Starting phenix.real_space_refine on Thu Jul 2 14:25:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khe_62337/07_2026/9khe_62337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khe_62337/07_2026/9khe_62337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9khe_62337/07_2026/9khe_62337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khe_62337/07_2026/9khe_62337.map" model { file = "/net/cci-nas-00/data/ceres_data/9khe_62337/07_2026/9khe_62337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khe_62337/07_2026/9khe_62337.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.057 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 40 5.16 5 C 5828 2.51 5 N 1384 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 2.10, per 1000 atoms: 0.24 Number of scatterers: 8670 At special positions: 0 Unit cell: (103.95, 103.95, 81.774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 40 16.00 O 1416 8.00 N 1384 7.00 C 5828 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: 0.70 Conformation dependent library (CDL) restraints added in 444.4 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 76.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 62 through 88 removed outlier: 3.698A pdb=" N ALA A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 117 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.807A pdb=" N TYR A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 161 removed outlier: 3.795A pdb=" N ILE A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.668A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 177 through 191 removed outlier: 4.202A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 removed outlier: 3.655A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.526A pdb=" N ILE A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.516A pdb=" N PHE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.683A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 88 removed outlier: 3.675A pdb=" N ALA B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 117 removed outlier: 3.747A pdb=" N ASP B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.585A pdb=" N ILE B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.522A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.795A pdb=" N ILE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.618A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 177 through 191 removed outlier: 4.156A pdb=" N VAL B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 removed outlier: 3.734A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 200 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.545A pdb=" N ILE B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.759A pdb=" N ALA B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.628A pdb=" N MET B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 88 removed outlier: 3.516A pdb=" N ALA C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 117 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.640A pdb=" N HIS C 143 " --> pdb=" O TYR C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.804A pdb=" N ILE C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.650A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 177 through 191 removed outlier: 4.164A pdb=" N VAL C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 226 removed outlier: 3.628A pdb=" N THR C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 224 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.506A pdb=" N ILE C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.513A pdb=" N PHE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 313 removed outlier: 4.275A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 88 removed outlier: 3.652A pdb=" N ALA D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 117 removed outlier: 3.768A pdb=" N ASP D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 142 removed outlier: 3.621A pdb=" N ILE D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 153 through 161 removed outlier: 3.743A pdb=" N ILE D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.629A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 177 through 191 removed outlier: 4.175A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 226 removed outlier: 3.742A pdb=" N THR D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 200 " --> pdb=" O TYR D 196 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.525A pdb=" N ILE D 252 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.533A pdb=" N PHE D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.689A pdb=" N MET D 285 " --> pdb=" O ASN D 281 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA3, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA4, first strand: chain 'D' and resid 240 through 241 510 hydrogen bonds defined for protein. 1458 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: 1.15 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1284 1.32 - 1.44: 2810 1.44 - 1.56: 4778 1.56 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8940 Sorted by residual: bond pdb=" C ILE B 236 " pdb=" N GLY B 237 " ideal model delta sigma weight residual 1.331 1.284 0.046 1.46e-02 4.69e+03 1.01e+01 bond pdb=" C ILE B 236 " pdb=" O ILE B 236 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.19e-02 7.06e+03 8.79e+00 bond pdb=" C THR C 268 " pdb=" O THR C 268 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.26e-02 6.30e+03 6.37e+00 bond pdb=" C LEU A 170 " pdb=" N LEU A 171 " ideal model delta sigma weight residual 1.335 1.303 0.032 1.33e-02 5.65e+03 5.79e+00 bond pdb=" C THR A 268 " pdb=" O THR A 268 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.46e-02 4.69e+03 5.35e+00 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11764 2.00 - 3.99: 301 3.99 - 5.99: 59 5.99 - 7.99: 7 7.99 - 9.98: 5 Bond angle restraints: 12136 Sorted by residual: angle pdb=" N THR D 268 " pdb=" CA THR D 268 " pdb=" C THR D 268 " ideal model delta sigma weight residual 113.18 104.56 8.62 1.33e+00 5.65e-01 4.20e+01 angle pdb=" N THR A 268 " pdb=" CA THR A 268 " pdb=" C THR A 268 " ideal model delta sigma weight residual 113.18 104.75 8.43 1.33e+00 5.65e-01 4.02e+01 angle pdb=" N THR B 268 " pdb=" CA THR B 268 " pdb=" C THR B 268 " ideal model delta sigma weight residual 113.18 105.30 7.88 1.33e+00 5.65e-01 3.51e+01 angle pdb=" N TYR A 274 " pdb=" CA TYR A 274 " pdb=" C TYR A 274 " ideal model delta sigma weight residual 111.36 105.59 5.77 1.09e+00 8.42e-01 2.80e+01 angle pdb=" N TYR C 274 " pdb=" CA TYR C 274 " pdb=" C TYR C 274 " ideal model delta sigma weight residual 111.36 105.69 5.67 1.09e+00 8.42e-01 2.71e+01 ... (remaining 12131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4274 17.95 - 35.90: 658 35.90 - 53.85: 146 53.85 - 71.80: 13 71.80 - 89.75: 9 Dihedral angle restraints: 5100 sinusoidal: 2056 harmonic: 3044 Sorted by residual: dihedral pdb=" CA PRO B 228 " pdb=" C PRO B 228 " pdb=" N GLU B 229 " pdb=" CA GLU B 229 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO D 228 " pdb=" C PRO D 228 " pdb=" N GLU D 229 " pdb=" CA GLU D 229 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " pdb=" CG ASP D 111 " pdb=" OD1 ASP D 111 " ideal model delta sinusoidal sigma weight residual -30.00 -87.24 57.24 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1162 0.064 - 0.128: 148 0.128 - 0.191: 13 0.191 - 0.255: 0 0.255 - 0.319: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA ILE B 236 " pdb=" N ILE B 236 " pdb=" C ILE B 236 " pdb=" CB ILE B 236 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE B 236 " pdb=" CA ILE B 236 " pdb=" CG1 ILE B 236 " pdb=" CG2 ILE B 236 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CB THR C 268 " pdb=" CA THR C 268 " pdb=" OG1 THR C 268 " pdb=" CG2 THR C 268 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1321 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 98 " 0.020 2.00e-02 2.50e+03 2.17e-02 8.22e+00 pdb=" CG PHE A 98 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 98 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 98 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 98 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 98 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 98 " -0.020 2.00e-02 2.50e+03 2.11e-02 7.80e+00 pdb=" CG PHE C 98 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 98 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 98 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 98 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 227 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO A 228 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " 0.036 5.00e-02 4.00e+02 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.77: 1801 2.77 - 3.36: 10163 3.36 - 3.95: 15870 3.95 - 4.55: 22734 4.55 - 5.14: 33672 Nonbonded interactions: 84240 Sorted by model distance: nonbonded pdb=" O SER C 161 " pdb=" OG SER C 161 " model vdw 2.173 3.040 nonbonded pdb=" O SER B 161 " pdb=" OG SER B 161 " model vdw 2.174 3.040 nonbonded pdb=" O SER A 161 " pdb=" OG SER A 161 " model vdw 2.175 3.040 nonbonded pdb=" O SER D 161 " pdb=" OG SER D 161 " model vdw 2.219 3.040 nonbonded pdb=" O ALA A 76 " pdb=" OG SER A 80 " model vdw 2.222 3.040 ... (remaining 84235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 58 through 313) selection = (chain 'B' and resid 58 through 313) selection = chain 'C' selection = chain 'D' } 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: 0.390 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.004 0.061 8940 Z= 0.225 Angle : 0.819 9.985 12136 Z= 0.519 Chirality : 0.043 0.319 1324 Planarity : 0.006 0.066 1464 Dihedral : 17.502 89.748 3156 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.33 % Allowed : 28.40 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.27), residues: 1016 helix: 0.90 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 134 TYR 0.024 0.002 TYR A 196 PHE 0.050 0.002 PHE A 98 TRP 0.033 0.002 TRP B 235 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.23 ( 8940) covalent geometry : angle 0.81896 / 0.52 (12136) hydrogen bonds : bond 0.16088 / 10.45 ( 510) hydrogen bonds : angle 5.38178 / 3.74 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7397 (mmtm) cc_final: 0.7065 (mmtm) REVERT: A 69 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8412 (mm-30) REVERT: A 85 MET cc_start: 0.8143 (ttm) cc_final: 0.7934 (ttm) REVERT: A 184 PHE cc_start: 0.8353 (t80) cc_final: 0.8116 (t80) REVERT: A 190 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7288 (mmtm) REVERT: A 229 GLU cc_start: 0.8737 (mp0) cc_final: 0.8524 (mp0) REVERT: A 301 TYR cc_start: 0.8213 (t80) cc_final: 0.7975 (t80) REVERT: B 66 LYS cc_start: 0.7848 (mmtm) cc_final: 0.6955 (mmtm) REVERT: B 85 MET cc_start: 0.8183 (ttm) cc_final: 0.7945 (ttm) REVERT: B 90 PHE cc_start: 0.8370 (m-80) cc_final: 0.8165 (m-10) REVERT: B 138 ARG cc_start: 0.8664 (ttt90) cc_final: 0.8373 (ttt-90) REVERT: B 144 PHE cc_start: 0.8680 (t80) cc_final: 0.8451 (t80) REVERT: B 173 ILE cc_start: 0.9012 (tp) cc_final: 0.8783 (tp) REVERT: B 190 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7756 (tptt) REVERT: B 247 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 85 MET cc_start: 0.8206 (ttm) cc_final: 0.7898 (ttm) REVERT: C 144 PHE cc_start: 0.8813 (t80) cc_final: 0.8533 (t80) REVERT: C 247 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7582 (mm-30) REVERT: C 281 ASN cc_start: 0.8482 (m-40) cc_final: 0.8116 (m110) REVERT: C 289 MET cc_start: 0.8889 (mtp) cc_final: 0.8669 (mtp) REVERT: D 138 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8120 (ttt-90) REVERT: D 281 ASN cc_start: 0.8142 (m-40) cc_final: 0.7939 (m110) outliers start: 3 outliers final: 2 residues processed: 243 average time/residue: 0.0993 time to fit residues: 32.1784 Evaluate side-chains 220 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain D residue 151 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN B 281 ASN C 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.186210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116509 restraints weight = 10238.812| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.04 r_work: 0.3098 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8940 Z= 0.144 Angle : 0.587 8.188 12136 Z= 0.313 Chirality : 0.040 0.135 1324 Planarity : 0.004 0.042 1464 Dihedral : 4.514 44.964 1170 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.41 % Allowed : 24.67 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.27), residues: 1016 helix: 1.26 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 134 TYR 0.015 0.002 TYR D 78 PHE 0.029 0.002 PHE A 98 TRP 0.008 0.001 TRP A 235 HIS 0.018 0.002 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8940) covalent geometry : angle 0.58739 / 0.31 (12136) hydrogen bonds : bond 0.05068 / 3.23 ( 510) hydrogen bonds : angle 4.00983 / 2.85 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.302 Fit side-chains REVERT: A 66 LYS cc_start: 0.7609 (mmtm) cc_final: 0.6916 (mmtm) REVERT: A 85 MET cc_start: 0.8519 (ttm) cc_final: 0.8243 (ttm) REVERT: A 183 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 245 SER cc_start: 0.8979 (t) cc_final: 0.8668 (p) REVERT: A 301 TYR cc_start: 0.8487 (t80) cc_final: 0.8239 (t80) REVERT: B 85 MET cc_start: 0.8472 (ttm) cc_final: 0.8192 (ttm) REVERT: B 93 LEU cc_start: 0.8076 (mp) cc_final: 0.7628 (tt) REVERT: B 138 ARG cc_start: 0.8644 (ttt90) cc_final: 0.8382 (ttt180) REVERT: B 144 PHE cc_start: 0.8779 (t80) cc_final: 0.8536 (t80) REVERT: B 147 ASP cc_start: 0.8119 (t0) cc_final: 0.7919 (t0) REVERT: B 234 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 240 LYS cc_start: 0.8536 (tptp) cc_final: 0.8257 (tptp) REVERT: B 247 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8094 (mm-30) REVERT: C 85 MET cc_start: 0.8638 (ttm) cc_final: 0.8322 (ttm) REVERT: C 144 PHE cc_start: 0.8768 (t80) cc_final: 0.8137 (t80) REVERT: C 170 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 231 GLU cc_start: 0.8846 (pt0) cc_final: 0.8542 (pt0) REVERT: C 247 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7893 (mm-30) REVERT: C 281 ASN cc_start: 0.8227 (m-40) cc_final: 0.7950 (m110) REVERT: D 66 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7089 (mmtm) REVERT: D 138 ARG cc_start: 0.8453 (ttt90) cc_final: 0.8059 (ttt-90) REVERT: D 281 ASN cc_start: 0.8104 (m-40) cc_final: 0.7884 (m110) outliers start: 22 outliers final: 14 residues processed: 253 average time/residue: 0.0930 time to fit residues: 31.2736 Evaluate side-chains 235 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.0070 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.187038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115301 restraints weight = 10111.886| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.18 r_work: 0.3094 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8940 Z= 0.129 Angle : 0.548 8.953 12136 Z= 0.289 Chirality : 0.039 0.140 1324 Planarity : 0.004 0.049 1464 Dihedral : 4.337 45.609 1169 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.41 % Allowed : 23.68 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.28), residues: 1016 helix: 1.42 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.68 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.014 0.001 TYR B 78 PHE 0.017 0.001 PHE C 137 TRP 0.009 0.001 TRP D 154 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8940) covalent geometry : angle 0.54772 / 0.29 (12136) hydrogen bonds : bond 0.04561 / 2.90 ( 510) hydrogen bonds : angle 3.77376 / 2.68 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8345 (mm-30) REVERT: A 85 MET cc_start: 0.8611 (ttm) cc_final: 0.8343 (ttm) REVERT: A 137 PHE cc_start: 0.7133 (m-80) cc_final: 0.6863 (m-80) REVERT: A 245 SER cc_start: 0.8967 (t) cc_final: 0.8710 (p) REVERT: A 284 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: B 61 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8372 (mmtm) REVERT: B 85 MET cc_start: 0.8508 (ttm) cc_final: 0.8222 (ttm) REVERT: B 93 LEU cc_start: 0.8176 (mp) cc_final: 0.7775 (tt) REVERT: B 138 ARG cc_start: 0.8584 (ttt90) cc_final: 0.8349 (ttt-90) REVERT: B 144 PHE cc_start: 0.8836 (t80) cc_final: 0.8631 (t80) REVERT: B 147 ASP cc_start: 0.8282 (t0) cc_final: 0.7993 (t0) REVERT: B 234 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8798 (p) REVERT: B 247 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8168 (mm-30) REVERT: C 85 MET cc_start: 0.8728 (ttm) cc_final: 0.8439 (ttm) REVERT: C 115 GLN cc_start: 0.7879 (tp40) cc_final: 0.7600 (mm-40) REVERT: C 138 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8411 (ptm-80) REVERT: C 144 PHE cc_start: 0.8802 (t80) cc_final: 0.8322 (t80) REVERT: C 170 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8417 (tp) REVERT: D 64 TRP cc_start: 0.8918 (m-10) cc_final: 0.8479 (m-10) REVERT: D 66 LYS cc_start: 0.7663 (mmtp) cc_final: 0.7069 (mmpt) REVERT: D 93 LEU cc_start: 0.8057 (mp) cc_final: 0.7524 (tt) REVERT: D 138 ARG cc_start: 0.8455 (ttt90) cc_final: 0.8115 (ttt-90) REVERT: D 144 PHE cc_start: 0.8395 (t80) cc_final: 0.8091 (t80) REVERT: D 157 ILE cc_start: 0.8611 (mt) cc_final: 0.8352 (mp) REVERT: D 301 TYR cc_start: 0.8455 (t80) cc_final: 0.8201 (t80) outliers start: 22 outliers final: 11 residues processed: 248 average time/residue: 0.0957 time to fit residues: 32.2085 Evaluate side-chains 231 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.185103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116715 restraints weight = 10288.280| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.39 r_work: 0.3034 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8940 Z= 0.158 Angle : 0.561 8.373 12136 Z= 0.295 Chirality : 0.040 0.143 1324 Planarity : 0.004 0.041 1464 Dihedral : 4.266 43.948 1169 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.85 % Allowed : 23.25 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.28), residues: 1016 helix: 1.40 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.015 0.001 TYR B 78 PHE 0.028 0.002 PHE A 98 TRP 0.008 0.001 TRP D 154 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 8940) covalent geometry : angle 0.56116 / 0.29 (12136) hydrogen bonds : bond 0.04526 / 2.88 ( 510) hydrogen bonds : angle 3.72484 / 2.65 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7578 (mmtm) cc_final: 0.7175 (mmpt) REVERT: A 85 MET cc_start: 0.8696 (ttm) cc_final: 0.8396 (ttm) REVERT: A 138 ARG cc_start: 0.8443 (ptm160) cc_final: 0.8020 (ptm-80) REVERT: A 245 SER cc_start: 0.9049 (t) cc_final: 0.8728 (p) REVERT: A 301 TYR cc_start: 0.8668 (t80) cc_final: 0.8320 (t80) REVERT: B 61 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8361 (mmtm) REVERT: B 66 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7314 (mmtm) REVERT: B 85 MET cc_start: 0.8656 (ttm) cc_final: 0.8371 (ttm) REVERT: B 93 LEU cc_start: 0.8226 (mp) cc_final: 0.8003 (mt) REVERT: B 144 PHE cc_start: 0.8832 (t80) cc_final: 0.8615 (t80) REVERT: B 147 ASP cc_start: 0.8349 (t0) cc_final: 0.7992 (t0) REVERT: B 234 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8873 (p) REVERT: B 247 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 301 TYR cc_start: 0.8417 (t80) cc_final: 0.8168 (t80) REVERT: C 85 MET cc_start: 0.8695 (ttm) cc_final: 0.8357 (ttm) REVERT: C 115 GLN cc_start: 0.7797 (tp40) cc_final: 0.7562 (mm-40) REVERT: C 138 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8373 (ptm-80) REVERT: C 144 PHE cc_start: 0.8784 (t80) cc_final: 0.8378 (t80) REVERT: C 170 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8500 (tp) REVERT: C 183 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8173 (mm-30) REVERT: D 66 LYS cc_start: 0.7539 (mmtp) cc_final: 0.7207 (mmpt) REVERT: D 69 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8504 (mt-10) REVERT: D 138 ARG cc_start: 0.8453 (ttt90) cc_final: 0.8119 (ttt-90) REVERT: D 144 PHE cc_start: 0.8425 (t80) cc_final: 0.8149 (t80) REVERT: D 157 ILE cc_start: 0.8628 (mt) cc_final: 0.8362 (mp) REVERT: D 301 TYR cc_start: 0.8506 (t80) cc_final: 0.8254 (t80) outliers start: 26 outliers final: 21 residues processed: 247 average time/residue: 0.0978 time to fit residues: 31.8820 Evaluate side-chains 235 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.0170 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113719 restraints weight = 10149.124| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.19 r_work: 0.3068 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8940 Z= 0.140 Angle : 0.539 8.859 12136 Z= 0.284 Chirality : 0.040 0.143 1324 Planarity : 0.003 0.039 1464 Dihedral : 4.198 44.845 1169 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.40 % Allowed : 23.03 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 1016 helix: 1.46 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.64 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.016 0.001 TYR B 78 PHE 0.015 0.001 PHE B 71 TRP 0.007 0.001 TRP D 154 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8940) covalent geometry : angle 0.53905 / 0.28 (12136) hydrogen bonds : bond 0.04360 / 2.77 ( 510) hydrogen bonds : angle 3.65427 / 2.59 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7360 (mmpt) REVERT: A 85 MET cc_start: 0.8677 (ttm) cc_final: 0.8360 (ttm) REVERT: A 138 ARG cc_start: 0.8511 (ptm160) cc_final: 0.8186 (ptm-80) REVERT: A 245 SER cc_start: 0.9036 (t) cc_final: 0.8684 (p) REVERT: B 61 LYS cc_start: 0.8844 (ptpp) cc_final: 0.8338 (mmtm) REVERT: B 66 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7318 (mmtm) REVERT: B 85 MET cc_start: 0.8685 (ttm) cc_final: 0.8375 (ttm) REVERT: B 138 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8245 (ptm-80) REVERT: B 144 PHE cc_start: 0.8831 (t80) cc_final: 0.8227 (t80) REVERT: B 147 ASP cc_start: 0.8417 (t0) cc_final: 0.8152 (t0) REVERT: B 152 PHE cc_start: 0.8005 (m-10) cc_final: 0.7741 (m-10) REVERT: B 234 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8892 (p) REVERT: B 247 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 301 TYR cc_start: 0.8438 (t80) cc_final: 0.8162 (t80) REVERT: C 85 MET cc_start: 0.8678 (ttm) cc_final: 0.8341 (ttm) REVERT: C 115 GLN cc_start: 0.7869 (tp40) cc_final: 0.7597 (mm-40) REVERT: C 138 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8349 (ptm-80) REVERT: C 144 PHE cc_start: 0.8739 (t80) cc_final: 0.8403 (t80) REVERT: C 154 TRP cc_start: 0.7943 (m100) cc_final: 0.7660 (m100) REVERT: C 170 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8543 (tp) REVERT: C 183 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8138 (mm-30) REVERT: C 282 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8013 (tp) REVERT: D 66 LYS cc_start: 0.7720 (mmtp) cc_final: 0.7291 (mmpt) REVERT: D 69 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8633 (mt-10) REVERT: D 115 GLN cc_start: 0.7932 (tp40) cc_final: 0.7638 (mm-40) REVERT: D 138 ARG cc_start: 0.8449 (ttt90) cc_final: 0.8125 (ttt-90) REVERT: D 157 ILE cc_start: 0.8623 (mt) cc_final: 0.8364 (mp) REVERT: D 282 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8039 (tp) REVERT: D 301 TYR cc_start: 0.8464 (t80) cc_final: 0.8244 (t80) outliers start: 31 outliers final: 22 residues processed: 241 average time/residue: 0.1031 time to fit residues: 33.2810 Evaluate side-chains 233 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN C 230 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.185108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117866 restraints weight = 10155.043| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.04 r_work: 0.2943 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8940 Z= 0.142 Angle : 0.541 8.940 12136 Z= 0.284 Chirality : 0.040 0.168 1324 Planarity : 0.003 0.038 1464 Dihedral : 4.155 44.789 1169 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.17 % Allowed : 22.81 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 1016 helix: 1.46 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.64 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.015 0.001 TYR A 196 PHE 0.015 0.001 PHE D 71 TRP 0.008 0.001 TRP C 154 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8940) covalent geometry : angle 0.54066 / 0.28 (12136) hydrogen bonds : bond 0.04326 / 2.75 ( 510) hydrogen bonds : angle 3.61825 / 2.57 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7596 (mmpt) REVERT: A 69 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8405 (mm-30) REVERT: A 85 MET cc_start: 0.8899 (ttm) cc_final: 0.8578 (ttm) REVERT: A 138 ARG cc_start: 0.8551 (ptm160) cc_final: 0.8219 (ptm-80) REVERT: A 245 SER cc_start: 0.9025 (t) cc_final: 0.8686 (p) REVERT: B 61 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8298 (mmtm) REVERT: B 66 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7631 (mmpt) REVERT: B 85 MET cc_start: 0.8903 (ttm) cc_final: 0.8574 (ttm) REVERT: B 135 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8114 (pt) REVERT: B 138 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.8190 (ptm-80) REVERT: B 144 PHE cc_start: 0.8911 (t80) cc_final: 0.8378 (t80) REVERT: B 147 ASP cc_start: 0.8481 (t0) cc_final: 0.8215 (t0) REVERT: B 190 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7930 (mmtm) REVERT: B 234 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8894 (p) REVERT: B 247 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8113 (tp30) REVERT: C 66 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7815 (mmpt) REVERT: C 85 MET cc_start: 0.8888 (ttm) cc_final: 0.8543 (ttm) REVERT: C 115 GLN cc_start: 0.8014 (tp40) cc_final: 0.7699 (mm-40) REVERT: C 138 ARG cc_start: 0.8655 (ttt180) cc_final: 0.8328 (ptm-80) REVERT: C 144 PHE cc_start: 0.8785 (t80) cc_final: 0.8483 (t80) REVERT: C 154 TRP cc_start: 0.8110 (m100) cc_final: 0.7854 (m100) REVERT: C 163 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8223 (mttt) REVERT: C 170 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8724 (tp) REVERT: C 183 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7911 (mm-30) REVERT: C 282 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8073 (tp) REVERT: D 69 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8631 (mt-10) REVERT: D 115 GLN cc_start: 0.7923 (tp40) cc_final: 0.7584 (mm-40) REVERT: D 144 PHE cc_start: 0.8425 (t80) cc_final: 0.8142 (t80) REVERT: D 157 ILE cc_start: 0.8783 (mt) cc_final: 0.8552 (mp) REVERT: D 282 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8112 (tp) outliers start: 38 outliers final: 29 residues processed: 248 average time/residue: 0.1080 time to fit residues: 35.7133 Evaluate side-chains 242 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 63 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 98 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN C 230 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.187384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123483 restraints weight = 10274.430| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.31 r_work: 0.3108 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8940 Z= 0.116 Angle : 0.535 9.481 12136 Z= 0.280 Chirality : 0.039 0.138 1324 Planarity : 0.004 0.038 1464 Dihedral : 4.137 45.062 1169 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.40 % Allowed : 23.90 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.27), residues: 1016 helix: 1.54 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.60 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.016 0.001 TYR C 196 PHE 0.017 0.001 PHE D 71 TRP 0.007 0.001 TRP D 154 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 8940) covalent geometry : angle 0.53516 / 0.28 (12136) hydrogen bonds : bond 0.04085 / 2.60 ( 510) hydrogen bonds : angle 3.56507 / 2.52 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7622 (mmpt) REVERT: A 69 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8415 (mm-30) REVERT: A 85 MET cc_start: 0.8961 (ttm) cc_final: 0.8631 (ttm) REVERT: A 138 ARG cc_start: 0.8624 (ptm160) cc_final: 0.8385 (ptm-80) REVERT: A 245 SER cc_start: 0.8960 (t) cc_final: 0.8640 (p) REVERT: B 61 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8287 (mmtm) REVERT: B 66 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7620 (mmpt) REVERT: B 85 MET cc_start: 0.8949 (ttm) cc_final: 0.8572 (ttm) REVERT: B 93 LEU cc_start: 0.7750 (mp) cc_final: 0.7389 (tt) REVERT: B 115 GLN cc_start: 0.7794 (tp40) cc_final: 0.7546 (mm-40) REVERT: B 144 PHE cc_start: 0.8894 (t80) cc_final: 0.8376 (t80) REVERT: B 147 ASP cc_start: 0.8416 (t0) cc_final: 0.8123 (t0) REVERT: B 234 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (p) REVERT: C 66 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7823 (mmpt) REVERT: C 85 MET cc_start: 0.8909 (ttm) cc_final: 0.8538 (ttm) REVERT: C 115 GLN cc_start: 0.7971 (tp40) cc_final: 0.7657 (mm-40) REVERT: C 144 PHE cc_start: 0.8782 (t80) cc_final: 0.8504 (t80) REVERT: C 154 TRP cc_start: 0.8107 (m100) cc_final: 0.7877 (m100) REVERT: C 163 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8209 (mttt) REVERT: C 170 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8646 (tp) REVERT: C 179 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.6484 (mpt180) REVERT: D 115 GLN cc_start: 0.7900 (tp40) cc_final: 0.7554 (mm-40) REVERT: D 144 PHE cc_start: 0.8411 (t80) cc_final: 0.8124 (t80) REVERT: D 157 ILE cc_start: 0.8816 (mt) cc_final: 0.8568 (mp) REVERT: D 282 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8065 (tp) REVERT: D 301 TYR cc_start: 0.8742 (t80) cc_final: 0.8514 (t80) outliers start: 31 outliers final: 21 residues processed: 231 average time/residue: 0.1054 time to fit residues: 32.3906 Evaluate side-chains 223 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN C 230 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.183544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.113686 restraints weight = 10187.183| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.09 r_work: 0.3048 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8940 Z= 0.175 Angle : 0.579 9.455 12136 Z= 0.304 Chirality : 0.041 0.197 1324 Planarity : 0.004 0.037 1464 Dihedral : 4.190 44.499 1169 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.40 % Allowed : 22.92 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 1016 helix: 1.45 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 138 TYR 0.014 0.002 TYR B 196 PHE 0.023 0.002 PHE C 108 TRP 0.008 0.001 TRP C 154 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 8940) covalent geometry : angle 0.57855 / 0.30 (12136) hydrogen bonds : bond 0.04376 / 2.78 ( 510) hydrogen bonds : angle 3.63579 / 2.58 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8428 (mm-30) REVERT: A 85 MET cc_start: 0.8973 (ttm) cc_final: 0.8638 (ttm) REVERT: A 138 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8383 (ptm-80) REVERT: A 245 SER cc_start: 0.8975 (t) cc_final: 0.8661 (p) REVERT: B 61 LYS cc_start: 0.8798 (ptpp) cc_final: 0.8228 (mmtm) REVERT: B 66 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7788 (mmpt) REVERT: B 85 MET cc_start: 0.9015 (ttm) cc_final: 0.8648 (ttm) REVERT: B 93 LEU cc_start: 0.7909 (mp) cc_final: 0.7386 (tt) REVERT: B 138 ARG cc_start: 0.8409 (ttt-90) cc_final: 0.8073 (ptm-80) REVERT: B 144 PHE cc_start: 0.8875 (t80) cc_final: 0.8364 (t80) REVERT: B 147 ASP cc_start: 0.8520 (t0) cc_final: 0.8202 (t0) REVERT: B 234 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8947 (p) REVERT: C 66 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7862 (mmpt) REVERT: C 85 MET cc_start: 0.8959 (ttm) cc_final: 0.8595 (ttm) REVERT: C 115 GLN cc_start: 0.8034 (tp40) cc_final: 0.7710 (mm-40) REVERT: C 138 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8325 (ptm-80) REVERT: C 144 PHE cc_start: 0.8767 (t80) cc_final: 0.8504 (t80) REVERT: C 154 TRP cc_start: 0.8201 (m100) cc_final: 0.7947 (m100) REVERT: C 163 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8122 (mttt) REVERT: C 170 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8795 (tp) REVERT: C 282 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (tp) REVERT: D 115 GLN cc_start: 0.7951 (tp40) cc_final: 0.7598 (mm-40) REVERT: D 144 PHE cc_start: 0.8434 (t80) cc_final: 0.8155 (t80) REVERT: D 157 ILE cc_start: 0.8836 (mt) cc_final: 0.8596 (mp) REVERT: D 282 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8145 (tp) outliers start: 31 outliers final: 23 residues processed: 238 average time/residue: 0.0958 time to fit residues: 30.5801 Evaluate side-chains 233 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN C 230 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.184583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118273 restraints weight = 10128.788| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.49 r_work: 0.3047 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8940 Z= 0.139 Angle : 0.565 9.136 12136 Z= 0.296 Chirality : 0.040 0.182 1324 Planarity : 0.004 0.037 1464 Dihedral : 4.191 44.299 1169 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.51 % Allowed : 22.15 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.28), residues: 1016 helix: 1.46 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 138 TYR 0.015 0.001 TYR B 196 PHE 0.019 0.001 PHE C 108 TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8940) covalent geometry : angle 0.56546 / 0.30 (12136) hydrogen bonds : bond 0.04239 / 2.70 ( 510) hydrogen bonds : angle 3.62605 / 2.56 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.8906 (ttm) cc_final: 0.8556 (ttm) REVERT: A 138 ARG cc_start: 0.8569 (ptm160) cc_final: 0.8335 (ptm-80) REVERT: A 245 SER cc_start: 0.9024 (t) cc_final: 0.8708 (p) REVERT: B 61 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8240 (mmtm) REVERT: B 66 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7721 (mmpt) REVERT: B 85 MET cc_start: 0.8957 (ttm) cc_final: 0.8593 (ttm) REVERT: B 93 LEU cc_start: 0.7894 (mp) cc_final: 0.7492 (tt) REVERT: B 115 GLN cc_start: 0.7719 (tp40) cc_final: 0.7478 (mm-40) REVERT: B 138 ARG cc_start: 0.8423 (ttt-90) cc_final: 0.8084 (ptm-80) REVERT: B 144 PHE cc_start: 0.8924 (t80) cc_final: 0.8420 (t80) REVERT: B 147 ASP cc_start: 0.8486 (t0) cc_final: 0.8147 (t0) REVERT: B 234 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8986 (p) REVERT: C 85 MET cc_start: 0.8814 (ttm) cc_final: 0.8442 (ttm) REVERT: C 115 GLN cc_start: 0.7894 (tp40) cc_final: 0.7601 (mm-40) REVERT: C 144 PHE cc_start: 0.8772 (t80) cc_final: 0.8518 (t80) REVERT: C 154 TRP cc_start: 0.8100 (m100) cc_final: 0.7765 (m100) REVERT: C 170 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8623 (tp) REVERT: C 282 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8062 (tp) REVERT: C 284 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: D 95 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 115 GLN cc_start: 0.7969 (tp40) cc_final: 0.7649 (mm-40) REVERT: D 144 PHE cc_start: 0.8409 (t80) cc_final: 0.8125 (t80) REVERT: D 282 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8096 (tp) outliers start: 32 outliers final: 23 residues processed: 227 average time/residue: 0.0960 time to fit residues: 29.4206 Evaluate side-chains 225 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN C 230 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.183572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113809 restraints weight = 10252.593| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.37 r_work: 0.2904 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8940 Z= 0.182 Angle : 0.600 9.098 12136 Z= 0.316 Chirality : 0.042 0.164 1324 Planarity : 0.004 0.037 1464 Dihedral : 4.258 44.425 1169 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.18 % Allowed : 22.59 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1016 helix: 1.33 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.015 0.002 TYR B 196 PHE 0.020 0.002 PHE A 98 TRP 0.007 0.001 TRP C 154 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8940) covalent geometry : angle 0.60012 / 0.32 (12136) hydrogen bonds : bond 0.04462 / 2.83 ( 510) hydrogen bonds : angle 3.69496 / 2.61 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.8819 (ttm) cc_final: 0.8472 (ttm) REVERT: A 138 ARG cc_start: 0.8597 (ptm160) cc_final: 0.8353 (ptm-80) REVERT: A 245 SER cc_start: 0.9032 (t) cc_final: 0.8726 (p) REVERT: B 61 LYS cc_start: 0.8819 (ptpp) cc_final: 0.8215 (mmtm) REVERT: B 85 MET cc_start: 0.8989 (ttm) cc_final: 0.8636 (ttm) REVERT: B 138 ARG cc_start: 0.8411 (ttt-90) cc_final: 0.8080 (ptm-80) REVERT: B 144 PHE cc_start: 0.8922 (t80) cc_final: 0.8410 (t80) REVERT: B 147 ASP cc_start: 0.8541 (t0) cc_final: 0.8220 (t0) REVERT: B 234 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8891 (p) REVERT: C 66 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7745 (mmpt) REVERT: C 85 MET cc_start: 0.8851 (ttm) cc_final: 0.8492 (ttm) REVERT: C 115 GLN cc_start: 0.7917 (tp40) cc_final: 0.7614 (mm-40) REVERT: C 144 PHE cc_start: 0.8776 (t80) cc_final: 0.8521 (t80) REVERT: C 154 TRP cc_start: 0.8179 (m100) cc_final: 0.7632 (m100) REVERT: C 157 ILE cc_start: 0.8726 (mt) cc_final: 0.8501 (mp) REVERT: C 163 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8095 (mttt) REVERT: C 170 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8485 (tt) REVERT: C 282 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8114 (tp) REVERT: C 284 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: C 301 TYR cc_start: 0.8527 (t80) cc_final: 0.8309 (t80) REVERT: D 95 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 115 GLN cc_start: 0.7998 (tp40) cc_final: 0.7678 (mm-40) REVERT: D 138 ARG cc_start: 0.8500 (ptm160) cc_final: 0.8271 (ptm160) REVERT: D 144 PHE cc_start: 0.8425 (t80) cc_final: 0.8134 (t80) REVERT: D 165 GLU cc_start: 0.7741 (tp30) cc_final: 0.7168 (tp30) REVERT: D 282 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8137 (tp) outliers start: 29 outliers final: 23 residues processed: 228 average time/residue: 0.0868 time to fit residues: 26.9315 Evaluate side-chains 228 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN C 230 ASN D 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.185837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116449 restraints weight = 10167.407| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.04 r_work: 0.3051 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8940 Z= 0.130 Angle : 0.574 9.064 12136 Z= 0.301 Chirality : 0.040 0.162 1324 Planarity : 0.004 0.038 1464 Dihedral : 4.224 44.801 1169 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.29 % Allowed : 22.81 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.28), residues: 1016 helix: 1.41 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.69 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 134 TYR 0.017 0.001 TYR D 196 PHE 0.050 0.002 PHE A 98 TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8940) covalent geometry : angle 0.57379 / 0.30 (12136) hydrogen bonds : bond 0.04192 / 2.67 ( 510) hydrogen bonds : angle 3.64201 / 2.56 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.25 seconds wall clock time: 43 minutes 34.93 seconds (2614.93 seconds total)