Starting phenix.real_space_refine on Wed Feb 4 04:57:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khe_62337/02_2026/9khe_62337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khe_62337/02_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_62337/02_2026/9khe_62337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khe_62337/02_2026/9khe_62337.map" model { file = "/net/cci-nas-00/data/ceres_data/9khe_62337/02_2026/9khe_62337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khe_62337/02_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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.19 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: 0.91 Conformation dependent library (CDL) restraints added in 277.4 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: 0.26 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: 1.29 Time building geometry restraints manager: 1.07 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: 0.460 Set stop_for_unknowns flag: 0.010 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: 0.030 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.160 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 covalent geometry : bond 0.00422 ( 8940) covalent geometry : angle 0.81896 (12136) hydrogen bonds : bond 0.16088 ( 510) hydrogen bonds : angle 5.38178 ( 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 : 0.284 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: 0.0926 time to fit residues: 29.8399 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 : 0.234 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4040 r_free = 0.4040 target = 0.187098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116321 restraints weight = 10272.839| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.19 r_work: 0.3083 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8940 Z= 0.141 Angle : 0.584 8.108 12136 Z= 0.311 Chirality : 0.040 0.136 1324 Planarity : 0.004 0.043 1464 Dihedral : 4.475 44.081 1170 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 25.55 % Favored : 72.37 % 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: 0.71 (0.27), residues: 1016 helix: 1.24 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.30 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 134 TYR 0.015 0.001 TYR B 233 PHE 0.027 0.002 PHE A 98 TRP 0.008 0.001 TRP A 235 HIS 0.011 0.002 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8940) covalent geometry : angle 0.58363 (12136) hydrogen bonds : bond 0.05030 ( 510) hydrogen bonds : angle 4.00307 ( 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 257 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.344 Fit side-chains REVERT: A 66 LYS cc_start: 0.7569 (mmtm) cc_final: 0.6865 (mmtm) REVERT: A 85 MET cc_start: 0.8506 (ttm) cc_final: 0.8243 (ttm) REVERT: A 138 ARG cc_start: 0.8510 (ptm160) cc_final: 0.8287 (ptm160) REVERT: A 183 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 245 SER cc_start: 0.8992 (t) cc_final: 0.8701 (p) REVERT: A 301 TYR cc_start: 0.8446 (t80) cc_final: 0.8190 (t80) REVERT: B 66 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7121 (mmtm) REVERT: B 85 MET cc_start: 0.8397 (ttm) cc_final: 0.8137 (ttm) REVERT: B 93 LEU cc_start: 0.8074 (mp) cc_final: 0.7608 (tt) REVERT: B 144 PHE cc_start: 0.8785 (t80) cc_final: 0.8535 (t80) REVERT: B 147 ASP cc_start: 0.8071 (t0) cc_final: 0.7860 (t0) REVERT: B 234 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8880 (p) REVERT: B 240 LYS cc_start: 0.8528 (tptp) cc_final: 0.8252 (tptp) REVERT: B 247 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 85 MET cc_start: 0.8572 (ttm) cc_final: 0.8261 (ttm) REVERT: C 144 PHE cc_start: 0.8761 (t80) cc_final: 0.8137 (t80) REVERT: C 170 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8390 (tp) REVERT: C 231 GLU cc_start: 0.8881 (pt0) cc_final: 0.8554 (pt0) REVERT: C 247 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 281 ASN cc_start: 0.8256 (m-40) cc_final: 0.8019 (m110) REVERT: D 66 LYS cc_start: 0.7956 (mmtp) cc_final: 0.7041 (mmtm) REVERT: D 138 ARG cc_start: 0.8428 (ttt90) cc_final: 0.8157 (ttt-90) REVERT: D 281 ASN cc_start: 0.8137 (m-40) cc_final: 0.7911 (m110) outliers start: 19 outliers final: 12 residues processed: 253 average time/residue: 0.1084 time to fit residues: 36.2895 Evaluate side-chains 234 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4042 r_free = 0.4042 target = 0.187233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114897 restraints weight = 10121.228| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.23 r_work: 0.3086 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8940 Z= 0.129 Angle : 0.544 9.087 12136 Z= 0.288 Chirality : 0.039 0.137 1324 Planarity : 0.004 0.049 1464 Dihedral : 4.323 45.829 1169 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.41 % Allowed : 23.46 % Favored : 74.12 % 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: 1.00 (0.27), residues: 1016 helix: 1.41 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.11 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 covalent geometry : bond 0.00268 ( 8940) covalent geometry : angle 0.54441 (12136) hydrogen bonds : bond 0.04532 ( 510) hydrogen bonds : angle 3.75460 ( 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 249 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8334 (mm-30) REVERT: A 85 MET cc_start: 0.8575 (ttm) cc_final: 0.8295 (ttm) REVERT: A 137 PHE cc_start: 0.7158 (m-80) cc_final: 0.6894 (m-80) REVERT: A 138 ARG cc_start: 0.8494 (ptm160) cc_final: 0.8166 (ptm-80) REVERT: A 245 SER cc_start: 0.8954 (t) cc_final: 0.8694 (p) REVERT: B 61 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8384 (mmtm) REVERT: B 66 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7099 (mmtm) REVERT: B 85 MET cc_start: 0.8486 (ttm) cc_final: 0.8207 (ttm) REVERT: B 93 LEU cc_start: 0.8169 (mp) cc_final: 0.7759 (tt) REVERT: B 147 ASP cc_start: 0.8297 (t0) cc_final: 0.8007 (t0) REVERT: B 234 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8793 (p) REVERT: B 247 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 85 MET cc_start: 0.8625 (ttm) cc_final: 0.8324 (ttm) REVERT: C 115 GLN cc_start: 0.7792 (tp40) cc_final: 0.7555 (mm-40) REVERT: C 138 ARG cc_start: 0.8664 (ttt180) cc_final: 0.8407 (ptm-80) REVERT: C 144 PHE cc_start: 0.8796 (t80) cc_final: 0.8303 (t80) REVERT: C 170 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 64 TRP cc_start: 0.8992 (m-10) cc_final: 0.8523 (m-10) REVERT: D 66 LYS cc_start: 0.7655 (mmtp) cc_final: 0.7096 (mmpt) REVERT: D 93 LEU cc_start: 0.8049 (mp) cc_final: 0.7520 (tt) REVERT: D 138 ARG cc_start: 0.8458 (ttt90) cc_final: 0.8120 (ttt-90) REVERT: D 144 PHE cc_start: 0.8387 (t80) cc_final: 0.8087 (t80) REVERT: D 157 ILE cc_start: 0.8586 (mt) cc_final: 0.8332 (mp) REVERT: D 301 TYR cc_start: 0.8447 (t80) cc_final: 0.8195 (t80) outliers start: 22 outliers final: 13 residues processed: 244 average time/residue: 0.0925 time to fit residues: 30.0344 Evaluate side-chains 228 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 CYS Chi-restraints excluded: chain B residue 169 TYR 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 234 THR Chi-restraints excluded: chain C residue 284 GLU 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: 0.5980 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.183296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110760 restraints weight = 10321.958| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.14 r_work: 0.3036 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8940 Z= 0.197 Angle : 0.590 8.483 12136 Z= 0.310 Chirality : 0.042 0.154 1324 Planarity : 0.004 0.040 1464 Dihedral : 4.314 43.637 1169 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.18 % Allowed : 23.36 % Favored : 73.46 % 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: 0.85 (0.27), residues: 1016 helix: 1.34 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.25 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 138 TYR 0.014 0.002 TYR D 210 PHE 0.028 0.002 PHE A 98 TRP 0.008 0.001 TRP D 154 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 8940) covalent geometry : angle 0.59010 (12136) hydrogen bonds : bond 0.04702 ( 510) hydrogen bonds : angle 3.78670 ( 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 256 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7451 (mmpt) REVERT: A 85 MET cc_start: 0.8725 (ttm) cc_final: 0.8397 (ttm) REVERT: A 138 ARG cc_start: 0.8518 (ptm160) cc_final: 0.8047 (ptm-80) REVERT: A 245 SER cc_start: 0.9064 (t) cc_final: 0.8710 (p) REVERT: A 283 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7638 (mtt90) REVERT: B 61 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8314 (mmtm) REVERT: B 66 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7504 (mmpt) REVERT: B 85 MET cc_start: 0.8734 (ttm) cc_final: 0.8424 (ttm) REVERT: B 138 ARG cc_start: 0.8629 (ttt180) cc_final: 0.8333 (ptm-80) REVERT: B 144 PHE cc_start: 0.8734 (t80) cc_final: 0.8291 (t80) REVERT: B 147 ASP cc_start: 0.8415 (t0) cc_final: 0.8029 (t0) REVERT: B 234 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8858 (p) REVERT: B 247 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8165 (mm-30) REVERT: B 301 TYR cc_start: 0.8531 (t80) cc_final: 0.8303 (t80) REVERT: C 85 MET cc_start: 0.8747 (ttm) cc_final: 0.8406 (ttm) REVERT: C 115 GLN cc_start: 0.7843 (tp40) cc_final: 0.7605 (mm-40) REVERT: C 138 ARG cc_start: 0.8625 (ttt180) cc_final: 0.8377 (ptm-80) REVERT: C 144 PHE cc_start: 0.8795 (t80) cc_final: 0.8379 (t80) REVERT: C 154 TRP cc_start: 0.8004 (m100) cc_final: 0.7692 (m100) REVERT: C 165 GLU cc_start: 0.7935 (tp30) cc_final: 0.7276 (tp30) REVERT: C 170 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8648 (tp) REVERT: C 179 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7357 (ttp-170) REVERT: C 183 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 69 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8541 (mt-10) REVERT: D 138 ARG cc_start: 0.8488 (ttt90) cc_final: 0.8140 (ttt-90) REVERT: D 144 PHE cc_start: 0.8461 (t80) cc_final: 0.8203 (t80) REVERT: D 157 ILE cc_start: 0.8646 (mt) cc_final: 0.8379 (mp) REVERT: D 301 TYR cc_start: 0.8561 (t80) cc_final: 0.8316 (t80) outliers start: 29 outliers final: 23 residues processed: 250 average time/residue: 0.0873 time to fit residues: 28.8626 Evaluate side-chains 239 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 283 ARG 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 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 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 Chi-restraints excluded: chain D residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4038 r_free = 0.4038 target = 0.187045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115101 restraints weight = 10129.290| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.18 r_work: 0.3075 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2345 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= 0.121 Angle : 0.535 8.823 12136 Z= 0.280 Chirality : 0.039 0.136 1324 Planarity : 0.003 0.040 1464 Dihedral : 4.179 45.191 1169 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.40 % Allowed : 23.57 % 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: 1.08 (0.27), residues: 1016 helix: 1.47 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.013 0.001 TYR C 196 PHE 0.016 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 covalent geometry : bond 0.00260 ( 8940) covalent geometry : angle 0.53463 (12136) hydrogen bonds : bond 0.04299 ( 510) hydrogen bonds : angle 3.61817 ( 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 249 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7417 (mmpt) REVERT: A 85 MET cc_start: 0.8704 (ttm) cc_final: 0.8394 (ttm) REVERT: A 138 ARG cc_start: 0.8498 (ptm160) cc_final: 0.8082 (ptm-80) REVERT: A 245 SER cc_start: 0.9045 (t) cc_final: 0.8696 (p) REVERT: A 254 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8088 (tp) REVERT: B 61 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8292 (mmtm) REVERT: B 66 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7540 (mmpt) REVERT: B 85 MET cc_start: 0.8674 (ttm) cc_final: 0.8356 (ttm) REVERT: B 135 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8083 (pt) REVERT: B 138 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8266 (ptm-80) REVERT: B 144 PHE cc_start: 0.8725 (t80) cc_final: 0.8303 (t80) REVERT: B 147 ASP cc_start: 0.8415 (t0) cc_final: 0.8167 (t0) REVERT: B 152 PHE cc_start: 0.7977 (m-10) cc_final: 0.7717 (m-10) REVERT: B 234 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8914 (p) REVERT: B 247 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8208 (mm-30) REVERT: B 289 MET cc_start: 0.8693 (mtp) cc_final: 0.8481 (mtp) REVERT: C 66 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7612 (mmpt) REVERT: C 85 MET cc_start: 0.8673 (ttm) cc_final: 0.8328 (ttm) REVERT: C 115 GLN cc_start: 0.7850 (tp40) cc_final: 0.7586 (mm-40) REVERT: C 134 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8201 (ptm-80) REVERT: C 144 PHE cc_start: 0.8725 (t80) cc_final: 0.8400 (t80) REVERT: C 154 TRP cc_start: 0.7933 (m100) cc_final: 0.7637 (m100) REVERT: C 163 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8225 (mttt) REVERT: C 170 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8501 (tp) REVERT: C 183 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 282 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7949 (tp) REVERT: D 115 GLN cc_start: 0.7910 (tp40) cc_final: 0.7632 (mm-40) REVERT: D 138 ARG cc_start: 0.8463 (ttt90) cc_final: 0.8133 (ttt-90) REVERT: D 157 ILE cc_start: 0.8606 (mt) cc_final: 0.8353 (mp) REVERT: D 282 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7982 (tp) REVERT: D 301 TYR cc_start: 0.8461 (t80) cc_final: 0.8246 (t80) outliers start: 31 outliers final: 19 residues processed: 241 average time/residue: 0.0889 time to fit residues: 28.3473 Evaluate side-chains 235 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 83 THR 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 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 181 VAL Chi-restraints excluded: chain C residue 194 ILE 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 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: 1.9990 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4019 r_free = 0.4019 target = 0.185250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113033 restraints weight = 10203.728| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.21 r_work: 0.3061 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8940 Z= 0.138 Angle : 0.541 9.107 12136 Z= 0.284 Chirality : 0.039 0.134 1324 Planarity : 0.003 0.040 1464 Dihedral : 4.131 44.969 1169 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.95 % Allowed : 23.25 % Favored : 72.81 % 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: 1.08 (0.27), residues: 1016 helix: 1.48 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.014 0.001 TYR D 196 PHE 0.017 0.001 PHE D 71 TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8940) covalent geometry : angle 0.54097 (12136) hydrogen bonds : bond 0.04284 ( 510) hydrogen bonds : angle 3.60208 ( 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 249 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7716 (mmtm) cc_final: 0.7501 (mmpt) REVERT: A 85 MET cc_start: 0.8751 (ttm) cc_final: 0.8447 (ttm) REVERT: A 138 ARG cc_start: 0.8543 (ptm160) cc_final: 0.8103 (ptm-80) REVERT: A 245 SER cc_start: 0.9052 (t) cc_final: 0.8709 (p) REVERT: A 254 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8162 (tp) REVERT: B 61 LYS cc_start: 0.8810 (ptpp) cc_final: 0.8281 (mmtm) REVERT: B 85 MET cc_start: 0.8767 (ttm) cc_final: 0.8455 (ttm) REVERT: B 138 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8254 (ptm-80) REVERT: B 144 PHE cc_start: 0.8717 (t80) cc_final: 0.8308 (t80) REVERT: B 147 ASP cc_start: 0.8378 (t0) cc_final: 0.8087 (t0) REVERT: B 152 PHE cc_start: 0.8024 (m-80) cc_final: 0.7738 (m-10) REVERT: B 234 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8865 (p) REVERT: B 247 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8134 (tp30) REVERT: B 289 MET cc_start: 0.8730 (mtp) cc_final: 0.8522 (mtp) REVERT: B 301 TYR cc_start: 0.8443 (t80) cc_final: 0.8234 (t80) REVERT: C 66 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7677 (mmpt) REVERT: C 85 MET cc_start: 0.8713 (ttm) cc_final: 0.8371 (ttm) REVERT: C 115 GLN cc_start: 0.7900 (tp40) cc_final: 0.7618 (mm-40) REVERT: C 134 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8208 (ptm-80) REVERT: C 138 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8317 (ptm-80) REVERT: C 144 PHE cc_start: 0.8737 (t80) cc_final: 0.8431 (t80) REVERT: C 154 TRP cc_start: 0.8013 (m100) cc_final: 0.7722 (m100) REVERT: C 163 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8193 (mttt) REVERT: C 170 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 183 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 282 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8005 (tp) REVERT: D 115 GLN cc_start: 0.7967 (tp40) cc_final: 0.7672 (mm-40) REVERT: D 138 ARG cc_start: 0.8583 (ttt90) cc_final: 0.8376 (ttt-90) REVERT: D 144 PHE cc_start: 0.8402 (t80) cc_final: 0.8129 (t80) REVERT: D 157 ILE cc_start: 0.8655 (mt) cc_final: 0.8398 (mp) REVERT: D 282 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8020 (tp) outliers start: 36 outliers final: 26 residues processed: 242 average time/residue: 0.0944 time to fit residues: 30.4749 Evaluate side-chains 237 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 175 LEU 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 254 LEU 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 151 CYS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 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 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: 1.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 63 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4035 r_free = 0.4035 target = 0.186743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116157 restraints weight = 10288.737| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.28 r_work: 0.3070 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8940 Z= 0.122 Angle : 0.530 8.265 12136 Z= 0.278 Chirality : 0.039 0.153 1324 Planarity : 0.004 0.040 1464 Dihedral : 4.132 44.819 1169 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.06 % Allowed : 22.26 % 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: 1.15 (0.27), residues: 1016 helix: 1.52 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.03 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.015 0.001 TYR D 196 PHE 0.021 0.001 PHE A 98 TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8940) covalent geometry : angle 0.53014 (12136) hydrogen bonds : bond 0.04157 ( 510) hydrogen bonds : angle 3.56656 ( 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 246 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7481 (mmpt) REVERT: A 69 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8341 (mm-30) REVERT: A 85 MET cc_start: 0.8747 (ttm) cc_final: 0.8437 (ttm) REVERT: A 138 ARG cc_start: 0.8540 (ptm160) cc_final: 0.8167 (ptm-80) REVERT: A 245 SER cc_start: 0.9044 (t) cc_final: 0.8712 (p) REVERT: A 254 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 61 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8298 (mmtm) REVERT: B 85 MET cc_start: 0.8756 (ttm) cc_final: 0.8404 (ttm) REVERT: B 93 LEU cc_start: 0.7954 (mp) cc_final: 0.7575 (tt) REVERT: B 115 GLN cc_start: 0.7693 (tp40) cc_final: 0.7463 (mm-40) REVERT: B 144 PHE cc_start: 0.8711 (t80) cc_final: 0.8312 (t80) REVERT: B 147 ASP cc_start: 0.8465 (t0) cc_final: 0.8155 (t0) REVERT: B 234 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8849 (p) REVERT: B 247 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8160 (tp30) REVERT: B 289 MET cc_start: 0.8737 (mtp) cc_final: 0.8509 (mtp) REVERT: B 301 TYR cc_start: 0.8457 (t80) cc_final: 0.8168 (t80) REVERT: C 66 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7658 (mmpt) REVERT: C 85 MET cc_start: 0.8719 (ttm) cc_final: 0.8367 (ttm) REVERT: C 115 GLN cc_start: 0.7851 (tp40) cc_final: 0.7574 (mm-40) REVERT: C 144 PHE cc_start: 0.8763 (t80) cc_final: 0.8502 (t80) REVERT: C 154 TRP cc_start: 0.7968 (m100) cc_final: 0.7665 (m100) REVERT: C 163 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8190 (mttt) REVERT: C 170 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8520 (tp) REVERT: C 282 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7965 (tp) REVERT: D 115 GLN cc_start: 0.7934 (tp40) cc_final: 0.7640 (mm-40) REVERT: D 144 PHE cc_start: 0.8375 (t80) cc_final: 0.8099 (t80) REVERT: D 157 ILE cc_start: 0.8636 (mt) cc_final: 0.8381 (mp) REVERT: D 282 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7948 (tp) REVERT: D 301 TYR cc_start: 0.8581 (t80) cc_final: 0.8358 (t80) outliers start: 37 outliers final: 28 residues processed: 239 average time/residue: 0.0896 time to fit residues: 28.6774 Evaluate side-chains 237 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 254 LEU 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 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 114 LEU Chi-restraints excluded: chain C residue 151 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4029 r_free = 0.4029 target = 0.186058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115423 restraints weight = 10150.147| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.32 r_work: 0.3036 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8940 Z= 0.140 Angle : 0.559 9.649 12136 Z= 0.293 Chirality : 0.040 0.137 1324 Planarity : 0.004 0.039 1464 Dihedral : 4.131 44.271 1169 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.28 % Allowed : 22.04 % 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: 1.11 (0.27), residues: 1016 helix: 1.50 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.07 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 138 TYR 0.015 0.001 TYR D 196 PHE 0.022 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 covalent geometry : bond 0.00317 ( 8940) covalent geometry : angle 0.55870 (12136) hydrogen bonds : bond 0.04217 ( 510) hydrogen bonds : angle 3.57283 ( 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 250 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7843 (mmtm) cc_final: 0.7585 (mmpt) REVERT: A 69 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8409 (mm-30) REVERT: A 85 MET cc_start: 0.8953 (ttm) cc_final: 0.8627 (ttm) REVERT: A 138 ARG cc_start: 0.8555 (ptm160) cc_final: 0.8271 (ptm-80) REVERT: A 245 SER cc_start: 0.9023 (t) cc_final: 0.8701 (p) REVERT: A 254 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 61 LYS cc_start: 0.8720 (ptpp) cc_final: 0.8272 (mmtm) REVERT: B 66 LYS cc_start: 0.8204 (mmpt) cc_final: 0.7550 (mmtm) REVERT: B 85 MET cc_start: 0.8900 (ttm) cc_final: 0.8536 (ttm) REVERT: B 93 LEU cc_start: 0.7872 (mp) cc_final: 0.7414 (tt) REVERT: B 115 GLN cc_start: 0.7765 (tp40) cc_final: 0.7515 (mm-40) REVERT: B 138 ARG cc_start: 0.8529 (ttt-90) cc_final: 0.8217 (ptm-80) REVERT: B 144 PHE cc_start: 0.8724 (t80) cc_final: 0.8333 (t80) REVERT: B 147 ASP cc_start: 0.8495 (t0) cc_final: 0.8173 (t0) REVERT: B 234 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 301 TYR cc_start: 0.8646 (t80) cc_final: 0.8444 (t80) REVERT: C 66 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7810 (mmpt) REVERT: C 85 MET cc_start: 0.8869 (ttm) cc_final: 0.8503 (ttm) REVERT: C 115 GLN cc_start: 0.7931 (tp40) cc_final: 0.7632 (mm-40) REVERT: C 134 ARG cc_start: 0.8551 (mtm110) cc_final: 0.8332 (ptm-80) REVERT: C 138 ARG cc_start: 0.8624 (ttt180) cc_final: 0.8396 (ptm-80) REVERT: C 144 PHE cc_start: 0.8774 (t80) cc_final: 0.8533 (t80) REVERT: C 154 TRP cc_start: 0.8130 (m100) cc_final: 0.7839 (m100) REVERT: C 163 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8215 (mttt) REVERT: C 170 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8640 (tp) REVERT: C 282 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (tp) REVERT: D 115 GLN cc_start: 0.8000 (tp40) cc_final: 0.7690 (mm-40) REVERT: D 144 PHE cc_start: 0.8420 (t80) cc_final: 0.8140 (t80) REVERT: D 157 ILE cc_start: 0.8763 (mt) cc_final: 0.8505 (mp) REVERT: D 282 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8121 (tp) outliers start: 39 outliers final: 29 residues processed: 243 average time/residue: 0.0981 time to fit residues: 31.7324 Evaluate side-chains 240 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 254 LEU 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 178 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3991 r_free = 0.3991 target = 0.182140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113898 restraints weight = 10157.611| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.23 r_work: 0.3002 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8940 Z= 0.200 Angle : 0.607 9.070 12136 Z= 0.319 Chirality : 0.042 0.144 1324 Planarity : 0.004 0.038 1464 Dihedral : 4.245 44.472 1169 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.40 % Allowed : 22.59 % Favored : 74.01 % 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: 1.01 (0.27), residues: 1016 helix: 1.42 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.00 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.017 0.002 TYR C 210 PHE 0.020 0.002 PHE C 108 TRP 0.009 0.001 TRP C 172 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8940) covalent geometry : angle 0.60685 (12136) hydrogen bonds : bond 0.04577 ( 510) hydrogen bonds : angle 3.70144 ( 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 244 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8378 (mm-30) REVERT: A 85 MET cc_start: 0.8822 (ttm) cc_final: 0.8471 (ttm) REVERT: A 138 ARG cc_start: 0.8577 (ptm160) cc_final: 0.8292 (ptm-80) REVERT: A 245 SER cc_start: 0.8935 (t) cc_final: 0.8639 (p) REVERT: A 254 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8311 (tp) REVERT: B 61 LYS cc_start: 0.8750 (ptpp) cc_final: 0.8285 (mmtm) REVERT: B 66 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7647 (mmtm) REVERT: B 85 MET cc_start: 0.8896 (ttm) cc_final: 0.8524 (ttm) REVERT: B 138 ARG cc_start: 0.8541 (ttt-90) cc_final: 0.8263 (ptm-80) REVERT: B 144 PHE cc_start: 0.8714 (t80) cc_final: 0.8331 (t80) REVERT: B 147 ASP cc_start: 0.8522 (t0) cc_final: 0.8179 (t0) REVERT: B 157 ILE cc_start: 0.8701 (mt) cc_final: 0.8500 (mp) REVERT: B 234 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 66 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7835 (mmpt) REVERT: C 85 MET cc_start: 0.8833 (ttm) cc_final: 0.8453 (ttm) REVERT: C 115 GLN cc_start: 0.7977 (tp40) cc_final: 0.7661 (mm-40) REVERT: C 138 ARG cc_start: 0.8631 (ttt180) cc_final: 0.8406 (ptm-80) REVERT: C 144 PHE cc_start: 0.8772 (t80) cc_final: 0.8535 (t80) REVERT: C 154 TRP cc_start: 0.8169 (m100) cc_final: 0.7205 (m100) REVERT: C 157 ILE cc_start: 0.8761 (mt) cc_final: 0.8553 (mp) REVERT: C 163 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8091 (mttt) REVERT: C 170 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8444 (tt) REVERT: C 180 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8396 (mptt) REVERT: C 282 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8080 (tp) REVERT: C 284 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: D 115 GLN cc_start: 0.8060 (tp40) cc_final: 0.7746 (mm-40) REVERT: D 121 ARG cc_start: 0.6500 (tmt170) cc_final: 0.6253 (tpt-90) REVERT: D 144 PHE cc_start: 0.8445 (t80) cc_final: 0.8191 (t80) REVERT: D 157 ILE cc_start: 0.8796 (mt) cc_final: 0.8575 (mp) outliers start: 31 outliers final: 21 residues processed: 240 average time/residue: 0.0956 time to fit residues: 30.7319 Evaluate side-chains 232 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 234 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 178 VAL 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 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 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 284 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4017 r_free = 0.4017 target = 0.184847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116698 restraints weight = 10207.913| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.11 r_work: 0.3055 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.003 0.041 8940 Z= 0.142 Angle : 0.582 9.203 12136 Z= 0.304 Chirality : 0.040 0.140 1324 Planarity : 0.004 0.038 1464 Dihedral : 4.190 44.370 1169 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.18 % Allowed : 22.92 % 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: 0.95 (0.27), residues: 1016 helix: 1.39 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.016 0.001 TYR B 196 PHE 0.050 0.002 PHE A 98 TRP 0.007 0.001 TRP C 154 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8940) covalent geometry : angle 0.58247 (12136) hydrogen bonds : bond 0.04322 ( 510) hydrogen bonds : angle 3.65725 ( 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 231 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8448 (mm-30) REVERT: A 85 MET cc_start: 0.8984 (ttm) cc_final: 0.8624 (ttm) REVERT: A 98 PHE cc_start: 0.8535 (t80) cc_final: 0.8313 (t80) REVERT: A 138 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8346 (ptm-80) REVERT: A 245 SER cc_start: 0.8973 (t) cc_final: 0.8670 (p) REVERT: A 254 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 61 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8278 (mmtm) REVERT: B 66 LYS cc_start: 0.8285 (mmpt) cc_final: 0.7727 (mmtm) REVERT: B 85 MET cc_start: 0.8999 (ttm) cc_final: 0.8614 (ttm) REVERT: B 93 LEU cc_start: 0.7955 (mp) cc_final: 0.7621 (tt) REVERT: B 138 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8247 (ptm-80) REVERT: B 144 PHE cc_start: 0.8698 (t80) cc_final: 0.8313 (t80) REVERT: B 147 ASP cc_start: 0.8600 (t0) cc_final: 0.8273 (t0) REVERT: B 234 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8893 (p) REVERT: C 66 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7827 (mmpt) REVERT: C 85 MET cc_start: 0.8955 (ttm) cc_final: 0.8581 (ttm) REVERT: C 138 ARG cc_start: 0.8652 (ttt180) cc_final: 0.8423 (ptm-80) REVERT: C 144 PHE cc_start: 0.8750 (t80) cc_final: 0.8513 (t80) REVERT: C 154 TRP cc_start: 0.8291 (m100) cc_final: 0.7352 (m100) REVERT: C 157 ILE cc_start: 0.8841 (mt) cc_final: 0.8543 (mp) REVERT: C 163 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8114 (mttt) REVERT: C 170 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8440 (tt) REVERT: C 229 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8138 (mp0) REVERT: C 284 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: C 301 TYR cc_start: 0.8590 (t80) cc_final: 0.8312 (t80) REVERT: D 115 GLN cc_start: 0.8082 (tp40) cc_final: 0.7737 (mm-40) REVERT: D 138 ARG cc_start: 0.8435 (ptm160) cc_final: 0.8191 (ptm160) REVERT: D 144 PHE cc_start: 0.8423 (t80) cc_final: 0.8152 (t80) REVERT: D 157 ILE cc_start: 0.8861 (mt) cc_final: 0.8630 (mp) outliers start: 29 outliers final: 22 residues processed: 228 average time/residue: 0.0958 time to fit residues: 29.4410 Evaluate side-chains 224 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 234 THR Chi-restraints excluded: chain A residue 254 LEU 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 179 ARG 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 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 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 178 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.184461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115657 restraints weight = 10154.478| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.26 r_work: 0.3031 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8940 Z= 0.144 Angle : 0.575 9.853 12136 Z= 0.301 Chirality : 0.040 0.135 1324 Planarity : 0.004 0.038 1464 Dihedral : 4.182 44.650 1169 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.96 % Allowed : 23.36 % 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: 0.97 (0.27), residues: 1016 helix: 1.39 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.016 0.001 TYR B 196 PHE 0.043 0.002 PHE A 98 TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8940) covalent geometry : angle 0.57512 (12136) hydrogen bonds : bond 0.04304 ( 510) hydrogen bonds : angle 3.65273 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.08 seconds wall clock time: 41 minutes 57.89 seconds (2517.89 seconds total)