Starting phenix.real_space_refine on Tue Nov 18 09:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5n9y_3605/11_2025/5n9y_3605.cif Found real_map, /net/cci-nas-00/data/ceres_data/5n9y_3605/11_2025/5n9y_3605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5n9y_3605/11_2025/5n9y_3605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5n9y_3605/11_2025/5n9y_3605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5n9y_3605/11_2025/5n9y_3605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5n9y_3605/11_2025/5n9y_3605.map" } resolution = 4.2 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 8080 2.51 5 N 2290 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "C" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "D" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Chain: "E" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2567 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 312} Time building chain proxies: 3.52, per 1000 atoms: 0.27 Number of scatterers: 12835 At special positions: 0 Unit cell: (118.69, 118.69, 127.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 2370 8.00 N 2290 7.00 C 8080 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: 1.11 Conformation dependent library (CDL) restraints added in 600.8 milliseconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 56.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 64 through 70 removed outlier: 4.207A pdb=" N ASP A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.927A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 167 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.602A pdb=" N ASN A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 176 " --> pdb=" O GLU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 186 through 213 removed outlier: 3.516A pdb=" N LEU A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 4.626A pdb=" N ASP A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 267 removed outlier: 3.569A pdb=" N GLY A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 4.278A pdb=" N ALA A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.524A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 removed outlier: 3.708A pdb=" N ILE A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 311 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 142 through 170 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.871A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 220 through 277 removed outlier: 3.655A pdb=" N ILE B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 4.021A pdb=" N THR B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 322 removed outlier: 4.171A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 311 " --> pdb=" O CYS B 307 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 59 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 68 through 72 removed outlier: 4.117A pdb=" N GLY C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 4.606A pdb=" N GLU C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 171 Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.825A pdb=" N ASN C 175 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 212 removed outlier: 3.568A pdb=" N LEU C 190 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Proline residue: C 203 - end of helix removed outlier: 4.099A pdb=" N ASP C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 277 removed outlier: 3.664A pdb=" N ALA C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 302 through 325 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 68 through 72 removed outlier: 4.032A pdb=" N GLY D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'D' and resid 142 through 172 Processing helix chain 'D' and resid 186 through 214 removed outlier: 3.599A pdb=" N LEU D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Proline residue: D 203 - end of helix removed outlier: 3.840A pdb=" N ASP D 206 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 277 Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.953A pdb=" N PHE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 324 removed outlier: 4.057A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 311 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 4.347A pdb=" N VAL E 9 " --> pdb=" O LYS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 142 through 170 Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.818A pdb=" N ASP E 174 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN E 175 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 213 removed outlier: 3.554A pdb=" N LEU E 190 " --> pdb=" O PHE E 186 " (cutoff:3.500A) Proline residue: E 203 - end of helix removed outlier: 4.620A pdb=" N ASP E 206 " --> pdb=" O ALA E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 276 removed outlier: 3.793A pdb=" N GLY E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 269 " --> pdb=" O ARG E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 288 removed outlier: 3.732A pdb=" N GLY E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 322 removed outlier: 4.737A pdb=" N VAL E 311 " --> pdb=" O CYS E 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 4.066A pdb=" N ILE A 4 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.029A pdb=" N LYS A 27 " --> pdb=" O MET A 19 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS A 41 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N SER A 118 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 43 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 105 " --> pdb=" O CYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.612A pdb=" N ILE B 4 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.901A pdb=" N LYS B 27 " --> pdb=" O MET B 19 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS B 41 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER B 118 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 43 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ARG B 120 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 45 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 removed outlier: 4.185A pdb=" N ILE C 4 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 35 " --> pdb=" O ILE C 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 28 removed outlier: 3.931A pdb=" N ILE C 116 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 43 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 118 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 120 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 105 " --> pdb=" O CYS C 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.841A pdb=" N ILE D 4 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 16 through 17 removed outlier: 3.592A pdb=" N PHE D 16 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS D 41 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER D 118 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU D 43 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ARG D 120 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU D 45 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'E' and resid 16 through 19 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 82 773 hydrogen bonds defined for protein. 2235 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: 2.12 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4265 1.34 - 1.46: 2240 1.46 - 1.57: 6420 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 13085 Sorted by residual: bond pdb=" CG1 ILE D 93 " pdb=" CD1 ILE D 93 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.08e+00 bond pdb=" C LEU B 61 " pdb=" N LEU B 62 " ideal model delta sigma weight residual 1.339 1.227 0.112 5.57e-02 3.22e+02 4.08e+00 bond pdb=" CB ARG C 78 " pdb=" CG ARG C 78 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.47e+00 bond pdb=" CB ASP C 239 " pdb=" CG ASP C 239 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 bond pdb=" CB TRP B 18 " pdb=" CG TRP B 18 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.31e+00 ... (remaining 13080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 17083 3.08 - 6.17: 579 6.17 - 9.25: 78 9.25 - 12.34: 16 12.34 - 15.42: 4 Bond angle restraints: 17760 Sorted by residual: angle pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" C ARG C 76 " ideal model delta sigma weight residual 108.13 113.89 -5.76 9.00e-01 1.23e+00 4.09e+01 angle pdb=" N ILE E 93 " pdb=" CA ILE E 93 " pdb=" C ILE E 93 " ideal model delta sigma weight residual 106.42 114.25 -7.83 1.51e+00 4.39e-01 2.69e+01 angle pdb=" C LEU A 238 " pdb=" N ASP A 239 " pdb=" CA ASP A 239 " ideal model delta sigma weight residual 121.14 112.63 8.51 1.75e+00 3.27e-01 2.36e+01 angle pdb=" N ILE D 93 " pdb=" CA ILE D 93 " pdb=" C ILE D 93 " ideal model delta sigma weight residual 106.42 113.55 -7.13 1.51e+00 4.39e-01 2.23e+01 angle pdb=" N ILE D 93 " pdb=" CA ILE D 93 " pdb=" CB ILE D 93 " ideal model delta sigma weight residual 112.65 107.98 4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 17755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 7196 17.18 - 34.35: 533 34.35 - 51.53: 116 51.53 - 68.71: 5 68.71 - 85.89: 10 Dihedral angle restraints: 7860 sinusoidal: 3205 harmonic: 4655 Sorted by residual: dihedral pdb=" CA GLY D 95 " pdb=" C GLY D 95 " pdb=" N SER D 96 " pdb=" CA SER D 96 " ideal model delta harmonic sigma weight residual 180.00 149.28 30.72 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA MET D 111 " pdb=" C MET D 111 " pdb=" N ASP D 112 " pdb=" CA ASP D 112 " ideal model delta harmonic sigma weight residual 180.00 149.55 30.45 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA ARG B 210 " pdb=" C ARG B 210 " pdb=" N LEU B 211 " pdb=" CA LEU B 211 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1460 0.071 - 0.141: 460 0.141 - 0.212: 73 0.212 - 0.283: 9 0.283 - 0.353: 3 Chirality restraints: 2005 Sorted by residual: chirality pdb=" CB ILE C 93 " pdb=" CA ILE C 93 " pdb=" CG1 ILE C 93 " pdb=" CG2 ILE C 93 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU C 104 " pdb=" CB LEU C 104 " pdb=" CD1 LEU C 104 " pdb=" CD2 LEU C 104 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 2002 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 76 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 77 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 202 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO E 203 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 203 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 203 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 202 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO B 203 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.044 5.00e-02 4.00e+02 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2625 2.77 - 3.30: 12882 3.30 - 3.83: 22989 3.83 - 4.37: 26135 4.37 - 4.90: 41431 Nonbonded interactions: 106062 Sorted by model distance: nonbonded pdb=" O CYS C 151 " pdb=" OG1 THR C 155 " model vdw 2.233 3.040 nonbonded pdb=" O GLN A 54 " pdb=" OG1 THR A 58 " model vdw 2.244 3.040 nonbonded pdb=" O CYS B 151 " pdb=" OG1 THR B 155 " model vdw 2.249 3.040 nonbonded pdb=" O ARG D 266 " pdb=" OG1 THR D 269 " model vdw 2.263 3.040 nonbonded pdb=" O GLN C 54 " pdb=" OG1 THR C 58 " model vdw 2.267 3.040 ... (remaining 106057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.600 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.008 0.112 13085 Z= 0.346 Angle : 1.295 15.421 17760 Z= 0.674 Chirality : 0.068 0.353 2005 Planarity : 0.009 0.082 2315 Dihedral : 12.872 85.887 4860 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.02 % Allowed : 10.40 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -5.18 (0.15), residues: 1625 helix: -3.34 (0.12), residues: 890 sheet: -2.62 (0.38), residues: 165 loop : -3.52 (0.19), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG A 199 TYR 0.020 0.003 TYR E 268 PHE 0.028 0.004 PHE C 306 TRP 0.031 0.004 TRP D 42 HIS 0.006 0.002 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00773 (13085) covalent geometry : angle 1.29467 (17760) hydrogen bonds : bond 0.10513 ( 773) hydrogen bonds : angle 11.02686 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 413 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8957 (p0) cc_final: 0.8743 (p0) REVERT: A 110 TYR cc_start: 0.8954 (t80) cc_final: 0.8637 (t80) REVERT: A 111 MET cc_start: 0.7796 (ppp) cc_final: 0.7134 (ptm) REVERT: A 178 ASP cc_start: 0.8519 (t70) cc_final: 0.7793 (t70) REVERT: A 227 MET cc_start: 0.8770 (tpt) cc_final: 0.8371 (tpp) REVERT: A 229 ASP cc_start: 0.8656 (p0) cc_final: 0.7887 (p0) REVERT: A 240 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 273 MET cc_start: 0.9140 (ttm) cc_final: 0.8880 (ttm) REVERT: A 278 LEU cc_start: 0.9131 (pp) cc_final: 0.8904 (pp) REVERT: A 305 ILE cc_start: 0.9122 (mt) cc_final: 0.8888 (mm) REVERT: B 16 PHE cc_start: 0.8492 (p90) cc_final: 0.8291 (p90) REVERT: B 65 ASN cc_start: 0.9186 (p0) cc_final: 0.8794 (p0) REVERT: B 132 SER cc_start: 0.9538 (m) cc_final: 0.9247 (p) REVERT: B 156 ASP cc_start: 0.8161 (m-30) cc_final: 0.7927 (t0) REVERT: B 157 HIS cc_start: 0.8028 (m170) cc_final: 0.7312 (m90) REVERT: B 160 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8697 (pt0) REVERT: B 189 LEU cc_start: 0.9014 (pt) cc_final: 0.8056 (tt) REVERT: B 192 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8767 (tmtt) REVERT: B 208 TYR cc_start: 0.8826 (m-10) cc_final: 0.8532 (m-10) REVERT: B 232 ASP cc_start: 0.8917 (m-30) cc_final: 0.8204 (m-30) REVERT: B 254 GLU cc_start: 0.7983 (pp20) cc_final: 0.7656 (pp20) REVERT: B 282 PHE cc_start: 0.8859 (m-80) cc_final: 0.8579 (m-10) REVERT: C 19 MET cc_start: 0.8617 (mmm) cc_final: 0.8325 (mmm) REVERT: C 41 CYS cc_start: 0.8066 (p) cc_final: 0.7818 (p) REVERT: C 68 ASP cc_start: 0.8319 (t70) cc_final: 0.7950 (t0) REVERT: C 123 LYS cc_start: 0.9015 (mtpm) cc_final: 0.8667 (tppp) REVERT: C 132 SER cc_start: 0.9343 (t) cc_final: 0.9098 (p) REVERT: C 157 HIS cc_start: 0.7258 (m170) cc_final: 0.6691 (m-70) REVERT: C 160 GLU cc_start: 0.8684 (pp20) cc_final: 0.8437 (pp20) REVERT: C 163 GLU cc_start: 0.9294 (tp30) cc_final: 0.9017 (tp30) REVERT: C 177 LEU cc_start: 0.9336 (mm) cc_final: 0.9091 (mm) REVERT: C 229 ASP cc_start: 0.8740 (p0) cc_final: 0.8105 (p0) REVERT: C 240 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8208 (mm-30) REVERT: C 259 MET cc_start: 0.9270 (mmt) cc_final: 0.8968 (mmp) REVERT: C 287 PHE cc_start: 0.8639 (m-80) cc_final: 0.8378 (m-80) REVERT: C 326 TRP cc_start: 0.7898 (m100) cc_final: 0.7457 (m100) REVERT: D 18 TRP cc_start: 0.8953 (m100) cc_final: 0.8562 (m100) REVERT: D 46 ASN cc_start: 0.9359 (t0) cc_final: 0.8121 (t0) REVERT: D 49 HIS cc_start: 0.8402 (m170) cc_final: 0.7827 (m-70) REVERT: D 111 MET cc_start: 0.7860 (tmt) cc_final: 0.7485 (tmm) REVERT: D 123 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8881 (mmmm) REVERT: D 151 CYS cc_start: 0.8983 (m) cc_final: 0.8063 (m) REVERT: D 157 HIS cc_start: 0.8106 (m170) cc_final: 0.7518 (m170) REVERT: D 189 LEU cc_start: 0.9294 (pt) cc_final: 0.8341 (tt) REVERT: D 194 LEU cc_start: 0.9722 (tp) cc_final: 0.9117 (tp) REVERT: D 200 TYR cc_start: 0.8490 (m-80) cc_final: 0.8282 (m-10) REVERT: D 227 MET cc_start: 0.8816 (tpt) cc_final: 0.8409 (tpp) REVERT: D 244 CYS cc_start: 0.9214 (m) cc_final: 0.8497 (t) REVERT: D 305 ILE cc_start: 0.9035 (mt) cc_final: 0.8772 (mm) REVERT: E 5 LYS cc_start: 0.9215 (ttmp) cc_final: 0.8824 (ttmm) REVERT: E 64 ASN cc_start: 0.9266 (m-40) cc_final: 0.9052 (m-40) REVERT: E 65 ASN cc_start: 0.9301 (p0) cc_final: 0.9034 (p0) REVERT: E 68 ASP cc_start: 0.8101 (t70) cc_final: 0.7802 (t0) REVERT: E 76 ARG cc_start: 0.8706 (pmt100) cc_final: 0.7859 (ptt180) REVERT: E 132 SER cc_start: 0.9266 (m) cc_final: 0.9053 (p) REVERT: E 151 CYS cc_start: 0.9245 (m) cc_final: 0.9003 (m) REVERT: E 157 HIS cc_start: 0.8365 (m170) cc_final: 0.7654 (m90) REVERT: E 160 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 197 MET cc_start: 0.8978 (ttp) cc_final: 0.8469 (ttp) REVERT: E 253 ASP cc_start: 0.8830 (t70) cc_final: 0.8510 (t70) REVERT: E 261 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7744 (tm-30) REVERT: E 262 ASN cc_start: 0.9467 (m-40) cc_final: 0.8840 (m-40) REVERT: E 273 MET cc_start: 0.8900 (ttm) cc_final: 0.8448 (ttm) outliers start: 28 outliers final: 8 residues processed: 430 average time/residue: 0.1309 time to fit residues: 78.5497 Evaluate side-chains 325 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 317 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 39 HIS A 166 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS C 39 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 166 HIS E 50 HIS E 103 GLN E 166 HIS E 193 GLN E 204 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064378 restraints weight = 46575.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066566 restraints weight = 27950.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068073 restraints weight = 19091.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.069152 restraints weight = 14223.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.069903 restraints weight = 11283.616| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13085 Z= 0.160 Angle : 0.834 8.768 17760 Z= 0.424 Chirality : 0.048 0.214 2005 Planarity : 0.008 0.097 2315 Dihedral : 7.089 83.659 1795 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.36 % Allowed : 5.27 % Favored : 94.37 % 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: -3.25 (0.18), residues: 1625 helix: -1.50 (0.15), residues: 850 sheet: -1.56 (0.45), residues: 135 loop : -3.13 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 184 TYR 0.018 0.002 TYR A 268 PHE 0.029 0.002 PHE A 306 TRP 0.023 0.002 TRP C 146 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00351 (13085) covalent geometry : angle 0.83368 (17760) hydrogen bonds : bond 0.04330 ( 773) hydrogen bonds : angle 6.63102 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 430 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9226 (t0) cc_final: 0.8896 (t0) REVERT: A 65 ASN cc_start: 0.9018 (p0) cc_final: 0.8787 (p0) REVERT: A 105 VAL cc_start: 0.9067 (t) cc_final: 0.8392 (t) REVERT: A 110 TYR cc_start: 0.8859 (t80) cc_final: 0.8599 (t80) REVERT: A 111 MET cc_start: 0.7591 (ppp) cc_final: 0.6814 (ptm) REVERT: A 169 ILE cc_start: 0.9675 (pt) cc_final: 0.9415 (pt) REVERT: A 178 ASP cc_start: 0.8359 (t70) cc_final: 0.7810 (t70) REVERT: A 197 MET cc_start: 0.9016 (mtp) cc_final: 0.7662 (mtp) REVERT: A 200 TYR cc_start: 0.8560 (m-80) cc_final: 0.7869 (m-80) REVERT: A 273 MET cc_start: 0.8936 (ttm) cc_final: 0.7768 (mtp) REVERT: A 305 ILE cc_start: 0.8903 (mt) cc_final: 0.8629 (mm) REVERT: A 307 CYS cc_start: 0.8847 (m) cc_final: 0.8518 (p) REVERT: B 65 ASN cc_start: 0.9114 (p0) cc_final: 0.8824 (p0) REVERT: B 92 CYS cc_start: 0.8153 (t) cc_final: 0.7693 (m) REVERT: B 151 CYS cc_start: 0.9288 (m) cc_final: 0.8815 (m) REVERT: B 157 HIS cc_start: 0.7830 (m170) cc_final: 0.7228 (m170) REVERT: B 160 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8663 (pt0) REVERT: B 189 LEU cc_start: 0.9027 (pt) cc_final: 0.7963 (tt) REVERT: B 192 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8456 (tmtt) REVERT: B 253 ASP cc_start: 0.8614 (t70) cc_final: 0.8371 (t70) REVERT: B 268 TYR cc_start: 0.8969 (t80) cc_final: 0.8754 (t80) REVERT: B 282 PHE cc_start: 0.8834 (m-80) cc_final: 0.8587 (m-10) REVERT: C 18 TRP cc_start: 0.8221 (m100) cc_final: 0.7368 (m100) REVERT: C 68 ASP cc_start: 0.8134 (t70) cc_final: 0.7734 (t0) REVERT: C 107 MET cc_start: 0.8970 (tmm) cc_final: 0.8734 (tmm) REVERT: C 111 MET cc_start: 0.8067 (ppp) cc_final: 0.7775 (ppp) REVERT: C 123 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8656 (tppp) REVERT: C 157 HIS cc_start: 0.7323 (m170) cc_final: 0.6650 (m-70) REVERT: C 160 GLU cc_start: 0.8624 (pp20) cc_final: 0.8389 (pp20) REVERT: C 167 ASP cc_start: 0.8813 (p0) cc_final: 0.8544 (p0) REVERT: C 194 LEU cc_start: 0.9696 (tp) cc_final: 0.9174 (tp) REVERT: C 200 TYR cc_start: 0.8433 (m-80) cc_final: 0.8032 (m-80) REVERT: C 215 ARG cc_start: 0.7746 (mmp80) cc_final: 0.7295 (mmm160) REVERT: C 229 ASP cc_start: 0.8671 (p0) cc_final: 0.8315 (p0) REVERT: C 232 ASP cc_start: 0.8349 (m-30) cc_final: 0.8039 (m-30) REVERT: C 259 MET cc_start: 0.9060 (mmt) cc_final: 0.8793 (mmp) REVERT: C 326 TRP cc_start: 0.7564 (m100) cc_final: 0.7208 (m100) REVERT: D 1 MET cc_start: 0.7628 (ppp) cc_final: 0.7193 (ppp) REVERT: D 18 TRP cc_start: 0.9061 (m100) cc_final: 0.8108 (m100) REVERT: D 46 ASN cc_start: 0.9349 (t0) cc_final: 0.9007 (t0) REVERT: D 76 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8148 (mtp180) REVERT: D 78 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8207 (ttp-110) REVERT: D 92 CYS cc_start: 0.8757 (t) cc_final: 0.8436 (t) REVERT: D 111 MET cc_start: 0.8131 (ttt) cc_final: 0.6357 (ttt) REVERT: D 123 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8853 (mmmm) REVERT: D 125 LEU cc_start: 0.9455 (mp) cc_final: 0.9244 (mp) REVERT: D 151 CYS cc_start: 0.8986 (m) cc_final: 0.8776 (m) REVERT: D 157 HIS cc_start: 0.8097 (m170) cc_final: 0.7710 (m170) REVERT: D 160 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8844 (mt-10) REVERT: D 169 ILE cc_start: 0.9491 (pt) cc_final: 0.9208 (pt) REVERT: D 189 LEU cc_start: 0.9348 (pt) cc_final: 0.8389 (tt) REVERT: D 194 LEU cc_start: 0.9565 (tp) cc_final: 0.8888 (tp) REVERT: D 200 TYR cc_start: 0.8322 (m-80) cc_final: 0.8058 (m-10) REVERT: D 227 MET cc_start: 0.8679 (tpt) cc_final: 0.8320 (tpp) REVERT: D 244 CYS cc_start: 0.8968 (m) cc_final: 0.8497 (t) REVERT: D 260 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8600 (tm-30) REVERT: D 282 PHE cc_start: 0.8558 (m-80) cc_final: 0.8336 (m-80) REVERT: E 5 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8830 (ttmm) REVERT: E 42 TRP cc_start: 0.9015 (t60) cc_final: 0.8517 (t60) REVERT: E 65 ASN cc_start: 0.9196 (p0) cc_final: 0.8938 (p0) REVERT: E 76 ARG cc_start: 0.8245 (ptt-90) cc_final: 0.7411 (mpp80) REVERT: E 92 CYS cc_start: 0.8521 (t) cc_final: 0.8225 (t) REVERT: E 132 SER cc_start: 0.9253 (m) cc_final: 0.9028 (p) REVERT: E 151 CYS cc_start: 0.9180 (m) cc_final: 0.8491 (m) REVERT: E 157 HIS cc_start: 0.8157 (m170) cc_final: 0.6719 (m-70) REVERT: E 160 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8439 (pt0) REVERT: E 169 ILE cc_start: 0.9540 (pt) cc_final: 0.9295 (pt) REVERT: E 200 TYR cc_start: 0.9035 (m-80) cc_final: 0.8784 (m-80) REVERT: E 232 ASP cc_start: 0.8774 (m-30) cc_final: 0.8305 (m-30) REVERT: E 254 GLU cc_start: 0.8706 (pp20) cc_final: 0.8494 (pp20) REVERT: E 257 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8734 (tm-30) REVERT: E 261 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 262 ASN cc_start: 0.9423 (m-40) cc_final: 0.8742 (m-40) outliers start: 5 outliers final: 0 residues processed: 433 average time/residue: 0.1073 time to fit residues: 66.9123 Evaluate side-chains 363 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070734 restraints weight = 47418.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072755 restraints weight = 29862.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074158 restraints weight = 21354.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075166 restraints weight = 16616.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075841 restraints weight = 13713.541| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13085 Z= 0.187 Angle : 0.818 8.360 17760 Z= 0.419 Chirality : 0.048 0.192 2005 Planarity : 0.006 0.063 2315 Dihedral : 6.668 80.503 1795 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % 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: -2.52 (0.19), residues: 1625 helix: -0.84 (0.16), residues: 880 sheet: -1.42 (0.44), residues: 135 loop : -2.91 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 199 TYR 0.017 0.002 TYR A 268 PHE 0.024 0.002 PHE E 306 TRP 0.035 0.002 TRP D 218 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00412 (13085) covalent geometry : angle 0.81827 (17760) hydrogen bonds : bond 0.04142 ( 773) hydrogen bonds : angle 5.97015 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8123 (p90) cc_final: 0.7734 (p90) REVERT: A 46 ASN cc_start: 0.9217 (t0) cc_final: 0.8922 (t0) REVERT: A 65 ASN cc_start: 0.9032 (p0) cc_final: 0.8749 (p0) REVERT: A 110 TYR cc_start: 0.8917 (t80) cc_final: 0.8670 (t80) REVERT: A 111 MET cc_start: 0.7795 (ppp) cc_final: 0.7106 (ptm) REVERT: A 157 HIS cc_start: 0.8120 (m-70) cc_final: 0.7567 (m90) REVERT: A 169 ILE cc_start: 0.9694 (pt) cc_final: 0.9420 (pt) REVERT: A 178 ASP cc_start: 0.8587 (t70) cc_final: 0.8188 (t70) REVERT: A 282 PHE cc_start: 0.8638 (m-80) cc_final: 0.8384 (m-80) REVERT: A 305 ILE cc_start: 0.8925 (mt) cc_final: 0.8676 (mm) REVERT: B 46 ASN cc_start: 0.9200 (t0) cc_final: 0.8683 (t0) REVERT: B 65 ASN cc_start: 0.8989 (p0) cc_final: 0.8601 (p0) REVERT: B 76 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7557 (ptt-90) REVERT: B 92 CYS cc_start: 0.8071 (t) cc_final: 0.7708 (m) REVERT: B 160 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 189 LEU cc_start: 0.9074 (pt) cc_final: 0.8182 (tt) REVERT: B 192 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8491 (tmtt) REVERT: B 197 MET cc_start: 0.9158 (ttm) cc_final: 0.8720 (mmm) REVERT: B 200 TYR cc_start: 0.7846 (m-10) cc_final: 0.7394 (m-10) REVERT: B 268 TYR cc_start: 0.8970 (t80) cc_final: 0.8717 (t80) REVERT: B 278 LEU cc_start: 0.8954 (tt) cc_final: 0.8734 (tt) REVERT: B 282 PHE cc_start: 0.8600 (m-80) cc_final: 0.8251 (m-10) REVERT: C 18 TRP cc_start: 0.8245 (m100) cc_final: 0.7800 (m100) REVERT: C 68 ASP cc_start: 0.8265 (t70) cc_final: 0.7817 (t0) REVERT: C 111 MET cc_start: 0.8099 (ppp) cc_final: 0.7745 (ppp) REVERT: C 123 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8681 (tppp) REVERT: C 157 HIS cc_start: 0.7626 (m170) cc_final: 0.7063 (m-70) REVERT: C 163 GLU cc_start: 0.9011 (tp30) cc_final: 0.8713 (tp30) REVERT: C 176 LEU cc_start: 0.9302 (pp) cc_final: 0.9063 (pp) REVERT: C 201 MET cc_start: 0.8325 (mmt) cc_final: 0.8110 (mmm) REVERT: C 208 TYR cc_start: 0.9012 (m-10) cc_final: 0.8618 (m-10) REVERT: C 229 ASP cc_start: 0.8827 (p0) cc_final: 0.8588 (p0) REVERT: C 259 MET cc_start: 0.9025 (mmt) cc_final: 0.8771 (mmp) REVERT: C 270 MET cc_start: 0.8847 (ttt) cc_final: 0.8349 (ttp) REVERT: D 1 MET cc_start: 0.7573 (ppp) cc_final: 0.7156 (ppp) REVERT: D 18 TRP cc_start: 0.9055 (m100) cc_final: 0.8554 (m100) REVERT: D 46 ASN cc_start: 0.9366 (t0) cc_final: 0.9037 (t0) REVERT: D 50 HIS cc_start: 0.7662 (p-80) cc_final: 0.7449 (p-80) REVERT: D 65 ASN cc_start: 0.9143 (p0) cc_final: 0.8765 (p0) REVERT: D 76 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8106 (mtt180) REVERT: D 78 ARG cc_start: 0.8733 (ttp-110) cc_final: 0.8449 (ttp-110) REVERT: D 92 CYS cc_start: 0.8718 (t) cc_final: 0.8472 (t) REVERT: D 111 MET cc_start: 0.8181 (ttt) cc_final: 0.6574 (ttt) REVERT: D 123 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8875 (mmmm) REVERT: D 157 HIS cc_start: 0.8250 (m170) cc_final: 0.7917 (m170) REVERT: D 189 LEU cc_start: 0.9395 (pt) cc_final: 0.8520 (tt) REVERT: D 192 LYS cc_start: 0.9409 (tttm) cc_final: 0.9107 (tttt) REVERT: D 194 LEU cc_start: 0.9690 (tp) cc_final: 0.8952 (tp) REVERT: D 200 TYR cc_start: 0.8425 (m-80) cc_final: 0.8169 (m-10) REVERT: D 238 LEU cc_start: 0.9690 (pp) cc_final: 0.9483 (pp) REVERT: D 244 CYS cc_start: 0.9034 (m) cc_final: 0.8595 (t) REVERT: D 251 MET cc_start: 0.8323 (mmt) cc_final: 0.8071 (mmt) REVERT: D 260 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8530 (tm-30) REVERT: D 270 MET cc_start: 0.9012 (ttt) cc_final: 0.8751 (ttt) REVERT: D 282 PHE cc_start: 0.8559 (m-80) cc_final: 0.8151 (m-80) REVERT: E 5 LYS cc_start: 0.9118 (ttmm) cc_final: 0.8863 (ttmm) REVERT: E 42 TRP cc_start: 0.9006 (t60) cc_final: 0.8520 (t60) REVERT: E 51 ASP cc_start: 0.8569 (m-30) cc_final: 0.7992 (t0) REVERT: E 65 ASN cc_start: 0.9190 (p0) cc_final: 0.8970 (p0) REVERT: E 132 SER cc_start: 0.9420 (m) cc_final: 0.9144 (p) REVERT: E 157 HIS cc_start: 0.8098 (m170) cc_final: 0.7050 (m-70) REVERT: E 169 ILE cc_start: 0.9599 (pt) cc_final: 0.9332 (pt) REVERT: E 179 GLN cc_start: 0.7965 (mp10) cc_final: 0.6847 (mp10) REVERT: E 232 ASP cc_start: 0.8735 (m-30) cc_final: 0.8347 (m-30) REVERT: E 234 LEU cc_start: 0.9625 (tp) cc_final: 0.9312 (tp) REVERT: E 254 GLU cc_start: 0.8747 (pp20) cc_final: 0.8542 (pp20) REVERT: E 261 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8043 (tm-30) REVERT: E 262 ASN cc_start: 0.9407 (m-40) cc_final: 0.8570 (m110) REVERT: E 270 MET cc_start: 0.9220 (tpt) cc_final: 0.8907 (tpt) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.0995 time to fit residues: 58.9901 Evaluate side-chains 327 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN E 31 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071746 restraints weight = 47376.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073779 restraints weight = 29648.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075202 restraints weight = 21108.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076209 restraints weight = 16410.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076941 restraints weight = 13516.739| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13085 Z= 0.173 Angle : 0.812 9.029 17760 Z= 0.411 Chirality : 0.049 0.221 2005 Planarity : 0.006 0.059 2315 Dihedral : 6.530 77.013 1795 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.14 % Allowed : 4.33 % Favored : 95.52 % 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: -1.94 (0.20), residues: 1625 helix: -0.21 (0.17), residues: 845 sheet: -1.33 (0.44), residues: 135 loop : -2.74 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.015 0.002 TYR A 268 PHE 0.024 0.002 PHE D 306 TRP 0.041 0.002 TRP B 146 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00387 (13085) covalent geometry : angle 0.81233 (17760) hydrogen bonds : bond 0.04046 ( 773) hydrogen bonds : angle 5.68399 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 420 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9198 (t0) cc_final: 0.8952 (t0) REVERT: A 65 ASN cc_start: 0.8977 (p0) cc_final: 0.8709 (p0) REVERT: A 110 TYR cc_start: 0.8837 (t80) cc_final: 0.8437 (t80) REVERT: A 178 ASP cc_start: 0.8576 (t70) cc_final: 0.8029 (t70) REVERT: A 273 MET cc_start: 0.8400 (mtp) cc_final: 0.8066 (mtm) REVERT: A 282 PHE cc_start: 0.8612 (m-80) cc_final: 0.8370 (m-80) REVERT: A 305 ILE cc_start: 0.8952 (mt) cc_final: 0.8708 (mm) REVERT: B 1 MET cc_start: 0.4667 (ppp) cc_final: 0.3616 (ppp) REVERT: B 46 ASN cc_start: 0.9205 (t0) cc_final: 0.8747 (t0) REVERT: B 65 ASN cc_start: 0.8912 (p0) cc_final: 0.8448 (p0) REVERT: B 92 CYS cc_start: 0.8061 (t) cc_final: 0.7649 (m) REVERT: B 160 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8762 (pt0) REVERT: B 189 LEU cc_start: 0.9078 (pt) cc_final: 0.8134 (tt) REVERT: B 192 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8556 (tmtt) REVERT: B 197 MET cc_start: 0.9181 (ttm) cc_final: 0.8570 (tpp) REVERT: B 200 TYR cc_start: 0.7704 (m-10) cc_final: 0.7103 (m-10) REVERT: B 219 MET cc_start: 0.8474 (mmm) cc_final: 0.8229 (mmm) REVERT: B 232 ASP cc_start: 0.8577 (m-30) cc_final: 0.8367 (m-30) REVERT: B 270 MET cc_start: 0.8702 (ttt) cc_final: 0.8483 (ttt) REVERT: B 273 MET cc_start: 0.9172 (mtp) cc_final: 0.8922 (mtt) REVERT: B 282 PHE cc_start: 0.8482 (m-80) cc_final: 0.8249 (m-10) REVERT: C 18 TRP cc_start: 0.8269 (m100) cc_final: 0.7911 (m100) REVERT: C 46 ASN cc_start: 0.9072 (t0) cc_final: 0.8865 (t0) REVERT: C 68 ASP cc_start: 0.8291 (t70) cc_final: 0.7824 (t0) REVERT: C 123 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8707 (tppp) REVERT: C 157 HIS cc_start: 0.7624 (m170) cc_final: 0.7136 (m-70) REVERT: C 208 TYR cc_start: 0.8808 (m-10) cc_final: 0.8270 (m-80) REVERT: C 229 ASP cc_start: 0.8855 (p0) cc_final: 0.8630 (p0) REVERT: C 240 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 259 MET cc_start: 0.8980 (mmt) cc_final: 0.8776 (mmp) REVERT: C 270 MET cc_start: 0.8849 (ttt) cc_final: 0.8340 (ttm) REVERT: C 326 TRP cc_start: 0.7492 (m100) cc_final: 0.7026 (m100) REVERT: D 1 MET cc_start: 0.7542 (ppp) cc_final: 0.7083 (ppp) REVERT: D 18 TRP cc_start: 0.8988 (m100) cc_final: 0.8504 (m100) REVERT: D 46 ASN cc_start: 0.9367 (t0) cc_final: 0.9042 (t0) REVERT: D 50 HIS cc_start: 0.7913 (p-80) cc_final: 0.7463 (p90) REVERT: D 65 ASN cc_start: 0.9164 (p0) cc_final: 0.8838 (p0) REVERT: D 76 ARG cc_start: 0.8897 (mtp85) cc_final: 0.8114 (mtm180) REVERT: D 78 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8377 (ttp-110) REVERT: D 111 MET cc_start: 0.8004 (ttt) cc_final: 0.6618 (ttt) REVERT: D 123 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8862 (mmmm) REVERT: D 157 HIS cc_start: 0.8175 (m170) cc_final: 0.7771 (m90) REVERT: D 170 ILE cc_start: 0.9243 (tp) cc_final: 0.8680 (mm) REVERT: D 194 LEU cc_start: 0.9723 (tp) cc_final: 0.9138 (tp) REVERT: D 200 TYR cc_start: 0.8613 (m-80) cc_final: 0.7931 (m-80) REVERT: D 227 MET cc_start: 0.8491 (tpp) cc_final: 0.8147 (tpt) REVERT: D 244 CYS cc_start: 0.9040 (m) cc_final: 0.8535 (t) REVERT: D 245 ILE cc_start: 0.9430 (pt) cc_final: 0.9193 (pt) REVERT: D 260 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 275 MET cc_start: 0.9013 (mmm) cc_final: 0.8715 (mmm) REVERT: D 278 LEU cc_start: 0.8892 (tt) cc_final: 0.8168 (tt) REVERT: D 282 PHE cc_start: 0.8598 (m-80) cc_final: 0.8091 (m-80) REVERT: E 5 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8888 (ttmm) REVERT: E 18 TRP cc_start: 0.7841 (m-10) cc_final: 0.7503 (m-10) REVERT: E 65 ASN cc_start: 0.9161 (p0) cc_final: 0.8899 (p0) REVERT: E 132 SER cc_start: 0.9426 (m) cc_final: 0.9137 (p) REVERT: E 157 HIS cc_start: 0.8008 (m170) cc_final: 0.7646 (m-70) REVERT: E 161 PHE cc_start: 0.8945 (t80) cc_final: 0.8722 (t80) REVERT: E 169 ILE cc_start: 0.9631 (pt) cc_final: 0.9356 (pt) REVERT: E 179 GLN cc_start: 0.8353 (mp10) cc_final: 0.7421 (mp10) REVERT: E 197 MET cc_start: 0.8971 (ttm) cc_final: 0.8186 (ttm) REVERT: E 232 ASP cc_start: 0.8657 (m-30) cc_final: 0.8193 (m-30) REVERT: E 257 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8725 (tm-30) REVERT: E 261 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8116 (tm-30) REVERT: E 262 ASN cc_start: 0.9327 (m-40) cc_final: 0.8520 (m110) REVERT: E 270 MET cc_start: 0.9141 (tpt) cc_final: 0.8926 (tpt) outliers start: 2 outliers final: 1 residues processed: 422 average time/residue: 0.1031 time to fit residues: 64.0270 Evaluate side-chains 328 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063045 restraints weight = 48255.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065094 restraints weight = 29818.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066514 restraints weight = 20822.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067521 restraints weight = 15827.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068245 restraints weight = 12825.281| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13085 Z= 0.184 Angle : 0.820 10.146 17760 Z= 0.414 Chirality : 0.049 0.189 2005 Planarity : 0.006 0.054 2315 Dihedral : 6.430 77.928 1795 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -1.72 (0.20), residues: 1625 helix: 0.00 (0.17), residues: 845 sheet: -1.71 (0.38), residues: 165 loop : -2.58 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 184 TYR 0.014 0.002 TYR A 268 PHE 0.031 0.002 PHE B 306 TRP 0.047 0.002 TRP D 218 HIS 0.010 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00414 (13085) covalent geometry : angle 0.82014 (17760) hydrogen bonds : bond 0.03934 ( 773) hydrogen bonds : angle 5.51667 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9184 (t0) cc_final: 0.8948 (t0) REVERT: A 65 ASN cc_start: 0.9013 (p0) cc_final: 0.8688 (p0) REVERT: A 110 TYR cc_start: 0.8975 (t80) cc_final: 0.8621 (t80) REVERT: A 111 MET cc_start: 0.8529 (ptm) cc_final: 0.6579 (ptm) REVERT: A 178 ASP cc_start: 0.8430 (t70) cc_final: 0.7920 (t70) REVERT: A 282 PHE cc_start: 0.8636 (m-80) cc_final: 0.8389 (m-80) REVERT: A 305 ILE cc_start: 0.8995 (mt) cc_final: 0.8753 (mm) REVERT: B 1 MET cc_start: 0.4840 (ppp) cc_final: 0.3746 (ppp) REVERT: B 46 ASN cc_start: 0.9203 (t0) cc_final: 0.8817 (t0) REVERT: B 160 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8684 (mt-10) REVERT: B 189 LEU cc_start: 0.9028 (pt) cc_final: 0.8172 (tt) REVERT: B 192 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8514 (tmtt) REVERT: B 197 MET cc_start: 0.8802 (ttm) cc_final: 0.8385 (tpp) REVERT: B 232 ASP cc_start: 0.8518 (m-30) cc_final: 0.8315 (m-30) REVERT: B 273 MET cc_start: 0.9179 (mtp) cc_final: 0.8957 (mtt) REVERT: C 18 TRP cc_start: 0.8432 (m100) cc_final: 0.8083 (m100) REVERT: C 46 ASN cc_start: 0.9094 (t0) cc_final: 0.8884 (t0) REVERT: C 68 ASP cc_start: 0.8223 (t70) cc_final: 0.7990 (t0) REVERT: C 123 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8732 (tppp) REVERT: C 157 HIS cc_start: 0.7607 (m170) cc_final: 0.7046 (m-70) REVERT: C 176 LEU cc_start: 0.9421 (pp) cc_final: 0.9113 (pp) REVERT: C 197 MET cc_start: 0.8999 (tpp) cc_final: 0.8778 (tpp) REVERT: C 208 TYR cc_start: 0.8735 (m-10) cc_final: 0.8368 (m-80) REVERT: C 229 ASP cc_start: 0.8759 (p0) cc_final: 0.8501 (p0) REVERT: C 240 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 270 MET cc_start: 0.8872 (ttt) cc_final: 0.8449 (ttp) REVERT: D 1 MET cc_start: 0.7542 (ppp) cc_final: 0.6971 (ppp) REVERT: D 18 TRP cc_start: 0.8902 (m100) cc_final: 0.8344 (m100) REVERT: D 46 ASN cc_start: 0.9330 (t0) cc_final: 0.9048 (t0) REVERT: D 65 ASN cc_start: 0.9170 (p0) cc_final: 0.8946 (p0) REVERT: D 78 ARG cc_start: 0.8789 (ttp-110) cc_final: 0.8027 (ttp-110) REVERT: D 92 CYS cc_start: 0.8576 (t) cc_final: 0.8364 (t) REVERT: D 111 MET cc_start: 0.8069 (ttt) cc_final: 0.7392 (ttt) REVERT: D 123 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8902 (mmmm) REVERT: D 157 HIS cc_start: 0.8225 (m170) cc_final: 0.7598 (m90) REVERT: D 189 LEU cc_start: 0.9322 (pp) cc_final: 0.8602 (tt) REVERT: D 194 LEU cc_start: 0.9711 (tp) cc_final: 0.9096 (tp) REVERT: D 200 TYR cc_start: 0.8479 (m-80) cc_final: 0.7707 (m-80) REVERT: D 244 CYS cc_start: 0.9126 (m) cc_final: 0.8538 (t) REVERT: D 254 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 270 MET cc_start: 0.8896 (ttt) cc_final: 0.8628 (ttt) REVERT: D 275 MET cc_start: 0.8944 (mmm) cc_final: 0.8709 (mmm) REVERT: D 278 LEU cc_start: 0.9108 (tt) cc_final: 0.8405 (tt) REVERT: D 282 PHE cc_start: 0.8752 (m-80) cc_final: 0.8377 (m-80) REVERT: E 5 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8757 (ttmm) REVERT: E 18 TRP cc_start: 0.7593 (m-10) cc_final: 0.7172 (m-10) REVERT: E 51 ASP cc_start: 0.8503 (m-30) cc_final: 0.8293 (t0) REVERT: E 65 ASN cc_start: 0.9064 (p0) cc_final: 0.8818 (p0) REVERT: E 123 LYS cc_start: 0.9251 (tptt) cc_final: 0.8743 (tppt) REVERT: E 132 SER cc_start: 0.9419 (m) cc_final: 0.9134 (p) REVERT: E 169 ILE cc_start: 0.9634 (pt) cc_final: 0.9286 (pt) REVERT: E 179 GLN cc_start: 0.8321 (mp10) cc_final: 0.7486 (mp10) REVERT: E 261 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 262 ASN cc_start: 0.9306 (m-40) cc_final: 0.8665 (m-40) REVERT: E 270 MET cc_start: 0.9084 (tpt) cc_final: 0.8850 (tpt) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1020 time to fit residues: 60.0348 Evaluate side-chains 327 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065546 restraints weight = 47243.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067665 restraints weight = 29620.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069146 restraints weight = 20927.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070206 restraints weight = 15983.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071002 restraints weight = 12994.030| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13085 Z= 0.145 Angle : 0.817 11.077 17760 Z= 0.402 Chirality : 0.048 0.219 2005 Planarity : 0.005 0.057 2315 Dihedral : 6.302 77.990 1795 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -1.47 (0.20), residues: 1625 helix: 0.24 (0.17), residues: 845 sheet: -1.52 (0.38), residues: 165 loop : -2.54 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 184 TYR 0.014 0.002 TYR B 110 PHE 0.028 0.002 PHE B 306 TRP 0.050 0.002 TRP B 146 HIS 0.007 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00327 (13085) covalent geometry : angle 0.81712 (17760) hydrogen bonds : bond 0.03754 ( 773) hydrogen bonds : angle 5.35224 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7991 (p90) cc_final: 0.7760 (p90) REVERT: A 31 ASN cc_start: 0.8088 (m110) cc_final: 0.7738 (t0) REVERT: A 46 ASN cc_start: 0.9197 (t0) cc_final: 0.8941 (t0) REVERT: A 65 ASN cc_start: 0.8959 (p0) cc_final: 0.8591 (p0) REVERT: A 110 TYR cc_start: 0.8753 (t80) cc_final: 0.8377 (t80) REVERT: A 111 MET cc_start: 0.8232 (ptm) cc_final: 0.6920 (ptm) REVERT: A 169 ILE cc_start: 0.9636 (pt) cc_final: 0.9395 (pt) REVERT: A 178 ASP cc_start: 0.8451 (t70) cc_final: 0.7876 (t70) REVERT: A 305 ILE cc_start: 0.8919 (mt) cc_final: 0.8683 (mm) REVERT: B 1 MET cc_start: 0.4799 (ppp) cc_final: 0.3733 (ppp) REVERT: B 46 ASN cc_start: 0.9237 (t0) cc_final: 0.8844 (t0) REVERT: B 65 ASN cc_start: 0.8665 (p0) cc_final: 0.8036 (p0) REVERT: B 160 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8648 (mt-10) REVERT: B 192 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8427 (tmtt) REVERT: B 197 MET cc_start: 0.8904 (ttm) cc_final: 0.8256 (ttm) REVERT: B 259 MET cc_start: 0.8556 (ttp) cc_final: 0.8188 (ppp) REVERT: B 275 MET cc_start: 0.8446 (tpt) cc_final: 0.7721 (tpt) REVERT: C 68 ASP cc_start: 0.8172 (t70) cc_final: 0.7934 (t0) REVERT: C 123 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8766 (tppp) REVERT: C 160 GLU cc_start: 0.8376 (pm20) cc_final: 0.8123 (pm20) REVERT: C 197 MET cc_start: 0.8605 (tpp) cc_final: 0.8231 (tpp) REVERT: C 200 TYR cc_start: 0.8435 (m-80) cc_final: 0.8079 (m-80) REVERT: C 208 TYR cc_start: 0.8696 (m-10) cc_final: 0.8307 (m-80) REVERT: C 229 ASP cc_start: 0.8720 (p0) cc_final: 0.8429 (p0) REVERT: C 270 MET cc_start: 0.8800 (ttt) cc_final: 0.8290 (ttp) REVERT: C 326 TRP cc_start: 0.7479 (m100) cc_final: 0.6619 (m100) REVERT: D 1 MET cc_start: 0.7474 (ppp) cc_final: 0.6916 (ppp) REVERT: D 18 TRP cc_start: 0.8730 (m100) cc_final: 0.8426 (m100) REVERT: D 46 ASN cc_start: 0.9288 (t0) cc_final: 0.9067 (t0) REVERT: D 65 ASN cc_start: 0.9019 (p0) cc_final: 0.8792 (p0) REVERT: D 78 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8200 (ttp-110) REVERT: D 92 CYS cc_start: 0.8466 (t) cc_final: 0.8228 (t) REVERT: D 111 MET cc_start: 0.8066 (ttt) cc_final: 0.7045 (ttt) REVERT: D 157 HIS cc_start: 0.8101 (m-70) cc_final: 0.7426 (m90) REVERT: D 194 LEU cc_start: 0.9716 (tp) cc_final: 0.9164 (tp) REVERT: D 200 TYR cc_start: 0.8213 (m-80) cc_final: 0.7626 (m-80) REVERT: D 219 MET cc_start: 0.7934 (mtm) cc_final: 0.7623 (mtm) REVERT: D 244 CYS cc_start: 0.8988 (m) cc_final: 0.8420 (t) REVERT: D 245 ILE cc_start: 0.9480 (pt) cc_final: 0.9245 (pt) REVERT: D 278 LEU cc_start: 0.8961 (tt) cc_final: 0.8280 (tt) REVERT: D 282 PHE cc_start: 0.8702 (m-80) cc_final: 0.8466 (m-80) REVERT: E 5 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8720 (ttmm) REVERT: E 65 ASN cc_start: 0.8955 (p0) cc_final: 0.8701 (p0) REVERT: E 132 SER cc_start: 0.9335 (m) cc_final: 0.8980 (p) REVERT: E 157 HIS cc_start: 0.8129 (m-70) cc_final: 0.7584 (m90) REVERT: E 169 ILE cc_start: 0.9640 (pt) cc_final: 0.9356 (pt) REVERT: E 197 MET cc_start: 0.8756 (ttm) cc_final: 0.7979 (ttm) REVERT: E 232 ASP cc_start: 0.8422 (m-30) cc_final: 0.8209 (m-30) REVERT: E 261 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 262 ASN cc_start: 0.9241 (m-40) cc_final: 0.8642 (m-40) REVERT: E 273 MET cc_start: 0.8446 (ttm) cc_final: 0.8196 (ttm) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.0945 time to fit residues: 58.6497 Evaluate side-chains 334 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073648 restraints weight = 46724.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.075682 restraints weight = 29763.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077110 restraints weight = 21307.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078119 restraints weight = 16567.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078854 restraints weight = 13643.988| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13085 Z= 0.151 Angle : 0.820 10.701 17760 Z= 0.407 Chirality : 0.048 0.275 2005 Planarity : 0.005 0.052 2315 Dihedral : 6.235 78.112 1795 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -1.33 (0.20), residues: 1625 helix: 0.35 (0.18), residues: 845 sheet: -1.44 (0.38), residues: 165 loop : -2.48 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 184 TYR 0.016 0.002 TYR B 110 PHE 0.050 0.003 PHE C 306 TRP 0.050 0.002 TRP D 218 HIS 0.007 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00344 (13085) covalent geometry : angle 0.81983 (17760) hydrogen bonds : bond 0.03759 ( 773) hydrogen bonds : angle 5.34708 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.9487 (pttp) cc_final: 0.9228 (ptpp) REVERT: A 16 PHE cc_start: 0.8240 (p90) cc_final: 0.7770 (p90) REVERT: A 46 ASN cc_start: 0.9198 (t0) cc_final: 0.8954 (t0) REVERT: A 65 ASN cc_start: 0.9063 (p0) cc_final: 0.8706 (p0) REVERT: A 110 TYR cc_start: 0.8834 (t80) cc_final: 0.8422 (t80) REVERT: A 111 MET cc_start: 0.8402 (ptm) cc_final: 0.6804 (ptm) REVERT: A 169 ILE cc_start: 0.9674 (pt) cc_final: 0.9417 (pt) REVERT: A 178 ASP cc_start: 0.8512 (t70) cc_final: 0.8140 (t70) REVERT: A 282 PHE cc_start: 0.8548 (m-80) cc_final: 0.8330 (m-80) REVERT: A 305 ILE cc_start: 0.8936 (mt) cc_final: 0.8712 (mm) REVERT: B 1 MET cc_start: 0.4832 (ppp) cc_final: 0.3785 (ppp) REVERT: B 41 CYS cc_start: 0.7550 (m) cc_final: 0.7261 (m) REVERT: B 46 ASN cc_start: 0.9213 (t0) cc_final: 0.8602 (t0) REVERT: B 65 ASN cc_start: 0.8872 (p0) cc_final: 0.8331 (p0) REVERT: B 92 CYS cc_start: 0.7974 (t) cc_final: 0.7764 (t) REVERT: B 107 MET cc_start: 0.8692 (tmm) cc_final: 0.8229 (tmm) REVERT: B 134 LEU cc_start: 0.9384 (pp) cc_final: 0.9159 (pp) REVERT: B 160 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8707 (mt-10) REVERT: B 192 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8614 (tttm) REVERT: B 197 MET cc_start: 0.9026 (ttm) cc_final: 0.8482 (ttm) REVERT: B 200 TYR cc_start: 0.8446 (m-10) cc_final: 0.8156 (m-80) REVERT: B 232 ASP cc_start: 0.8460 (m-30) cc_final: 0.8202 (m-30) REVERT: C 18 TRP cc_start: 0.8299 (m100) cc_final: 0.8059 (m100) REVERT: C 46 ASN cc_start: 0.9109 (t0) cc_final: 0.8689 (t0) REVERT: C 68 ASP cc_start: 0.8323 (t70) cc_final: 0.8069 (t0) REVERT: C 123 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8742 (tppp) REVERT: C 171 ASP cc_start: 0.9104 (t70) cc_final: 0.8854 (t0) REVERT: C 200 TYR cc_start: 0.8393 (m-80) cc_final: 0.6991 (m-80) REVERT: C 201 MET cc_start: 0.8300 (mmm) cc_final: 0.8015 (mmm) REVERT: C 208 TYR cc_start: 0.8822 (m-10) cc_final: 0.8493 (m-80) REVERT: C 229 ASP cc_start: 0.8863 (p0) cc_final: 0.8522 (p0) REVERT: C 259 MET cc_start: 0.9077 (mmt) cc_final: 0.8788 (mmp) REVERT: C 270 MET cc_start: 0.8899 (ttt) cc_final: 0.8480 (ttp) REVERT: C 326 TRP cc_start: 0.7685 (m100) cc_final: 0.6194 (m100) REVERT: D 1 MET cc_start: 0.7501 (ppp) cc_final: 0.6922 (ppp) REVERT: D 18 TRP cc_start: 0.8896 (m100) cc_final: 0.8482 (m100) REVERT: D 46 ASN cc_start: 0.9345 (t0) cc_final: 0.9014 (t0) REVERT: D 78 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8445 (ttp-110) REVERT: D 92 CYS cc_start: 0.8532 (t) cc_final: 0.8210 (t) REVERT: D 169 ILE cc_start: 0.9584 (pt) cc_final: 0.9339 (pt) REVERT: D 189 LEU cc_start: 0.9354 (pp) cc_final: 0.8662 (tt) REVERT: D 194 LEU cc_start: 0.9704 (tp) cc_final: 0.9128 (tp) REVERT: D 200 TYR cc_start: 0.8279 (m-80) cc_final: 0.7556 (m-80) REVERT: D 244 CYS cc_start: 0.9061 (m) cc_final: 0.8498 (t) REVERT: D 278 LEU cc_start: 0.8973 (tt) cc_final: 0.8521 (tt) REVERT: D 282 PHE cc_start: 0.8679 (m-80) cc_final: 0.8378 (m-80) REVERT: E 5 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8743 (ttmm) REVERT: E 65 ASN cc_start: 0.9045 (p0) cc_final: 0.8819 (p0) REVERT: E 129 ASP cc_start: 0.8942 (t70) cc_final: 0.8678 (t0) REVERT: E 132 SER cc_start: 0.9396 (m) cc_final: 0.9067 (p) REVERT: E 157 HIS cc_start: 0.8262 (m-70) cc_final: 0.7802 (m-70) REVERT: E 169 ILE cc_start: 0.9660 (pt) cc_final: 0.9368 (pt) REVERT: E 177 LEU cc_start: 0.9175 (mt) cc_final: 0.8942 (mt) REVERT: E 229 ASP cc_start: 0.8530 (p0) cc_final: 0.8330 (p0) REVERT: E 232 ASP cc_start: 0.8623 (m-30) cc_final: 0.8350 (m-30) REVERT: E 257 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8678 (tm-30) REVERT: E 261 GLU cc_start: 0.8662 (tm-30) cc_final: 0.7960 (tm-30) REVERT: E 262 ASN cc_start: 0.9268 (m-40) cc_final: 0.8789 (m-40) REVERT: E 268 TYR cc_start: 0.7888 (t80) cc_final: 0.7645 (t80) REVERT: E 273 MET cc_start: 0.8459 (ttm) cc_final: 0.8177 (ttm) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.0972 time to fit residues: 58.1726 Evaluate side-chains 335 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 109 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064906 restraints weight = 47178.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067014 restraints weight = 29325.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068543 restraints weight = 20692.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069589 restraints weight = 15760.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070391 restraints weight = 12762.069| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13085 Z= 0.147 Angle : 0.824 11.522 17760 Z= 0.405 Chirality : 0.048 0.256 2005 Planarity : 0.005 0.052 2315 Dihedral : 6.153 78.202 1795 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -1.19 (0.21), residues: 1625 helix: 0.48 (0.18), residues: 845 sheet: -1.42 (0.38), residues: 165 loop : -2.43 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 76 TYR 0.019 0.002 TYR E 110 PHE 0.032 0.002 PHE D 306 TRP 0.042 0.002 TRP B 18 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00337 (13085) covalent geometry : angle 0.82424 (17760) hydrogen bonds : bond 0.03731 ( 773) hydrogen bonds : angle 5.21895 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9230 (t0) cc_final: 0.8944 (t0) REVERT: A 65 ASN cc_start: 0.9070 (p0) cc_final: 0.8777 (p0) REVERT: A 110 TYR cc_start: 0.8823 (t80) cc_final: 0.8379 (t80) REVERT: A 169 ILE cc_start: 0.9655 (pt) cc_final: 0.9409 (pt) REVERT: A 178 ASP cc_start: 0.8410 (t70) cc_final: 0.7817 (t70) REVERT: A 282 PHE cc_start: 0.8648 (m-80) cc_final: 0.8409 (m-80) REVERT: A 305 ILE cc_start: 0.8943 (mt) cc_final: 0.8717 (mm) REVERT: B 1 MET cc_start: 0.4755 (ppp) cc_final: 0.3712 (ppp) REVERT: B 41 CYS cc_start: 0.7550 (m) cc_final: 0.7134 (m) REVERT: B 46 ASN cc_start: 0.9104 (t0) cc_final: 0.8430 (t0) REVERT: B 76 ARG cc_start: 0.8247 (pmt170) cc_final: 0.7838 (ptt-90) REVERT: B 134 LEU cc_start: 0.9416 (pp) cc_final: 0.9180 (pp) REVERT: B 160 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8715 (mt-10) REVERT: B 192 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8604 (tttt) REVERT: B 197 MET cc_start: 0.9088 (ttm) cc_final: 0.8374 (tpp) REVERT: B 200 TYR cc_start: 0.8586 (m-10) cc_final: 0.8375 (m-80) REVERT: B 229 ASP cc_start: 0.8521 (p0) cc_final: 0.8289 (p0) REVERT: B 232 ASP cc_start: 0.8453 (m-30) cc_final: 0.8175 (m-30) REVERT: B 275 MET cc_start: 0.8576 (tpt) cc_final: 0.7783 (tpt) REVERT: C 18 TRP cc_start: 0.8521 (m100) cc_final: 0.8281 (m100) REVERT: C 46 ASN cc_start: 0.9104 (t0) cc_final: 0.8719 (t0) REVERT: C 68 ASP cc_start: 0.8352 (t70) cc_final: 0.8093 (t0) REVERT: C 171 ASP cc_start: 0.9112 (t70) cc_final: 0.8850 (t0) REVERT: C 200 TYR cc_start: 0.8312 (m-80) cc_final: 0.6885 (m-80) REVERT: C 204 GLN cc_start: 0.8965 (tt0) cc_final: 0.8725 (tt0) REVERT: C 228 GLN cc_start: 0.8890 (mt0) cc_final: 0.8636 (tp40) REVERT: C 229 ASP cc_start: 0.8806 (p0) cc_final: 0.8378 (p0) REVERT: C 232 ASP cc_start: 0.8166 (m-30) cc_final: 0.7949 (m-30) REVERT: C 259 MET cc_start: 0.9100 (mmt) cc_final: 0.8862 (mmp) REVERT: C 268 TYR cc_start: 0.9004 (t80) cc_final: 0.8729 (t80) REVERT: C 270 MET cc_start: 0.8819 (ttt) cc_final: 0.8531 (ttp) REVERT: C 326 TRP cc_start: 0.7659 (m100) cc_final: 0.6188 (m100) REVERT: D 1 MET cc_start: 0.7411 (ppp) cc_final: 0.6825 (ppp) REVERT: D 18 TRP cc_start: 0.8870 (m100) cc_final: 0.8372 (m100) REVERT: D 46 ASN cc_start: 0.9363 (t0) cc_final: 0.9012 (t0) REVERT: D 78 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8444 (ttp-110) REVERT: D 92 CYS cc_start: 0.8510 (t) cc_final: 0.8195 (t) REVERT: D 111 MET cc_start: 0.8614 (ttp) cc_final: 0.7698 (tmm) REVERT: D 169 ILE cc_start: 0.9570 (pt) cc_final: 0.9350 (pt) REVERT: D 189 LEU cc_start: 0.9322 (pp) cc_final: 0.8657 (tt) REVERT: D 194 LEU cc_start: 0.9689 (tp) cc_final: 0.9129 (tp) REVERT: D 227 MET cc_start: 0.8251 (tpt) cc_final: 0.8021 (tpt) REVERT: D 229 ASP cc_start: 0.8845 (p0) cc_final: 0.8251 (p0) REVERT: D 232 ASP cc_start: 0.8628 (m-30) cc_final: 0.8371 (p0) REVERT: D 244 CYS cc_start: 0.9084 (m) cc_final: 0.8544 (t) REVERT: D 278 LEU cc_start: 0.9018 (tt) cc_final: 0.8617 (tt) REVERT: D 282 PHE cc_start: 0.8716 (m-80) cc_final: 0.8438 (m-80) REVERT: E 5 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8839 (ttmm) REVERT: E 50 HIS cc_start: 0.8649 (p90) cc_final: 0.8394 (p90) REVERT: E 100 ARG cc_start: 0.7704 (mmp-170) cc_final: 0.7159 (mmm160) REVERT: E 123 LYS cc_start: 0.9102 (tptt) cc_final: 0.8543 (tppt) REVERT: E 129 ASP cc_start: 0.8936 (t70) cc_final: 0.8558 (t0) REVERT: E 132 SER cc_start: 0.9411 (m) cc_final: 0.9098 (p) REVERT: E 157 HIS cc_start: 0.8216 (m-70) cc_final: 0.7746 (m90) REVERT: E 169 ILE cc_start: 0.9616 (pt) cc_final: 0.9332 (pt) REVERT: E 208 TYR cc_start: 0.8495 (m-10) cc_final: 0.8006 (m-80) REVERT: E 229 ASP cc_start: 0.8580 (p0) cc_final: 0.8371 (p0) REVERT: E 232 ASP cc_start: 0.8637 (m-30) cc_final: 0.8379 (m-30) REVERT: E 261 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8083 (tm-30) REVERT: E 262 ASN cc_start: 0.9262 (m-40) cc_final: 0.8751 (m-40) REVERT: E 268 TYR cc_start: 0.8014 (t80) cc_final: 0.7619 (t80) REVERT: E 270 MET cc_start: 0.9063 (tpt) cc_final: 0.8833 (tpt) REVERT: E 273 MET cc_start: 0.8546 (ttm) cc_final: 0.8214 (ttm) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.1020 time to fit residues: 60.8304 Evaluate side-chains 320 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073038 restraints weight = 47147.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075050 restraints weight = 30364.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076452 restraints weight = 21966.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.077436 restraints weight = 17256.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078123 restraints weight = 14333.575| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13085 Z= 0.155 Angle : 0.837 12.401 17760 Z= 0.412 Chirality : 0.047 0.250 2005 Planarity : 0.006 0.061 2315 Dihedral : 6.141 78.353 1795 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.14 (0.21), residues: 1625 helix: 0.54 (0.18), residues: 845 sheet: -1.43 (0.38), residues: 165 loop : -2.42 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 184 TYR 0.017 0.002 TYR E 110 PHE 0.048 0.003 PHE C 306 TRP 0.040 0.002 TRP B 18 HIS 0.007 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00356 (13085) covalent geometry : angle 0.83747 (17760) hydrogen bonds : bond 0.03694 ( 773) hydrogen bonds : angle 5.21930 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9250 (t0) cc_final: 0.8947 (t0) REVERT: A 65 ASN cc_start: 0.9043 (p0) cc_final: 0.8732 (p0) REVERT: A 110 TYR cc_start: 0.8816 (t80) cc_final: 0.8341 (t80) REVERT: A 169 ILE cc_start: 0.9711 (pt) cc_final: 0.9465 (pt) REVERT: A 177 LEU cc_start: 0.9368 (mt) cc_final: 0.9142 (mt) REVERT: A 178 ASP cc_start: 0.8592 (t70) cc_final: 0.8071 (t70) REVERT: A 227 MET cc_start: 0.8834 (tpp) cc_final: 0.7970 (tmm) REVERT: A 273 MET cc_start: 0.8558 (mtp) cc_final: 0.8273 (mtm) REVERT: A 305 ILE cc_start: 0.8937 (mt) cc_final: 0.8716 (mm) REVERT: B 1 MET cc_start: 0.4747 (ppp) cc_final: 0.3733 (ppp) REVERT: B 26 VAL cc_start: 0.8136 (p) cc_final: 0.7917 (p) REVERT: B 41 CYS cc_start: 0.7591 (m) cc_final: 0.7106 (m) REVERT: B 46 ASN cc_start: 0.9110 (t0) cc_final: 0.8465 (t0) REVERT: B 76 ARG cc_start: 0.8146 (pmt170) cc_final: 0.7741 (ptt-90) REVERT: B 134 LEU cc_start: 0.9360 (pp) cc_final: 0.9077 (pp) REVERT: B 160 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8771 (mt-10) REVERT: B 192 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8671 (tmtt) REVERT: B 200 TYR cc_start: 0.8664 (m-10) cc_final: 0.8442 (m-80) REVERT: B 229 ASP cc_start: 0.8534 (p0) cc_final: 0.8257 (p0) REVERT: B 251 MET cc_start: 0.8143 (mmt) cc_final: 0.7850 (mmt) REVERT: B 253 ASP cc_start: 0.8703 (t70) cc_final: 0.8464 (t70) REVERT: B 268 TYR cc_start: 0.9015 (t80) cc_final: 0.8808 (t80) REVERT: B 270 MET cc_start: 0.8893 (ttt) cc_final: 0.8548 (ttt) REVERT: C 46 ASN cc_start: 0.9115 (t0) cc_final: 0.8733 (t0) REVERT: C 68 ASP cc_start: 0.8239 (t70) cc_final: 0.7890 (t0) REVERT: C 111 MET cc_start: 0.8158 (ptm) cc_final: 0.7819 (ppp) REVERT: C 121 GLN cc_start: 0.8304 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 200 TYR cc_start: 0.8400 (m-80) cc_final: 0.7226 (m-80) REVERT: C 228 GLN cc_start: 0.8845 (mt0) cc_final: 0.8573 (tp40) REVERT: C 229 ASP cc_start: 0.8845 (p0) cc_final: 0.8582 (p0) REVERT: C 232 ASP cc_start: 0.8118 (m-30) cc_final: 0.7899 (m-30) REVERT: C 259 MET cc_start: 0.9032 (mmt) cc_final: 0.8819 (mmp) REVERT: C 268 TYR cc_start: 0.9034 (t80) cc_final: 0.8807 (t80) REVERT: C 270 MET cc_start: 0.8843 (ttt) cc_final: 0.8459 (ttm) REVERT: C 275 MET cc_start: 0.8394 (mmp) cc_final: 0.8191 (mmp) REVERT: D 1 MET cc_start: 0.7361 (ppp) cc_final: 0.6771 (ppp) REVERT: D 46 ASN cc_start: 0.9381 (t0) cc_final: 0.9050 (t0) REVERT: D 65 ASN cc_start: 0.8993 (p0) cc_final: 0.8730 (p0) REVERT: D 76 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8317 (mtp-110) REVERT: D 78 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8339 (ttp-110) REVERT: D 92 CYS cc_start: 0.8416 (t) cc_final: 0.8089 (t) REVERT: D 169 ILE cc_start: 0.9595 (pt) cc_final: 0.9317 (pt) REVERT: D 194 LEU cc_start: 0.9721 (tp) cc_final: 0.9187 (tp) REVERT: D 200 TYR cc_start: 0.8259 (m-80) cc_final: 0.7679 (m-80) REVERT: D 227 MET cc_start: 0.8120 (tpt) cc_final: 0.7912 (tpt) REVERT: D 244 CYS cc_start: 0.9003 (m) cc_final: 0.8480 (t) REVERT: D 275 MET cc_start: 0.8751 (mmm) cc_final: 0.8523 (mmm) REVERT: D 278 LEU cc_start: 0.9096 (tt) cc_final: 0.8676 (tt) REVERT: D 282 PHE cc_start: 0.8670 (m-80) cc_final: 0.8405 (m-80) REVERT: E 5 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8844 (ttmm) REVERT: E 100 ARG cc_start: 0.7589 (mmp-170) cc_final: 0.7113 (mmm160) REVERT: E 129 ASP cc_start: 0.8943 (t70) cc_final: 0.8562 (t0) REVERT: E 132 SER cc_start: 0.9409 (m) cc_final: 0.9088 (p) REVERT: E 157 HIS cc_start: 0.8136 (m-70) cc_final: 0.7585 (m-70) REVERT: E 169 ILE cc_start: 0.9635 (pt) cc_final: 0.9346 (pt) REVERT: E 208 TYR cc_start: 0.8409 (m-10) cc_final: 0.8189 (m-80) REVERT: E 229 ASP cc_start: 0.8626 (p0) cc_final: 0.8361 (p0) REVERT: E 232 ASP cc_start: 0.8616 (m-30) cc_final: 0.8344 (m-30) REVERT: E 257 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8729 (tm-30) REVERT: E 261 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8116 (tm-30) REVERT: E 262 ASN cc_start: 0.9130 (m-40) cc_final: 0.8616 (m-40) REVERT: E 268 TYR cc_start: 0.8021 (t80) cc_final: 0.7573 (t80) REVERT: E 273 MET cc_start: 0.8511 (ttm) cc_final: 0.8218 (ttm) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.0966 time to fit residues: 56.5493 Evaluate side-chains 319 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 0.0970 chunk 4 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN C 260 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074248 restraints weight = 47115.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076276 restraints weight = 30329.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077647 restraints weight = 21982.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078651 restraints weight = 17283.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079392 restraints weight = 14358.920| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13085 Z= 0.152 Angle : 0.855 12.123 17760 Z= 0.417 Chirality : 0.048 0.270 2005 Planarity : 0.005 0.057 2315 Dihedral : 6.125 78.429 1795 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.07 % Allowed : 0.79 % Favored : 99.13 % 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: -1.21 (0.21), residues: 1625 helix: 0.34 (0.18), residues: 880 sheet: -1.41 (0.39), residues: 165 loop : -2.40 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 236 TYR 0.021 0.002 TYR D 110 PHE 0.034 0.002 PHE D 306 TRP 0.040 0.002 TRP B 18 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00350 (13085) covalent geometry : angle 0.85508 (17760) hydrogen bonds : bond 0.03698 ( 773) hydrogen bonds : angle 5.20554 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9262 (t0) cc_final: 0.8953 (t0) REVERT: A 65 ASN cc_start: 0.9069 (p0) cc_final: 0.8696 (p0) REVERT: A 107 MET cc_start: 0.8979 (tmm) cc_final: 0.8756 (tmm) REVERT: A 110 TYR cc_start: 0.8754 (t80) cc_final: 0.8289 (t80) REVERT: A 169 ILE cc_start: 0.9746 (pt) cc_final: 0.9502 (pt) REVERT: A 176 LEU cc_start: 0.9520 (pp) cc_final: 0.9312 (pp) REVERT: A 177 LEU cc_start: 0.9320 (mt) cc_final: 0.9111 (mt) REVERT: A 178 ASP cc_start: 0.8343 (t70) cc_final: 0.7878 (t70) REVERT: A 273 MET cc_start: 0.8571 (mtp) cc_final: 0.8292 (mtm) REVERT: A 305 ILE cc_start: 0.8940 (mt) cc_final: 0.8722 (mm) REVERT: B 1 MET cc_start: 0.4718 (ppp) cc_final: 0.3667 (ppp) REVERT: B 16 PHE cc_start: 0.8687 (p90) cc_final: 0.8237 (p90) REVERT: B 41 CYS cc_start: 0.7685 (m) cc_final: 0.7199 (m) REVERT: B 46 ASN cc_start: 0.9136 (t0) cc_final: 0.8516 (t0) REVERT: B 76 ARG cc_start: 0.8155 (pmt170) cc_final: 0.7750 (ptt-90) REVERT: B 160 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8754 (mt-10) REVERT: B 192 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8761 (tttm) REVERT: B 200 TYR cc_start: 0.8641 (m-10) cc_final: 0.8376 (m-80) REVERT: B 229 ASP cc_start: 0.8493 (p0) cc_final: 0.8212 (p0) REVERT: B 253 ASP cc_start: 0.8698 (t70) cc_final: 0.8470 (t70) REVERT: B 268 TYR cc_start: 0.8991 (t80) cc_final: 0.8735 (t80) REVERT: B 270 MET cc_start: 0.8886 (ttt) cc_final: 0.8557 (ttt) REVERT: C 18 TRP cc_start: 0.8376 (m100) cc_final: 0.8175 (m100) REVERT: C 68 ASP cc_start: 0.8351 (t70) cc_final: 0.8128 (t0) REVERT: C 76 ARG cc_start: 0.7195 (pmt170) cc_final: 0.6611 (ptt-90) REVERT: C 111 MET cc_start: 0.8169 (ptm) cc_final: 0.7774 (ppp) REVERT: C 121 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 197 MET cc_start: 0.8968 (tpp) cc_final: 0.8252 (tpp) REVERT: C 200 TYR cc_start: 0.8431 (m-80) cc_final: 0.7318 (m-80) REVERT: C 228 GLN cc_start: 0.8775 (mt0) cc_final: 0.8505 (tp40) REVERT: C 229 ASP cc_start: 0.8827 (p0) cc_final: 0.8570 (p0) REVERT: C 268 TYR cc_start: 0.8907 (t80) cc_final: 0.8683 (t80) REVERT: C 270 MET cc_start: 0.8799 (ttt) cc_final: 0.8468 (ttm) REVERT: D 1 MET cc_start: 0.7302 (ppp) cc_final: 0.6682 (ppp) REVERT: D 46 ASN cc_start: 0.9389 (t0) cc_final: 0.9053 (t0) REVERT: D 65 ASN cc_start: 0.8886 (p0) cc_final: 0.8547 (p0) REVERT: D 78 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8193 (ttp-110) REVERT: D 92 CYS cc_start: 0.8345 (t) cc_final: 0.8004 (t) REVERT: D 111 MET cc_start: 0.7970 (ttp) cc_final: 0.7553 (tmm) REVERT: D 169 ILE cc_start: 0.9578 (pt) cc_final: 0.9288 (pt) REVERT: D 189 LEU cc_start: 0.9351 (pp) cc_final: 0.8637 (tt) REVERT: D 194 LEU cc_start: 0.9713 (tp) cc_final: 0.9200 (tp) REVERT: D 200 TYR cc_start: 0.8259 (m-80) cc_final: 0.7808 (m-80) REVERT: D 219 MET cc_start: 0.7787 (mtm) cc_final: 0.7148 (mtm) REVERT: D 244 CYS cc_start: 0.8967 (m) cc_final: 0.8458 (t) REVERT: D 278 LEU cc_start: 0.9090 (tt) cc_final: 0.8770 (tt) REVERT: D 282 PHE cc_start: 0.8685 (m-80) cc_final: 0.8442 (m-80) REVERT: E 5 LYS cc_start: 0.9258 (ttmm) cc_final: 0.8901 (ttmm) REVERT: E 65 ASN cc_start: 0.8871 (p0) cc_final: 0.8624 (p0) REVERT: E 123 LYS cc_start: 0.9070 (tptt) cc_final: 0.8619 (tppt) REVERT: E 129 ASP cc_start: 0.8918 (t70) cc_final: 0.8548 (t0) REVERT: E 132 SER cc_start: 0.9401 (m) cc_final: 0.9100 (p) REVERT: E 169 ILE cc_start: 0.9630 (pt) cc_final: 0.9349 (pt) REVERT: E 178 ASP cc_start: 0.8005 (t70) cc_final: 0.7685 (t70) REVERT: E 208 TYR cc_start: 0.8236 (m-10) cc_final: 0.8000 (m-80) REVERT: E 229 ASP cc_start: 0.8623 (p0) cc_final: 0.8317 (p0) REVERT: E 232 ASP cc_start: 0.8567 (m-30) cc_final: 0.8279 (m-30) REVERT: E 257 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8748 (tm-30) REVERT: E 261 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8097 (tm-30) REVERT: E 262 ASN cc_start: 0.9135 (m-40) cc_final: 0.8836 (m-40) REVERT: E 268 TYR cc_start: 0.8090 (t80) cc_final: 0.7441 (t80) REVERT: E 270 MET cc_start: 0.8962 (tpt) cc_final: 0.8657 (tpp) REVERT: E 273 MET cc_start: 0.8539 (ttm) cc_final: 0.8247 (ttm) outliers start: 1 outliers final: 0 residues processed: 391 average time/residue: 0.0948 time to fit residues: 55.1427 Evaluate side-chains 318 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 36 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 157 optimal weight: 0.4980 chunk 38 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076210 restraints weight = 47239.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078252 restraints weight = 30340.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079678 restraints weight = 21848.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080713 restraints weight = 17018.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081411 restraints weight = 13999.828| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13085 Z= 0.151 Angle : 0.851 12.145 17760 Z= 0.418 Chirality : 0.048 0.261 2005 Planarity : 0.005 0.053 2315 Dihedral : 6.124 78.489 1795 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1625 helix: 0.35 (0.18), residues: 880 sheet: -1.30 (0.39), residues: 165 loop : -2.36 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 236 TYR 0.017 0.001 TYR D 110 PHE 0.048 0.002 PHE C 306 TRP 0.036 0.002 TRP B 18 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00344 (13085) covalent geometry : angle 0.85053 (17760) hydrogen bonds : bond 0.03685 ( 773) hydrogen bonds : angle 5.19428 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.31 seconds wall clock time: 35 minutes 49.35 seconds (2149.35 seconds total)