 11 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7947 (t0) REVERT: R 60 GLU cc_start: 0.8427 (tp30) cc_final: 0.7994 (tm-30) REVERT: R 83 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8406 (mp10) REVERT: S 11 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8167 (t0) REVERT: S 61 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8093 (mm-30) REVERT: T 10 GLN cc_start: 0.8377 (tt0) cc_final: 0.8130 (tt0) REVERT: T 11 ASN cc_start: 0.8487 (m-40) cc_final: 0.8036 (t0) REVERT: T 112 GLN cc_start: 0.8520 (tp40) cc_final: 0.8226 (mm-40) REVERT: T 125 THR cc_start: 0.8962 (p) cc_final: 0.8127 (t) REVERT: T 136 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.8363 (p90) REVERT: U 112 GLN cc_start: 0.8373 (tp40) cc_final: 0.8097 (tp40) REVERT: U 171 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8665 (tm-30) REVERT: V 12 TYR cc_start: 0.8772 (t80) cc_final: 0.8276 (t80) REVERT: V 68 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8126 (ttp-170) REVERT: V 79 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6933 (mmp-170) REVERT: V 112 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7830 (tp40) REVERT: W 112 GLN cc_start: 0.8448 (tp40) cc_final: 0.8097 (tp40) REVERT: W 156 HIS cc_start: 0.8599 (t70) cc_final: 0.8176 (t70) REVERT: X 15 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8370 (p0) REVERT: X 64 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8168 (mm-30) REVERT: X 162 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5900 (pm20) REVERT: X 171 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7617 (tm-30) outliers start: 63 outliers final: 26 residues processed: 420 average time/residue: 0.8082 time to fit residues: 400.5949 Evaluate side-chains 382 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 221 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 230 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 136 HIS ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN J 156 HIS ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS M 29 GLN P 83 GLN R 74 ASN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 83 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066031 restraints weight = 80321.057| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.28 r_work: 0.3099 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33816 Z= 0.129 Angle : 0.548 12.163 45480 Z= 0.282 Chirality : 0.037 0.273 4872 Planarity : 0.004 0.051 5952 Dihedral : 4.190 45.564 4521 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Rotamer: Outliers : 1.49 % Allowed : 20.89 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.13), residues: 4080 helix: 3.24 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.78 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.031 0.002 TYR N 66 PHE 0.020 0.002 PHE B 132 TRP 0.004 0.001 TRP X 93 HIS 0.012 0.001 HIS L 136 Details of bonding type rmsd covalent geometry : bond 0.00284 (33816) covalent geometry : angle 0.54781 (45480) hydrogen bonds : bond 0.03222 ( 2656) hydrogen bonds : angle 3.49529 ( 7968) ********************** 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 398 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 1.463 Fit side-chains REVERT: A 124 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8127 (mtp85) REVERT: A 148 MET cc_start: 0.8540 (mmm) cc_final: 0.8299 (mtt) REVERT: B 75 GLN cc_start: 0.8895 (mt0) cc_final: 0.8667 (mt0) REVERT: B 83 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7817 (mm-40) REVERT: B 136 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8315 (p90) REVERT: C 72 MET cc_start: 0.8722 (tmm) cc_final: 0.8479 (tmt) REVERT: C 124 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8465 (mtt-85) REVERT: D 64 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7984 (mm-30) REVERT: D 68 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7909 (mtm-85) REVERT: E 11 ASN cc_start: 0.8102 (m-40) cc_final: 0.7669 (t0) REVERT: E 83 GLN cc_start: 0.8826 (mm110) cc_final: 0.8532 (mm-40) REVERT: F 16 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8116 (p) REVERT: F 112 GLN cc_start: 0.8231 (tp40) cc_final: 0.7925 (tp40) REVERT: F 124 ARG cc_start: 0.8720 (mmt-90) cc_final: 0.8511 (mmt-90) REVERT: F 156 HIS cc_start: 0.8822 (t-90) cc_final: 0.8469 (t-90) REVERT: F 171 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8196 (tm-30) REVERT: H 112 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: H 156 HIS cc_start: 0.8791 (t70) cc_final: 0.8444 (t-90) REVERT: I 63 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: I 125 THR cc_start: 0.8817 (p) cc_final: 0.8599 (p) REVERT: I 148 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8010 (mtm) REVERT: J 7 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: K 34 TYR cc_start: 0.9147 (m-80) cc_final: 0.8764 (m-10) REVERT: K 72 MET cc_start: 0.8514 (tmt) cc_final: 0.8261 (tmm) REVERT: L 148 MET cc_start: 0.8653 (mtp) cc_final: 0.8347 (mtm) REVERT: M 68 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8036 (ttp-170) REVERT: M 86 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8901 (mppt) REVERT: M 135 THR cc_start: 0.8527 (m) cc_final: 0.8287 (p) REVERT: N 124 ARG cc_start: 0.8425 (mtt90) cc_final: 0.8216 (mtt90) REVERT: O 72 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: O 148 MET cc_start: 0.8794 (mtp) cc_final: 0.8373 (mtm) REVERT: P 124 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7972 (mtp85) REVERT: Q 83 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8458 (mm110) REVERT: Q 124 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8519 (tpp80) REVERT: R 7 GLN cc_start: 0.8022 (mt0) cc_final: 0.7658 (pt0) REVERT: R 60 GLU cc_start: 0.8432 (tp30) cc_final: 0.8188 (mm-30) REVERT: R 83 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8422 (mp10) REVERT: S 11 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8192 (t0) REVERT: S 61 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8078 (mm-30) REVERT: T 10 GLN cc_start: 0.8408 (tt0) cc_final: 0.8170 (tt0) REVERT: T 11 ASN cc_start: 0.8549 (m-40) cc_final: 0.8096 (t0) REVERT: T 112 GLN cc_start: 0.8484 (tp40) cc_final: 0.8183 (mm-40) REVERT: T 125 THR cc_start: 0.8932 (p) cc_final: 0.8098 (t) REVERT: T 136 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8375 (p90) REVERT: U 112 GLN cc_start: 0.8380 (tp40) cc_final: 0.8151 (tp40) REVERT: U 171 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: V 12 TYR cc_start: 0.8797 (t80) cc_final: 0.8284 (t80) REVERT: V 68 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8152 (ttp-170) REVERT: V 79 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6960 (mmp-170) REVERT: V 112 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7812 (tp40) REVERT: W 112 GLN cc_start: 0.8422 (tp40) cc_final: 0.8153 (tp40) REVERT: W 156 HIS cc_start: 0.8638 (t70) cc_final: 0.8225 (t70) REVERT: X 15 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8370 (p0) REVERT: X 64 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8169 (mm-30) REVERT: X 162 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5801 (pm20) REVERT: X 171 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7605 (tm-30) outliers start: 52 outliers final: 26 residues processed: 382 average time/residue: 0.8417 time to fit residues: 376.3129 Evaluate side-chains 374 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain S residue 11 ASN Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain U residue 100 MET Chi-restraints excluded: chain U residue 171 GLU Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 162 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0040 chunk 294 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 383 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 364 optimal weight: 0.0010 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 HIS J 75 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067413 restraints weight = 80000.231| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.28 r_work: 0.3133 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33816 Z= 0.110 Angle : 0.539 13.103 45480 Z= 0.278 Chirality : 0.036 0.232 4872 Planarity : 0.004 0.049 5952 Dihedral : 4.121 43.523 4521 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 1.38 % Allowed : 21.18 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.59 (0.13), residues: 4080 helix: 3.30 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.74 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.029 0.002 TYR N 66 PHE 0.020 0.002 PHE B 132 TRP 0.004 0.001 TRP X 93 HIS 0.013 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00236 (33816) covalent geometry : angle 0.53893 (45480) hydrogen bonds : bond 0.03094 ( 2656) hydrogen bonds : angle 3.45855 ( 7968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8770.07 seconds wall clock time: 151 minutes 29.76 seconds (9089.76 seconds total)