Starting phenix.real_space_refine on Fri Jun 27 23:00:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpj_44779/06_2025/9bpj_44779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpj_44779/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpj_44779/06_2025/9bpj_44779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpj_44779/06_2025/9bpj_44779.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpj_44779/06_2025/9bpj_44779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpj_44779/06_2025/9bpj_44779.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33192 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "D" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "J" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "N" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "P" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "R" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "T" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "V" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "X" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1383 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Time building chain proxies: 19.50, per 1000 atoms: 0.59 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: 8.02 Conformation dependent library (CDL) restraints added in 3.8 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 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: 12.77 Time building geometry restraints manager: 9.67 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.520 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 72.020 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:16.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (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 TRP 0.052 0.012 TRP B 93 HIS 0.018 0.004 HIS Q 53 PHE 0.113 0.020 PHE X 41 TYR 0.161 0.027 TYR R 34 ARG 0.017 0.002 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.10175 ( 2656) hydrogen bonds : angle 5.94390 ( 7968) covalent geometry : bond 0.01117 (33816) covalent geometry : angle 1.77475 (45480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 603 time to evaluate : 3.803 Fit side-chains REVERT: G 72 MET cc_start: 0.7236 (tmm) cc_final: 0.7019 (tmt) REVERT: I 162 GLU cc_start: 0.4599 (OUTLIER) cc_final: 0.4300 (pm20) REVERT: M 72 MET cc_start: 0.7030 (tmm) cc_final: 0.6388 (tmt) REVERT: S 72 MET cc_start: 0.7122 (tmm) cc_final: 0.6879 (tmt) REVERT: T 136 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7138 (p-80) REVERT: T 176 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6905 (ptmm) REVERT: X 162 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.3799 (pm20) outliers start: 99 outliers final: 9 residues processed: 689 average time/residue: 1.7707 time to fit residues: 1414.0929 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 : 3.815 ------------------------------------------------------------------------------- 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 344 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 136 HIS C 136 HIS D 7 GLN D 83 GLN ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065414 restraints weight = 81841.368| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.22 r_work: 0.3099 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2321 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= 0.147 Angle : 0.586 8.383 45480 Z= 0.313 Chirality : 0.039 0.175 4872 Planarity : 0.004 0.044 5952 Dihedral : 5.169 49.140 4544 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.13 % Favored : 97.55 % Rotamer: Outliers : 2.21 % Allowed : 12.30 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.13), residues: 4080 helix: 2.31 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -2.27 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 93 HIS 0.008 0.001 HIS R 128 PHE 0.018 0.002 PHE T 137 TYR 0.034 0.002 TYR N 66 ARG 0.008 0.001 ARG H 56 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 2656) hydrogen bonds : angle 3.85099 ( 7968) covalent geometry : bond 0.00323 (33816) covalent geometry : angle 0.58585 (45480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 431 time to evaluate : 3.792 Fit side-chains REVERT: A 56 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6481 (tmt170) REVERT: A 124 ARG cc_start: 0.8747 (mmt-90) cc_final: 0.8494 (mmt-90) REVERT: B 83 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7796 (mm-40) REVERT: B 136 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8404 (p90) REVERT: C 124 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8632 (mmt-90) REVERT: C 135 THR cc_start: 0.8755 (m) cc_final: 0.8553 (p) REVERT: C 136 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8749 (p90) REVERT: C 148 MET cc_start: 0.8688 (mtp) cc_final: 0.8472 (ttp) REVERT: D 68 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7480 (mtm-85) REVERT: E 11 ASN cc_start: 0.8295 (m110) cc_final: 0.7805 (t0) REVERT: E 27 TYR cc_start: 0.9035 (m-80) cc_final: 0.8741 (m-80) REVERT: E 83 GLN cc_start: 0.8568 (mm110) cc_final: 0.8325 (mm-40) REVERT: E 125 THR cc_start: 0.8869 (m) cc_final: 0.8082 (p) REVERT: E 136 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8613 (p90) REVERT: F 34 TYR cc_start: 0.8840 (m-10) cc_final: 0.8485 (m-10) REVERT: F 107 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: F 124 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.8528 (mmt-90) REVERT: F 156 HIS cc_start: 0.8902 (t-90) cc_final: 0.8460 (t-90) REVERT: G 104 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7447 (tpp) REVERT: H 63 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7379 (ttm-80) REVERT: H 135 THR cc_start: 0.9110 (m) cc_final: 0.8874 (p) REVERT: H 148 MET cc_start: 0.8661 (tpp) cc_final: 0.8420 (mmm) REVERT: I 63 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7407 (ttm-80) REVERT: I 124 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8679 (mmt-90) REVERT: I 136 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8554 (p90) REVERT: K 34 TYR cc_start: 0.8835 (m-80) cc_final: 0.8454 (m-10) REVERT: K 124 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8631 (mmt-90) REVERT: M 13 SER cc_start: 0.8338 (m) cc_final: 0.8129 (p) REVERT: M 68 ARG cc_start: 0.8042 (tpp80) cc_final: 0.7326 (ttp-170) REVERT: N 27 TYR cc_start: 0.8794 (m-80) cc_final: 0.8562 (m-80) REVERT: N 124 ARG cc_start: 0.8800 (mmt-90) cc_final: 0.8527 (mmt-90) REVERT: N 135 THR cc_start: 0.8787 (m) cc_final: 0.8536 (p) REVERT: O 72 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8367 (tmm) REVERT: O 148 MET cc_start: 0.8614 (mmm) cc_final: 0.8340 (mtm) REVERT: P 72 MET cc_start: 0.8855 (tmm) cc_final: 0.8590 (tmt) REVERT: P 124 ARG cc_start: 0.8802 (tpp-160) cc_final: 0.8600 (mtp85) REVERT: P 135 THR cc_start: 0.9025 (m) cc_final: 0.8806 (t) REVERT: P 148 MET cc_start: 0.8992 (tpp) cc_final: 0.8739 (mmm) REVERT: Q 83 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8478 (mm-40) REVERT: Q 124 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8455 (tpp80) REVERT: R 7 GLN cc_start: 0.7629 (mt0) cc_final: 0.7182 (pt0) REVERT: R 63 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.6999 (ttp80) REVERT: S 136 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8430 (p90) REVERT: T 112 GLN cc_start: 0.8398 (tp40) cc_final: 0.8179 (mm-40) REVERT: T 136 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (p-80) REVERT: U 57 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7764 (mm-30) REVERT: U 135 THR cc_start: 0.8990 (m) cc_final: 0.8754 (p) REVERT: U 171 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8648 (tm-30) REVERT: V 12 TYR cc_start: 0.8662 (t80) cc_final: 0.8218 (t80) REVERT: V 68 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7844 (ttp-170) REVERT: V 112 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7695 (tp40) REVERT: W 112 GLN cc_start: 0.8198 (tp40) cc_final: 0.7856 (tp-100) REVERT: W 124 ARG cc_start: 0.9072 (mmt-90) cc_final: 0.8864 (mmt-90) REVERT: X 104 MET cc_start: 0.7962 (ttp) cc_final: 0.7719 (ttp) REVERT: X 112 GLN cc_start: 0.8064 (tp40) cc_final: 0.7795 (tp40) REVERT: X 125 THR cc_start: 0.9179 (t) cc_final: 0.8948 (p) REVERT: X 136 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8813 (p90) REVERT: X 145 ILE cc_start: 0.8465 (mp) cc_final: 0.8210 (mp) REVERT: X 162 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6150 (pm20) REVERT: X 171 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7457 (tm-30) REVERT: X 174 THR cc_start: 0.8979 (m) cc_final: 0.8756 (p) outliers start: 77 outliers final: 25 residues processed: 484 average time/residue: 1.5892 time to fit residues: 905.8064 Evaluate side-chains 384 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain B residue 8 ILE 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 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 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 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 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 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 X residue 49 GLU Chi-restraints excluded: chain X residue 136 HIS 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 193 optimal weight: 0.9990 chunk 388 optimal weight: 0.9980 chunk 349 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 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 ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 HIS L 136 HIS Q 75 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 136 HIS T 83 GLN U 29 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 = 0.3474 r_free = 0.3474 target = 0.075223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066002 restraints weight = 81881.154| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.24 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: 0.7809 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33816 Z= 0.128 Angle : 0.531 7.856 45480 Z= 0.283 Chirality : 0.036 0.157 4872 Planarity : 0.003 0.038 5952 Dihedral : 4.523 54.305 4521 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.91 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 15.03 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.13), residues: 4080 helix: 2.75 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 93 HIS 0.014 0.001 HIS B 136 PHE 0.017 0.002 PHE S 137 TYR 0.028 0.002 TYR J 66 ARG 0.008 0.001 ARG J 56 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 2656) hydrogen bonds : angle 3.63531 ( 7968) covalent geometry : bond 0.00275 (33816) covalent geometry : angle 0.53131 (45480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 395 time to evaluate : 3.850 Fit side-chains REVERT: A 56 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6448 (tmt170) REVERT: A 148 MET cc_start: 0.8447 (tpp) cc_final: 0.7961 (mtt) REVERT: B 135 THR cc_start: 0.8882 (t) cc_final: 0.8671 (p) REVERT: C 136 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8591 (p90) REVERT: C 172 ARG cc_start: 0.8380 (mmp-170) cc_final: 0.8126 (mmm160) REVERT: D 15 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8039 (p0) REVERT: D 64 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7896 (mm-30) REVERT: D 68 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7611 (mtm-85) REVERT: E 11 ASN cc_start: 0.8248 (m110) cc_final: 0.7759 (t160) REVERT: E 27 TYR cc_start: 0.9020 (m-80) cc_final: 0.8764 (m-80) REVERT: E 83 GLN cc_start: 0.8718 (mm110) cc_final: 0.8426 (mm-40) REVERT: E 136 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8557 (p90) REVERT: F 34 TYR cc_start: 0.8878 (m-10) cc_final: 0.8517 (m-10) REVERT: F 107 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8180 (tp30) REVERT: F 112 GLN cc_start: 0.7987 (tp40) cc_final: 0.7671 (tp40) REVERT: F 156 HIS cc_start: 0.8839 (t-90) cc_final: 0.8386 (t-170) REVERT: F 171 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8175 (tm-30) REVERT: H 135 THR cc_start: 0.9097 (m) cc_final: 0.8837 (p) REVERT: H 148 MET cc_start: 0.8682 (tpp) cc_final: 0.8438 (mmm) REVERT: H 156 HIS cc_start: 0.8763 (t70) cc_final: 0.8364 (t-90) REVERT: I 27 TYR cc_start: 0.9021 (m-80) cc_final: 0.8756 (m-80) REVERT: I 63 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7357 (ttm-80) REVERT: I 124 ARG cc_start: 0.8921 (mmt-90) cc_final: 0.8720 (mmt-90) REVERT: K 34 TYR cc_start: 0.8855 (m-80) cc_final: 0.8558 (m-10) REVERT: K 124 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8691 (mmt-90) REVERT: L 27 TYR cc_start: 0.9032 (m-80) cc_final: 0.8826 (m-80) REVERT: L 136 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.8485 (p90) REVERT: M 56 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8047 (mmm-85) REVERT: M 68 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7340 (ttp-170) REVERT: N 27 TYR cc_start: 0.8774 (m-80) cc_final: 0.8547 (m-80) REVERT: N 124 ARG cc_start: 0.8844 (mmt-90) cc_final: 0.8638 (mmt-90) REVERT: N 135 THR cc_start: 0.8733 (m) cc_final: 0.8508 (p) REVERT: O 72 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8350 (tmm) REVERT: O 148 MET cc_start: 0.8574 (mmm) cc_final: 0.8294 (mtm) REVERT: P 12 TYR cc_start: 0.8998 (t80) cc_final: 0.8709 (t80) REVERT: P 72 MET cc_start: 0.8850 (tmm) cc_final: 0.8514 (tmt) REVERT: Q 83 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8450 (mm-40) REVERT: R 7 GLN cc_start: 0.7711 (mt0) cc_final: 0.7317 (pt0) REVERT: R 83 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8467 (mp10) REVERT: S 11 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.7839 (t0) REVERT: T 112 GLN cc_start: 0.8347 (tp40) cc_final: 0.8086 (mm-40) REVERT: T 132 PHE cc_start: 0.7900 (t80) cc_final: 0.7693 (t80) REVERT: T 136 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7280 (p-80) REVERT: U 57 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7808 (mm-30) REVERT: U 112 GLN cc_start: 0.8197 (tp40) cc_final: 0.7967 (tp40) REVERT: U 135 THR cc_start: 0.9040 (m) cc_final: 0.8807 (p) REVERT: U 171 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (tm-30) REVERT: V 12 TYR cc_start: 0.8690 (t80) cc_final: 0.8152 (t80) REVERT: V 68 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7859 (ttp-170) REVERT: V 112 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7655 (tp40) REVERT: W 112 GLN cc_start: 0.8236 (tp40) cc_final: 0.7953 (tp40) REVERT: X 112 GLN cc_start: 0.8022 (tp40) cc_final: 0.7758 (tp40) REVERT: X 145 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8229 (mp) REVERT: X 162 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6112 (pm20) REVERT: X 171 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7360 (tm-30) outliers start: 73 outliers final: 24 residues processed: 442 average time/residue: 1.5263 time to fit residues: 798.9984 Evaluate side-chains 391 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 136 HIS 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 D residue 68 ARG 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 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 L residue 100 MET Chi-restraints excluded: chain L residue 136 HIS 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 Q residue 22 SER 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 W residue 13 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 135 THR 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 402 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 207 optimal weight: 0.0980 chunk 254 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 247 optimal weight: 0.0020 chunk 116 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 11 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS H 11 ASN I 136 HIS J 75 GLN J 83 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 HIS L 136 HIS M 29 GLN M 83 GLN P 83 GLN P 136 HIS Q 75 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 156 HIS U 29 GLN U 83 GLN W 74 ASN X 136 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066597 restraints weight = 81827.316| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.22 r_work: 0.3125 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33816 Z= 0.117 Angle : 0.506 7.450 45480 Z= 0.269 Chirality : 0.035 0.147 4872 Planarity : 0.003 0.037 5952 Dihedral : 4.341 57.967 4521 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.08 % Favored : 97.75 % Rotamer: Outliers : 2.33 % Allowed : 16.29 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.13), residues: 4080 helix: 3.01 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.86 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 93 HIS 0.018 0.001 HIS C 136 PHE 0.018 0.002 PHE S 132 TYR 0.029 0.002 TYR P 66 ARG 0.009 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 2656) hydrogen bonds : angle 3.53234 ( 7968) covalent geometry : bond 0.00250 (33816) covalent geometry : angle 0.50644 (45480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 399 time to evaluate : 3.771 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8450 (tpp) cc_final: 0.8033 (mtt) REVERT: B 136 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8392 (p90) REVERT: C 34 TYR cc_start: 0.8868 (m-10) cc_final: 0.8639 (m-10) REVERT: C 72 MET cc_start: 0.8601 (tmm) cc_final: 0.8342 (tmt) REVERT: C 124 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8577 (mmt-90) REVERT: D 64 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7902 (mm-30) REVERT: D 68 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7690 (mtm-85) REVERT: E 11 ASN cc_start: 0.8241 (m110) cc_final: 0.7769 (t160) REVERT: E 27 TYR cc_start: 0.9018 (m-80) cc_final: 0.8798 (m-80) REVERT: E 83 GLN cc_start: 0.8762 (mm110) cc_final: 0.8456 (mm-40) REVERT: E 136 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.8431 (p90) REVERT: F 16 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7891 (p) REVERT: F 112 GLN cc_start: 0.7998 (tp40) cc_final: 0.7683 (tp40) REVERT: F 156 HIS cc_start: 0.8744 (t-90) cc_final: 0.8328 (t-170) REVERT: F 171 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8130 (tm-30) REVERT: H 83 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8432 (mp10) REVERT: H 112 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: H 144 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8495 (tp) REVERT: H 156 HIS cc_start: 0.8748 (t70) cc_final: 0.8363 (t-90) REVERT: I 63 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7383 (ttm-80) REVERT: I 136 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8522 (p90) REVERT: J 7 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: K 34 TYR cc_start: 0.8848 (m-80) cc_final: 0.8491 (m-10) REVERT: K 104 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7688 (ttm) REVERT: L 27 TYR cc_start: 0.9057 (m-80) cc_final: 0.8798 (m-80) REVERT: L 135 THR cc_start: 0.8979 (t) cc_final: 0.8690 (p) REVERT: M 68 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7680 (ttp-170) REVERT: N 27 TYR cc_start: 0.8794 (m-80) cc_final: 0.8560 (m-80) REVERT: O 72 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8338 (tmm) REVERT: O 148 MET cc_start: 0.8624 (mmm) cc_final: 0.8298 (mtm) REVERT: P 16 VAL cc_start: 0.8355 (t) cc_final: 0.8139 (t) REVERT: P 148 MET cc_start: 0.8987 (tpp) cc_final: 0.8722 (mmm) REVERT: Q 83 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8448 (mm-40) REVERT: Q 124 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8398 (tpp80) REVERT: R 7 GLN cc_start: 0.7681 (mt0) cc_final: 0.7340 (pt0) REVERT: R 60 GLU cc_start: 0.8319 (tp30) cc_final: 0.7808 (mm-30) REVERT: R 63 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7195 (ttp80) REVERT: R 83 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8394 (mp10) REVERT: S 11 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8015 (t0) REVERT: T 11 ASN cc_start: 0.8445 (m-40) cc_final: 0.7888 (t0) REVERT: T 112 GLN cc_start: 0.8350 (tp40) cc_final: 0.8079 (mm-40) REVERT: T 136 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7210 (p-80) REVERT: U 57 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7822 (mm-30) REVERT: U 112 GLN cc_start: 0.8145 (tp40) cc_final: 0.7910 (tp40) REVERT: U 135 THR cc_start: 0.9046 (m) cc_final: 0.8812 (p) REVERT: U 171 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: V 12 TYR cc_start: 0.8674 (t80) cc_final: 0.8148 (t80) REVERT: V 68 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7969 (ttp-170) REVERT: V 112 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7621 (tp40) REVERT: W 112 GLN cc_start: 0.8251 (tp40) cc_final: 0.7941 (tp40) REVERT: W 156 HIS cc_start: 0.8608 (t70) cc_final: 0.8342 (t70) REVERT: X 15 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8251 (p0) REVERT: X 64 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8136 (mm-30) REVERT: X 112 GLN cc_start: 0.8006 (tp40) cc_final: 0.7743 (tp40) REVERT: X 136 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8433 (p90) REVERT: X 162 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5936 (pm20) REVERT: X 171 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7381 (tm-30) REVERT: X 174 THR cc_start: 0.8965 (m) cc_final: 0.8731 (p) outliers start: 81 outliers final: 26 residues processed: 450 average time/residue: 1.5296 time to fit residues: 816.6600 Evaluate side-chains 401 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 356 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 81 LEU 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 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 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 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 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 P 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 63 ARG 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 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 162 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 268 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 291 optimal weight: 0.6980 chunk 336 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 B 136 HIS ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS I 136 HIS J 75 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 HIS L 136 HIS M 7 GLN M 29 GLN ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN T 83 GLN U 29 GLN X 136 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066036 restraints weight = 81697.051| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.22 r_work: 0.3110 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33816 Z= 0.135 Angle : 0.512 8.310 45480 Z= 0.269 Chirality : 0.036 0.165 4872 Planarity : 0.003 0.043 5952 Dihedral : 4.263 53.071 4521 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.16 % Favored : 97.72 % Rotamer: Outliers : 2.36 % Allowed : 17.70 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.13), residues: 4080 helix: 3.16 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -2.00 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP X 93 HIS 0.013 0.001 HIS L 136 PHE 0.019 0.002 PHE I 132 TYR 0.030 0.002 TYR P 66 ARG 0.009 0.001 ARG I 56 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 2656) hydrogen bonds : angle 3.50626 ( 7968) covalent geometry : bond 0.00295 (33816) covalent geometry : angle 0.51190 (45480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 382 time to evaluate : 4.018 Fit side-chains REVERT: A 56 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6456 (tmt170) REVERT: A 124 ARG cc_start: 0.8550 (mmt-90) cc_final: 0.8324 (mmt-90) REVERT: A 148 MET cc_start: 0.8464 (tpp) cc_final: 0.7847 (mtt) REVERT: B 135 THR cc_start: 0.8848 (t) cc_final: 0.8588 (p) REVERT: B 136 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7815 (p90) REVERT: C 34 TYR cc_start: 0.8865 (m-10) cc_final: 0.8655 (m-10) REVERT: C 72 MET cc_start: 0.8551 (tmm) cc_final: 0.8311 (tmt) REVERT: C 112 GLN cc_start: 0.8225 (tp40) cc_final: 0.8010 (mm-40) REVERT: C 124 ARG cc_start: 0.8863 (mmt-90) cc_final: 0.8508 (mmt-90) REVERT: D 64 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7871 (mm-30) REVERT: D 68 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7698 (mtm-85) REVERT: E 11 ASN cc_start: 0.8224 (m-40) cc_final: 0.7735 (t0) REVERT: E 62 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7944 (mptt) REVERT: E 83 GLN cc_start: 0.8787 (mm110) cc_final: 0.8457 (mm-40) REVERT: E 136 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8453 (p90) REVERT: F 16 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7892 (p) REVERT: F 112 GLN cc_start: 0.7954 (tp40) cc_final: 0.7596 (tp40) REVERT: F 156 HIS cc_start: 0.8755 (t-90) cc_final: 0.8322 (t-170) REVERT: F 171 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8054 (tm-30) REVERT: G 7 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: H 83 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8340 (mp10) REVERT: H 112 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: H 135 THR cc_start: 0.9050 (t) cc_final: 0.8787 (p) REVERT: H 156 HIS cc_start: 0.8744 (t70) cc_final: 0.8359 (t-90) REVERT: I 63 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7439 (ttm-80) REVERT: I 136 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8412 (p90) REVERT: J 7 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: J 136 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8705 (p90) REVERT: K 34 TYR cc_start: 0.8890 (m-80) cc_final: 0.8541 (m-10) REVERT: L 27 TYR cc_start: 0.9043 (m-80) cc_final: 0.8804 (m-80) REVERT: L 135 THR cc_start: 0.8994 (t) cc_final: 0.8703 (p) REVERT: M 68 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7713 (ttp-170) REVERT: N 27 TYR cc_start: 0.8792 (m-80) cc_final: 0.8552 (m-80) REVERT: N 124 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8545 (mmt-90) REVERT: O 7 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8816 (pm20) REVERT: O 72 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8330 (tmm) REVERT: O 104 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7963 (ttm) REVERT: O 148 MET cc_start: 0.8597 (mmm) cc_final: 0.8282 (mtm) REVERT: P 124 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7964 (mtp85) REVERT: P 148 MET cc_start: 0.8967 (tpp) cc_final: 0.8698 (mmm) REVERT: Q 83 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8464 (mm-40) REVERT: Q 124 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8261 (tpp80) REVERT: R 7 GLN cc_start: 0.7698 (mt0) cc_final: 0.7364 (pt0) REVERT: R 60 GLU cc_start: 0.8316 (tp30) cc_final: 0.7827 (mm-30) REVERT: R 63 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7179 (ttp80) REVERT: R 83 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8343 (mp10) REVERT: S 11 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8113 (t0) REVERT: T 11 ASN cc_start: 0.8525 (m-40) cc_final: 0.7980 (t0) REVERT: T 112 GLN cc_start: 0.8308 (tp40) cc_final: 0.8038 (mm-40) REVERT: T 124 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8356 (ptp-110) REVERT: T 136 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7968 (p90) REVERT: U 14 THR cc_start: 0.9242 (m) cc_final: 0.9011 (p) REVERT: U 57 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7743 (mm-30) REVERT: U 112 GLN cc_start: 0.8166 (tp40) cc_final: 0.7911 (tp40) REVERT: U 135 THR cc_start: 0.9055 (m) cc_final: 0.8826 (p) REVERT: U 171 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: V 12 TYR cc_start: 0.8705 (t80) cc_final: 0.8130 (t80) REVERT: V 68 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.7977 (ttp-170) REVERT: V 79 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6639 (mmp-170) REVERT: V 112 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7625 (tp40) REVERT: W 112 GLN cc_start: 0.8250 (tp40) cc_final: 0.7923 (tp40) REVERT: W 156 HIS cc_start: 0.8630 (t70) cc_final: 0.8367 (t70) REVERT: X 15 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8261 (p0) REVERT: X 64 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8099 (mm-30) REVERT: X 112 GLN cc_start: 0.7993 (tp40) cc_final: 0.7731 (tp40) REVERT: X 162 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6155 (pm20) REVERT: X 171 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7387 (tm-30) REVERT: X 174 THR cc_start: 0.8952 (m) cc_final: 0.8731 (p) outliers start: 82 outliers final: 29 residues processed: 432 average time/residue: 1.6321 time to fit residues: 827.5665 Evaluate side-chains 406 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 353 time to evaluate : 3.759 ------------------------------------------------------------------------------- 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 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 7 GLN 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 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 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 7 GLN 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 Q residue 124 ARG 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 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 X residue 15 ASP Chi-restraints excluded: chain X residue 135 THR 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 4 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 368 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 136 HIS ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS J 11 ASN J 75 GLN J 83 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 HIS J 156 HIS ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS M 25 ASN 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 29 GLN U 83 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066557 restraints weight = 81593.081| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.22 r_work: 0.3127 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33816 Z= 0.118 Angle : 0.505 10.579 45480 Z= 0.266 Chirality : 0.035 0.173 4872 Planarity : 0.003 0.040 5952 Dihedral : 4.194 50.318 4521 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 18.65 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.13), residues: 4080 helix: 3.24 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.95 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 93 HIS 0.012 0.001 HIS L 136 PHE 0.017 0.002 PHE L 132 TYR 0.030 0.002 TYR P 66 ARG 0.010 0.001 ARG L 56 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 2656) hydrogen bonds : angle 3.48561 ( 7968) covalent geometry : bond 0.00254 (33816) covalent geometry : angle 0.50523 (45480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 380 time to evaluate : 4.122 Fit side-chains REVERT: A 22 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8566 (p) REVERT: A 56 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6505 (tmt170) REVERT: A 148 MET cc_start: 0.8494 (tpp) cc_final: 0.7852 (mtt) REVERT: B 75 GLN cc_start: 0.8986 (mt0) cc_final: 0.8704 (mt0) REVERT: B 135 THR cc_start: 0.8802 (t) cc_final: 0.8585 (p) REVERT: C 34 TYR cc_start: 0.8873 (m-10) cc_final: 0.8668 (m-10) REVERT: C 112 GLN cc_start: 0.8201 (tp40) cc_final: 0.7992 (mm-40) REVERT: D 64 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7848 (mm-30) REVERT: D 68 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7775 (mtm-85) REVERT: E 11 ASN cc_start: 0.8214 (m-40) cc_final: 0.7611 (t0) REVERT: E 62 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7971 (mptt) REVERT: E 83 GLN cc_start: 0.8789 (mm110) cc_final: 0.8489 (mm-40) REVERT: E 136 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8477 (p90) REVERT: F 16 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7923 (p) REVERT: F 112 GLN cc_start: 0.7987 (tp40) cc_final: 0.7641 (tp40) REVERT: F 148 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7992 (ttm) REVERT: F 156 HIS cc_start: 0.8731 (t-90) cc_final: 0.8303 (t-170) REVERT: F 171 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8055 (tm-30) REVERT: G 7 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: G 53 HIS cc_start: 0.7773 (t70) cc_final: 0.7495 (t70) REVERT: G 124 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7931 (mmm-85) REVERT: H 83 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8353 (mt0) REVERT: H 112 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: H 135 THR cc_start: 0.9103 (t) cc_final: 0.8830 (p) REVERT: H 156 HIS cc_start: 0.8755 (t70) cc_final: 0.8377 (t-90) REVERT: I 63 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7449 (ttm-80) REVERT: I 136 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.8526 (p90) REVERT: J 7 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: J 136 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8621 (p90) REVERT: K 34 TYR cc_start: 0.8930 (m-80) cc_final: 0.8587 (m-10) REVERT: L 135 THR cc_start: 0.9001 (t) cc_final: 0.8720 (p) REVERT: M 68 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7785 (ttp-170) REVERT: M 135 THR cc_start: 0.8382 (m) cc_final: 0.8143 (p) REVERT: O 7 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: O 72 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8320 (tmm) REVERT: O 104 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8028 (ttp) REVERT: O 124 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7936 (mmt-90) REVERT: O 148 MET cc_start: 0.8602 (mmm) cc_final: 0.8315 (mtm) REVERT: P 148 MET cc_start: 0.8964 (tpp) cc_final: 0.8703 (mmm) REVERT: Q 83 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8462 (mm-40) REVERT: Q 124 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8351 (tpp80) REVERT: R 7 GLN cc_start: 0.7695 (mt0) cc_final: 0.7389 (pt0) REVERT: R 56 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7742 (mmm-85) REVERT: R 60 GLU cc_start: 0.8301 (tp30) cc_final: 0.7853 (mm-30) REVERT: R 63 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7161 (ttp80) REVERT: R 83 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8316 (mp10) REVERT: S 11 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8108 (t0) REVERT: T 11 ASN cc_start: 0.8503 (m-40) cc_final: 0.8005 (t0) REVERT: T 112 GLN cc_start: 0.8306 (tp40) cc_final: 0.8023 (mm-40) REVERT: T 124 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8388 (ptp-110) REVERT: T 136 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7529 (p-80) REVERT: U 14 THR cc_start: 0.9285 (m) cc_final: 0.9051 (p) REVERT: U 57 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7725 (mm-30) REVERT: U 112 GLN cc_start: 0.8143 (tp40) cc_final: 0.7873 (tp40) REVERT: U 135 THR cc_start: 0.9051 (m) cc_final: 0.8833 (p) REVERT: U 171 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: V 12 TYR cc_start: 0.8687 (t80) cc_final: 0.8186 (t80) REVERT: V 68 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8008 (ttp-170) REVERT: V 112 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7680 (tp40) REVERT: W 112 GLN cc_start: 0.8238 (tp40) cc_final: 0.7920 (tp40) REVERT: W 156 HIS cc_start: 0.8630 (t70) cc_final: 0.8216 (t70) REVERT: X 15 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8288 (p0) REVERT: X 64 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8104 (mm-30) REVERT: X 162 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6025 (pm20) REVERT: X 171 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7379 (tm-30) outliers start: 76 outliers final: 25 residues processed: 431 average time/residue: 1.6346 time to fit residues: 836.2344 Evaluate side-chains 397 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 348 time to evaluate : 4.230 ------------------------------------------------------------------------------- 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 136 HIS 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 F residue 148 MET Chi-restraints excluded: chain G residue 7 GLN 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 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 22 SER Chi-restraints excluded: chain J residue 136 HIS 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 7 GLN 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 Q residue 124 ARG 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 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 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 162 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 283 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 299 optimal weight: 0.9980 chunk 398 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 381 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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 ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS J 75 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 11 ASN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 74 ASN W 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063616 restraints weight = 82214.767| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.21 r_work: 0.3057 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33816 Z= 0.207 Angle : 0.559 9.649 45480 Z= 0.286 Chirality : 0.038 0.164 4872 Planarity : 0.004 0.043 5952 Dihedral : 4.361 50.417 4521 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 2.64 % Allowed : 18.85 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.13), residues: 4080 helix: 3.07 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 93 HIS 0.018 0.001 HIS E 136 PHE 0.018 0.002 PHE I 137 TYR 0.028 0.002 TYR F 66 ARG 0.010 0.001 ARG Q 56 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 2656) hydrogen bonds : angle 3.56616 ( 7968) covalent geometry : bond 0.00458 (33816) covalent geometry : angle 0.55863 (45480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 365 time to evaluate : 4.319 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6534 (tmt170) REVERT: B 75 GLN cc_start: 0.8898 (mt0) cc_final: 0.8628 (mt0) REVERT: B 83 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8096 (mm-40) REVERT: B 135 THR cc_start: 0.8903 (t) cc_final: 0.8607 (p) REVERT: B 136 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8182 (p90) REVERT: C 34 TYR cc_start: 0.8916 (m-10) cc_final: 0.8693 (m-10) REVERT: C 72 MET cc_start: 0.8618 (tmm) cc_final: 0.8383 (tmt) REVERT: C 112 GLN cc_start: 0.8227 (tp40) cc_final: 0.8015 (mm-40) REVERT: D 64 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7822 (mm-30) REVERT: D 68 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7696 (mtm-85) REVERT: E 11 ASN cc_start: 0.8286 (m-40) cc_final: 0.7824 (t0) REVERT: E 83 GLN cc_start: 0.8763 (mm110) cc_final: 0.8457 (mm-40) REVERT: F 16 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7985 (p) REVERT: F 112 GLN cc_start: 0.8030 (tp40) cc_final: 0.7685 (tp40) REVERT: F 148 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8035 (ttp) REVERT: F 156 HIS cc_start: 0.8859 (t-90) cc_final: 0.8468 (t-90) REVERT: F 171 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7983 (tm-30) REVERT: G 7 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: G 63 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7288 (ttm-80) REVERT: H 112 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: H 135 THR cc_start: 0.9054 (t) cc_final: 0.8770 (p) REVERT: H 156 HIS cc_start: 0.8871 (t70) cc_final: 0.8484 (t-90) REVERT: I 63 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7432 (ttm-80) REVERT: J 7 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: J 136 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.8167 (p90) REVERT: K 34 TYR cc_start: 0.8939 (m-80) cc_final: 0.8560 (m-10) REVERT: K 104 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: L 75 GLN cc_start: 0.8658 (mt0) cc_final: 0.8425 (mt0) REVERT: L 104 MET cc_start: 0.8364 (mmm) cc_final: 0.7963 (tpp) REVERT: M 34 TYR cc_start: 0.8963 (m-10) cc_final: 0.8744 (m-10) REVERT: M 68 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7727 (ttp-170) REVERT: O 72 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8393 (tmm) REVERT: O 104 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8096 (ttp) REVERT: O 124 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7891 (mmt-90) REVERT: O 148 MET cc_start: 0.8576 (mmm) cc_final: 0.8236 (mtm) REVERT: P 124 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8040 (mtp85) REVERT: Q 83 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8436 (mm-40) REVERT: Q 124 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8437 (tpp80) REVERT: R 7 GLN cc_start: 0.7751 (mt0) cc_final: 0.7406 (pt0) REVERT: R 60 GLU cc_start: 0.8298 (tp30) cc_final: 0.7906 (mm-30) REVERT: R 83 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8338 (mp10) REVERT: S 11 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.7781 (t0) REVERT: T 8 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8915 (pt) REVERT: T 10 GLN cc_start: 0.8250 (tt0) cc_final: 0.8013 (tt0) REVERT: T 11 ASN cc_start: 0.8564 (m-40) cc_final: 0.7964 (t0) REVERT: T 112 GLN cc_start: 0.8331 (tp40) cc_final: 0.8057 (mm-40) REVERT: T 124 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8455 (ptp-110) REVERT: T 136 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7605 (p-80) REVERT: U 14 THR cc_start: 0.9240 (m) cc_final: 0.9035 (p) REVERT: U 57 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7750 (mm-30) REVERT: U 171 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8583 (tm-30) REVERT: V 12 TYR cc_start: 0.8722 (t80) cc_final: 0.8211 (t80) REVERT: V 68 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.7999 (ttp-170) REVERT: V 79 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6688 (mmp-170) REVERT: V 112 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7651 (tp40) REVERT: W 112 GLN cc_start: 0.8281 (tp40) cc_final: 0.7997 (tp40) REVERT: W 156 HIS cc_start: 0.8680 (t70) cc_final: 0.8249 (t70) REVERT: X 64 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8085 (mm-30) REVERT: X 162 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6123 (pm20) REVERT: X 171 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7469 (tm-30) outliers start: 92 outliers final: 33 residues processed: 425 average time/residue: 1.6714 time to fit residues: 836.1911 Evaluate side-chains 393 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 4.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 68 ARG Chi-restraints excluded: chain E residue 31 SER 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 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 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 22 SER 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 63 ARG 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 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 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 19 optimal weight: 0.6980 chunk 301 optimal weight: 0.9980 chunk 364 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 HIS J 156 HIS ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065561 restraints weight = 80219.106| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.28 r_work: 0.3088 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3327 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= 0.128 Angle : 0.531 12.417 45480 Z= 0.274 Chirality : 0.036 0.156 4872 Planarity : 0.004 0.045 5952 Dihedral : 4.233 47.560 4521 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % Rotamer: Outliers : 1.87 % Allowed : 20.09 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.13), residues: 4080 helix: 3.18 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.88 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 93 HIS 0.010 0.001 HIS B 136 PHE 0.016 0.002 PHE L 132 TYR 0.029 0.002 TYR N 66 ARG 0.011 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 2656) hydrogen bonds : angle 3.49539 ( 7968) covalent geometry : bond 0.00281 (33816) covalent geometry : angle 0.53092 (45480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 373 time to evaluate : 5.117 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6659 (tmt170) REVERT: A 148 MET cc_start: 0.8675 (tpp) cc_final: 0.8299 (mtt) REVERT: B 75 GLN cc_start: 0.9002 (mt0) cc_final: 0.8743 (mt0) REVERT: B 83 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7987 (mm-40) REVERT: C 34 TYR cc_start: 0.9016 (m-10) cc_final: 0.8815 (m-10) REVERT: C 72 MET cc_start: 0.8717 (tmm) cc_final: 0.8457 (tmt) REVERT: C 112 GLN cc_start: 0.8427 (tp40) cc_final: 0.8205 (mm-40) REVERT: D 64 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8022 (mm-30) REVERT: D 68 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: E 11 ASN cc_start: 0.8230 (m-40) cc_final: 0.7677 (t160) REVERT: E 60 GLU cc_start: 0.8651 (tp30) cc_final: 0.8217 (tp30) REVERT: E 83 GLN cc_start: 0.8801 (mm110) cc_final: 0.8527 (mm-40) REVERT: E 136 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8097 (p90) REVERT: F 16 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8076 (p) REVERT: F 112 GLN cc_start: 0.8217 (tp40) cc_final: 0.7915 (tp40) REVERT: F 156 HIS cc_start: 0.8849 (t-90) cc_final: 0.8480 (t-90) REVERT: F 171 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8164 (tm-30) REVERT: G 7 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: G 63 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7538 (ttm-80) REVERT: H 112 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: H 135 THR cc_start: 0.9161 (t) cc_final: 0.8918 (p) REVERT: H 156 HIS cc_start: 0.8801 (t70) cc_final: 0.8439 (t-90) REVERT: I 63 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7713 (ttm-80) REVERT: J 7 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: K 34 TYR cc_start: 0.9113 (m-80) cc_final: 0.8761 (m-10) REVERT: K 104 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7753 (ttm) REVERT: M 68 ARG cc_start: 0.8410 (tpp80) cc_final: 0.7983 (ttp-170) REVERT: M 135 THR cc_start: 0.8500 (m) cc_final: 0.8277 (p) REVERT: O 72 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8496 (tmm) REVERT: O 124 ARG cc_start: 0.8202 (mmt-90) cc_final: 0.7973 (mmt-90) REVERT: O 148 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8420 (mtm) REVERT: P 124 ARG cc_start: 0.8208 (mtp85) cc_final: 0.8000 (mtp85) REVERT: Q 83 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8533 (mm-40) REVERT: Q 124 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8409 (tpp80) REVERT: R 7 GLN cc_start: 0.7982 (mt0) cc_final: 0.7637 (pt0) REVERT: R 60 GLU cc_start: 0.8400 (tp30) cc_final: 0.8096 (mm-30) REVERT: R 83 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8391 (mp10) REVERT: S 11 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8160 (t0) REVERT: T 8 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9086 (pt) REVERT: T 10 GLN cc_start: 0.8340 (tt0) cc_final: 0.8123 (tt0) REVERT: T 11 ASN cc_start: 0.8480 (m-40) cc_final: 0.8071 (t0) REVERT: T 112 GLN cc_start: 0.8520 (tp40) cc_final: 0.8230 (mm-40) REVERT: T 132 PHE cc_start: 0.8007 (t80) cc_final: 0.7794 (t80) REVERT: T 136 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7509 (p-80) REVERT: U 14 THR cc_start: 0.9349 (m) cc_final: 0.9092 (p) REVERT: U 112 GLN cc_start: 0.8307 (tp40) cc_final: 0.8032 (tp40) REVERT: U 171 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8670 (tm-30) REVERT: V 12 TYR cc_start: 0.8794 (t80) cc_final: 0.8319 (t80) REVERT: V 68 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8166 (ttp-170) REVERT: V 79 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6974 (mmp-170) REVERT: V 112 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7815 (tp40) REVERT: W 112 GLN cc_start: 0.8461 (tp40) cc_final: 0.8186 (tp40) REVERT: W 156 HIS cc_start: 0.8634 (t70) cc_final: 0.8213 (t70) REVERT: X 15 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8348 (p0) REVERT: X 64 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8180 (mm-30) REVERT: X 162 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: X 171 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7602 (tm-30) outliers start: 65 outliers final: 28 residues processed: 412 average time/residue: 2.5108 time to fit residues: 1229.0696 Evaluate side-chains 391 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 344 time to evaluate : 7.321 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain C residue 81 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 G residue 7 GLN 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 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 L residue 100 MET 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 O residue 148 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 148 MET 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 8 ILE 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 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 156 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 243 optimal weight: 8.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 HIS R 11 ASN ** 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 = 0.3459 r_free = 0.3459 target = 0.074590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065157 restraints weight = 80636.844| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.29 r_work: 0.3075 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33816 Z= 0.144 Angle : 0.539 12.101 45480 Z= 0.278 Chirality : 0.037 0.231 4872 Planarity : 0.003 0.043 5952 Dihedral : 4.223 46.196 4521 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.57 % Rotamer: Outliers : 1.72 % Allowed : 20.63 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.13), residues: 4080 helix: 3.18 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.82 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 93 HIS 0.010 0.001 HIS L 136 PHE 0.018 0.002 PHE B 132 TYR 0.030 0.002 TYR N 66 ARG 0.010 0.001 ARG Q 56 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 2656) hydrogen bonds : angle 3.49630 ( 7968) covalent geometry : bond 0.00318 (33816) covalent geometry : angle 0.53853 (45480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 3.973 Fit side-chains REVERT: A 56 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6702 (tmt170) REVERT: A 148 MET cc_start: 0.8682 (tpp) cc_final: 0.8303 (mtt) REVERT: B 75 GLN cc_start: 0.9037 (mt0) cc_final: 0.8766 (mt0) REVERT: B 83 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7922 (mm-40) REVERT: C 72 MET cc_start: 0.8699 (tmm) cc_final: 0.8457 (tmt) REVERT: C 112 GLN cc_start: 0.8466 (tp40) cc_final: 0.8253 (mm-40) REVERT: D 64 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8012 (mm-30) REVERT: D 68 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7987 (mtm-85) REVERT: E 11 ASN cc_start: 0.8172 (m-40) cc_final: 0.7682 (t0) REVERT: E 60 GLU cc_start: 0.8627 (tp30) cc_final: 0.8207 (tp30) REVERT: E 83 GLN cc_start: 0.8802 (mm110) cc_final: 0.8529 (mm-40) REVERT: E 148 MET cc_start: 0.8252 (mtp) cc_final: 0.7984 (mtp) REVERT: F 16 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8059 (p) REVERT: F 112 GLN cc_start: 0.8231 (tp40) cc_final: 0.7924 (tp40) REVERT: F 156 HIS cc_start: 0.8841 (t-90) cc_final: 0.8483 (t-90) REVERT: F 171 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 7 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: G 63 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7556 (ttm-80) REVERT: H 135 THR cc_start: 0.9162 (t) cc_final: 0.8892 (p) REVERT: H 156 HIS cc_start: 0.8803 (t70) cc_final: 0.8442 (t-90) REVERT: I 63 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7707 (ttm-80) REVERT: I 125 THR cc_start: 0.8854 (p) cc_final: 0.8649 (p) REVERT: I 148 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8014 (mtm) REVERT: J 7 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: K 34 TYR cc_start: 0.9125 (m-80) cc_final: 0.8740 (m-10) REVERT: L 75 GLN cc_start: 0.8758 (mt0) cc_final: 0.8506 (mt0) REVERT: M 29 GLN cc_start: 0.8395 (tt0) cc_final: 0.7932 (mt0) REVERT: M 68 ARG cc_start: 0.8424 (tpp80) cc_final: 0.7998 (ttp-170) REVERT: M 135 THR cc_start: 0.8503 (m) cc_final: 0.8267 (p) REVERT: O 72 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8498 (tmm) REVERT: O 124 ARG cc_start: 0.8249 (mmt-90) cc_final: 0.8023 (mmt-90) REVERT: O 148 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8300 (mtm) REVERT: P 72 MET cc_start: 0.8970 (tmm) cc_final: 0.8749 (tmt) REVERT: P 124 ARG cc_start: 0.8285 (mtp85) cc_final: 0.8084 (mtp85) REVERT: Q 83 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8446 (mm110) REVERT: Q 124 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8436 (tpp80) REVERT: R 7 GLN cc_start: 0.8078 (mt0) cc_final: 0.7705 (pt0) REVERT: R 60 GLU cc_start: 0.8355 (tp30) cc_final: 0.7943 (tm-30) REVERT: R 83 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8379 (mp10) REVERT: S 11 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8145 (t0) REVERT: T 8 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9154 (pt) REVERT: T 10 GLN cc_start: 0.8352 (tt0) cc_final: 0.8108 (tt0) REVERT: T 11 ASN cc_start: 0.8499 (m-40) cc_final: 0.8103 (t0) REVERT: T 112 GLN cc_start: 0.8529 (tp40) cc_final: 0.8231 (mm-40) REVERT: T 124 ARG cc_start: 0.8608 (ptp-110) cc_final: 0.8400 (ptp-110) REVERT: T 136 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7457 (p-80) REVERT: U 14 THR cc_start: 0.9343 (m) cc_final: 0.9087 (p) REVERT: U 112 GLN cc_start: 0.8305 (tp40) cc_final: 0.8018 (tp40) REVERT: U 171 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: V 12 TYR cc_start: 0.8813 (t80) cc_final: 0.8335 (t80) REVERT: V 68 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8130 (ttp-170) REVERT: V 79 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7032 (mmp-170) REVERT: V 112 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7782 (tp40) REVERT: W 112 GLN cc_start: 0.8476 (tp40) cc_final: 0.8178 (tp40) REVERT: W 156 HIS cc_start: 0.8691 (t70) cc_final: 0.8284 (t70) REVERT: X 15 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8352 (p0) REVERT: X 64 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8165 (mm-30) REVERT: X 104 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8024 (ttp) REVERT: X 171 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7580 (tm-30) outliers start: 60 outliers final: 30 residues processed: 395 average time/residue: 1.8565 time to fit residues: 864.2697 Evaluate side-chains 389 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 342 time to evaluate : 6.238 ------------------------------------------------------------------------------- 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 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 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 F residue 16 VAL Chi-restraints excluded: chain G residue 7 GLN 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 14 THR 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 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 O residue 148 MET Chi-restraints excluded: chain P residue 22 SER 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 8 ILE 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 31 SER Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 104 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 98 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 399 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 chunk 236 optimal weight: 0.0870 chunk 271 optimal weight: 10.0000 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 D 25 ASN D 83 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS L 83 GLN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.075458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066066 restraints weight = 80447.868| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.29 r_work: 0.3100 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33816 Z= 0.124 Angle : 0.539 12.170 45480 Z= 0.279 Chirality : 0.036 0.201 4872 Planarity : 0.004 0.047 5952 Dihedral : 4.080 44.041 4518 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 1.44 % Allowed : 21.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.13), residues: 4080 helix: 3.24 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.77 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 93 HIS 0.005 0.001 HIS J 156 PHE 0.028 0.002 PHE T 132 TYR 0.029 0.002 TYR N 66 ARG 0.011 0.001 ARG W 63 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 2656) hydrogen bonds : angle 3.49106 ( 7968) covalent geometry : bond 0.00272 (33816) covalent geometry : angle 0.53918 (45480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 4.139 Fit side-chains REVERT: A 56 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6665 (tmt170) REVERT: A 148 MET cc_start: 0.8666 (tpp) cc_final: 0.8313 (mtt) REVERT: B 75 GLN cc_start: 0.8992 (mt0) cc_final: 0.8707 (mt0) REVERT: B 83 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7841 (mm-40) REVERT: C 72 MET cc_start: 0.8697 (tmm) cc_final: 0.8462 (tmt) REVERT: C 112 GLN cc_start: 0.8528 (tp40) cc_final: 0.8310 (mm-40) REVERT: D 64 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8025 (mm-30) REVERT: E 11 ASN cc_start: 0.8156 (m-40) cc_final: 0.7697 (t0) REVERT: E 60 GLU cc_start: 0.8617 (tp30) cc_final: 0.8392 (tt0) REVERT: E 63 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7598 (ttm-80) REVERT: E 83 GLN cc_start: 0.8799 (mm110) cc_final: 0.8520 (mm-40) REVERT: E 148 MET cc_start: 0.8234 (mtp) cc_final: 0.7963 (mtp) REVERT: F 16 VAL cc_start: 0.8281 (t) cc_final: 0.8056 (p) REVERT: F 104 MET cc_start: 0.8307 (mmm) cc_final: 0.8061 (mmm) REVERT: F 112 GLN cc_start: 0.8216 (tp40) cc_final: 0.7917 (tp40) REVERT: F 156 HIS cc_start: 0.8887 (t-90) cc_final: 0.8525 (t-90) REVERT: F 171 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8157 (tm-30) REVERT: G 7 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: G 63 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: H 135 THR cc_start: 0.9130 (t) cc_final: 0.8862 (p) REVERT: H 156 HIS cc_start: 0.8801 (t70) cc_final: 0.8452 (t-90) REVERT: I 63 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7710 (ttm-80) REVERT: I 125 THR cc_start: 0.8850 (p) cc_final: 0.8644 (p) REVERT: I 148 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8017 (mtm) REVERT: J 7 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: K 34 TYR cc_start: 0.9139 (m-80) cc_final: 0.8747 (m-10) REVERT: L 75 GLN cc_start: 0.8782 (mt0) cc_final: 0.8509 (mt0) REVERT: M 29 GLN cc_start: 0.8385 (tt0) cc_final: 0.7872 (mt0) REVERT: M 68 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8022 (ttp-170) REVERT: M 135 THR cc_start: 0.8493 (m) cc_final: 0.8260 (p) REVERT: N 124 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8130 (mtt-85) REVERT: O 72 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8471 (tmm) REVERT: P 124 ARG cc_start: 0.8205 (mtp85) cc_final: 0.8002 (mtp85) REVERT: Q 83 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8437 (mm110) REVERT: Q 124 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8428 (tpp80) REVERT: R 7 GLN cc_start: 0.8104 (mt0) cc_final: 0.7741 (pt0) REVERT: R 83 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8395 (mp10) REVERT: S 11 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8172 (t0) REVERT: T 10 GLN cc_start: 0.8336 (tt0) cc_final: 0.8112 (tt0) REVERT: T 11 ASN cc_start: 0.8491 (m-40) cc_final: 0.8090 (t0) REVERT: T 112 GLN cc_start: 0.8507 (tp40) cc_final: 0.8204 (mm-40) REVERT: T 136 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8281 (p90) REVERT: U 112 GLN cc_start: 0.8297 (tp40) cc_final: 0.8010 (tp40) REVERT: U 171 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: V 68 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8134 (ttp-170) REVERT: V 79 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6966 (mmp-170) REVERT: V 112 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7790 (tp40) REVERT: V 124 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8418 (mmt90) REVERT: W 112 GLN cc_start: 0.8450 (tp40) cc_final: 0.8102 (tp40) REVERT: W 156 HIS cc_start: 0.8680 (t70) cc_final: 0.8270 (t70) REVERT: X 15 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8355 (p0) REVERT: X 64 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8187 (mm-30) REVERT: X 171 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7632 (tm-30) outliers start: 50 outliers final: 27 residues processed: 391 average time/residue: 1.6413 time to fit residues: 754.7573 Evaluate side-chains 376 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 136 HIS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 144 LEU 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 K 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 N residue 13 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 148 MET 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 V residue 79 ARG Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain X residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 345 optimal weight: 0.9980 chunk 303 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 338 optimal weight: 0.0970 chunk 258 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 383 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 349 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN R 29 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066798 restraints weight = 80363.753| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.28 r_work: 0.3118 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 33816 Z= 0.115 Angle : 0.540 11.806 45480 Z= 0.280 Chirality : 0.036 0.242 4872 Planarity : 0.004 0.051 5952 Dihedral : 3.983 37.706 4516 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 1.18 % Allowed : 21.61 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.13), residues: 4080 helix: 3.28 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -1.76 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 93 HIS 0.008 0.001 HIS W 151 PHE 0.027 0.002 PHE T 132 TYR 0.029 0.002 TYR N 66 ARG 0.011 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 2656) hydrogen bonds : angle 3.45906 ( 7968) covalent geometry : bond 0.00248 (33816) covalent geometry : angle 0.54002 (45480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20103.29 seconds wall clock time: 355 minutes 34.29 seconds (21334.29 seconds total)