Starting phenix.real_space_refine on Wed Jul 30 22:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5n9y_3605/07_2025/5n9y_3605.cif Found real_map, /net/cci-nas-00/data/ceres_data/5n9y_3605/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5n9y_3605/07_2025/5n9y_3605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5n9y_3605/07_2025/5n9y_3605.map" model { file = "/net/cci-nas-00/data/ceres_data/5n9y_3605/07_2025/5n9y_3605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5n9y_3605/07_2025/5n9y_3605.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.68, per 1000 atoms: 0.60 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: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.21 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: 3.69 Time building geometry restraints manager: 3.49 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: 0.02 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: 0.420 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.470 Find NCS groups from input model: 0.430 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- 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 : 12.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP D 42 HIS 0.006 0.002 HIS A 166 PHE 0.028 0.004 PHE C 306 TYR 0.020 0.003 TYR E 268 ARG 0.045 0.001 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.10513 ( 773) hydrogen bonds : angle 11.02686 ( 2235) covalent geometry : bond 0.00773 (13085) covalent geometry : angle 1.29467 (17760) *********************** 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 : 1.481 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: 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: 0.8742 (p0) REVERT: A 110 TYR cc_start: 0.8954 (t80) cc_final: 0.8638 (t80) REVERT: A 111 MET cc_start: 0.7796 (ppp) cc_final: 0.7132 (ptm) REVERT: A 178 ASP cc_start: 0.8519 (t70) cc_final: 0.7792 (t70) REVERT: A 227 MET cc_start: 0.8770 (tpt) cc_final: 0.8369 (tpp) REVERT: A 229 ASP cc_start: 0.8656 (p0) cc_final: 0.7897 (p0) REVERT: A 240 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8415 (mm-30) REVERT: A 273 MET cc_start: 0.9140 (ttm) cc_final: 0.8879 (ttm) REVERT: A 278 LEU cc_start: 0.9131 (pp) cc_final: 0.8907 (pp) REVERT: A 305 ILE cc_start: 0.9122 (mt) cc_final: 0.8887 (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: 0.8792 (p0) REVERT: B 132 SER cc_start: 0.9538 (m) cc_final: 0.9249 (p) REVERT: B 156 ASP cc_start: 0.8161 (m-30) cc_final: 0.7926 (t0) REVERT: B 157 HIS cc_start: 0.8028 (m170) cc_final: 0.7314 (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: 0.8054 (tt) REVERT: B 192 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8765 (tmtt) REVERT: B 208 TYR cc_start: 0.8826 (m-10) cc_final: 0.8533 (m-10) REVERT: B 232 ASP cc_start: 0.8917 (m-30) cc_final: 0.8203 (m-30) REVERT: B 254 GLU cc_start: 0.7983 (pp20) cc_final: 0.7653 (pp20) REVERT: B 282 PHE cc_start: 0.8859 (m-80) cc_final: 0.8582 (m-10) REVERT: C 19 MET cc_start: 0.8617 (mmm) cc_final: 0.8319 (mmm) REVERT: C 41 CYS cc_start: 0.8066 (p) cc_final: 0.7809 (p) REVERT: C 68 ASP cc_start: 0.8319 (t70) cc_final: 0.7951 (t0) REVERT: C 123 LYS cc_start: 0.9015 (mtpm) cc_final: 0.8670 (tptp) REVERT: C 132 SER cc_start: 0.9343 (t) cc_final: 0.9090 (p) REVERT: C 157 HIS cc_start: 0.7258 (m170) cc_final: 0.6688 (m-70) REVERT: C 160 GLU cc_start: 0.8684 (pp20) cc_final: 0.8442 (pp20) REVERT: C 163 GLU cc_start: 0.9294 (tp30) cc_final: 0.9017 (tp30) REVERT: C 229 ASP cc_start: 0.8740 (p0) cc_final: 0.8103 (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: 0.8967 (mmp) REVERT: C 326 TRP cc_start: 0.7898 (m100) cc_final: 0.7458 (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: 0.8119 (t0) REVERT: D 49 HIS cc_start: 0.8402 (m170) cc_final: 0.7828 (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: 0.8062 (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: 0.8339 (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: 0.8499 (t) REVERT: D 305 ILE cc_start: 0.9035 (mt) cc_final: 0.8766 (mm) REVERT: E 5 LYS cc_start: 0.9215 (ttmp) cc_final: 0.8828 (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: 0.7805 (t0) REVERT: E 76 ARG cc_start: 0.8706 (pmt100) cc_final: 0.7813 (ptt180) REVERT: E 132 SER cc_start: 0.9266 (m) cc_final: 0.9051 (p) REVERT: E 151 CYS cc_start: 0.9245 (m) cc_final: 0.8990 (m) REVERT: E 197 MET cc_start: 0.8978 (ttp) cc_final: 0.8474 (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: 0.7743 (tm-30) REVERT: E 262 ASN cc_start: 0.9467 (m-40) cc_final: 0.8841 (m-40) REVERT: E 273 MET cc_start: 0.8900 (ttm) cc_final: 0.8447 (ttm) outliers start: 28 outliers final: 8 residues processed: 430 average time/residue: 0.2668 time to fit residues: 159.0649 Evaluate side-chains 324 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 316 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.1980 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 103 GLN ** 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 103 GLN E 157 HIS 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 = 0.3415 r_free = 0.3415 target = 0.085315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071457 restraints weight = 46295.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073547 restraints weight = 28428.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.074999 restraints weight = 19850.153| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13085 Z= 0.177 Angle : 0.834 11.168 17760 Z= 0.427 Chirality : 0.048 0.206 2005 Planarity : 0.008 0.095 2315 Dihedral : 7.038 82.951 1795 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.29 % Allowed : 5.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.18), residues: 1625 helix: -1.44 (0.16), residues: 850 sheet: -1.59 (0.45), residues: 135 loop : -3.10 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 146 HIS 0.004 0.001 HIS E 157 PHE 0.029 0.002 PHE A 306 TYR 0.016 0.002 TYR A 268 ARG 0.006 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 773) hydrogen bonds : angle 6.55767 ( 2235) covalent geometry : bond 0.00383 (13085) covalent geometry : angle 0.83403 (17760) *********************** 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 432 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 428 time to evaluate : 1.354 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: 0.9234 (t0) cc_final: 0.8864 (t0) REVERT: A 65 ASN cc_start: 0.9056 (p0) cc_final: 0.8802 (p0) REVERT: A 105 VAL cc_start: 0.9074 (t) cc_final: 0.8280 (t) REVERT: A 110 TYR cc_start: 0.8880 (t80) cc_final: 0.8608 (t80) REVERT: A 111 MET cc_start: 0.7640 (ppp) cc_final: 0.6890 (ptm) REVERT: A 169 ILE cc_start: 0.9683 (pt) cc_final: 0.9428 (pt) REVERT: A 178 ASP cc_start: 0.8539 (t70) cc_final: 0.8013 (t70) REVERT: A 197 MET cc_start: 0.8905 (mtp) cc_final: 0.7452 (mtp) REVERT: A 227 MET cc_start: 0.8647 (tpt) cc_final: 0.8447 (tpp) REVERT: A 273 MET cc_start: 0.8878 (ttm) cc_final: 0.7842 (mtp) REVERT: A 287 PHE cc_start: 0.7944 (m-10) cc_final: 0.7695 (m-10) REVERT: A 305 ILE cc_start: 0.8978 (mt) cc_final: 0.8723 (mm) REVERT: B 46 ASN cc_start: 0.9283 (t0) cc_final: 0.8960 (t0) REVERT: B 65 ASN cc_start: 0.9144 (p0) cc_final: 0.8866 (p0) REVERT: B 92 CYS cc_start: 0.8187 (t) cc_final: 0.7703 (m) REVERT: B 151 CYS cc_start: 0.9328 (m) cc_final: 0.8882 (m) REVERT: B 157 HIS cc_start: 0.7847 (m170) cc_final: 0.7147 (m-70) REVERT: B 160 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8605 (pt0) REVERT: B 189 LEU cc_start: 0.9038 (pt) cc_final: 0.7946 (tt) REVERT: B 192 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8540 (tmtt) REVERT: B 253 ASP cc_start: 0.8699 (t70) cc_final: 0.8471 (t70) REVERT: B 278 LEU cc_start: 0.8966 (tt) cc_final: 0.8764 (tt) REVERT: B 282 PHE cc_start: 0.8653 (m-80) cc_final: 0.8326 (m-10) REVERT: C 18 TRP cc_start: 0.8235 (m100) cc_final: 0.7367 (m100) REVERT: C 68 ASP cc_start: 0.8241 (t70) cc_final: 0.7804 (t0) REVERT: C 111 MET cc_start: 0.8113 (ppp) cc_final: 0.7810 (ppp) REVERT: C 123 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8669 (tppp) REVERT: C 157 HIS cc_start: 0.7396 (m170) cc_final: 0.6734 (m-70) REVERT: C 160 GLU cc_start: 0.8699 (pp20) cc_final: 0.8416 (pp20) REVERT: C 200 TYR cc_start: 0.8431 (m-80) cc_final: 0.8054 (m-80) REVERT: C 208 TYR cc_start: 0.9006 (m-10) cc_final: 0.8755 (m-10) REVERT: C 229 ASP cc_start: 0.8836 (p0) cc_final: 0.8627 (p0) REVERT: C 232 ASP cc_start: 0.8431 (m-30) cc_final: 0.8138 (m-30) REVERT: C 259 MET cc_start: 0.9013 (mmt) cc_final: 0.8751 (mmp) REVERT: C 326 TRP cc_start: 0.7617 (m100) cc_final: 0.6799 (m100) REVERT: D 1 MET cc_start: 0.7648 (ppp) cc_final: 0.7192 (ppp) REVERT: D 18 TRP cc_start: 0.9101 (m100) cc_final: 0.8256 (m100) REVERT: D 41 CYS cc_start: 0.7870 (p) cc_final: 0.6786 (p) REVERT: D 46 ASN cc_start: 0.9374 (t0) cc_final: 0.9032 (t0) REVERT: D 76 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8289 (mmm-85) REVERT: D 78 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8220 (ttp-110) REVERT: D 92 CYS cc_start: 0.8692 (t) cc_final: 0.8343 (t) REVERT: D 111 MET cc_start: 0.8208 (ttt) cc_final: 0.6458 (ttt) REVERT: D 123 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8863 (mmmm) REVERT: D 125 LEU cc_start: 0.9462 (mp) cc_final: 0.9248 (mp) REVERT: D 157 HIS cc_start: 0.8146 (m170) cc_final: 0.7787 (m170) REVERT: D 169 ILE cc_start: 0.9523 (pt) cc_final: 0.9213 (pt) REVERT: D 189 LEU cc_start: 0.9387 (pt) cc_final: 0.8454 (tt) REVERT: D 194 LEU cc_start: 0.9613 (tp) cc_final: 0.8944 (tp) REVERT: D 200 TYR cc_start: 0.8300 (m-80) cc_final: 0.8066 (m-10) REVERT: D 227 MET cc_start: 0.8723 (tpt) cc_final: 0.8364 (tpp) REVERT: D 244 CYS cc_start: 0.8937 (m) cc_final: 0.8451 (t) REVERT: D 260 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 282 PHE cc_start: 0.8492 (m-80) cc_final: 0.8253 (m-80) REVERT: E 5 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8852 (ttmm) REVERT: E 16 PHE cc_start: 0.8029 (m-10) cc_final: 0.7794 (m-10) REVERT: E 41 CYS cc_start: 0.8044 (m) cc_final: 0.7831 (m) REVERT: E 42 TRP cc_start: 0.9112 (t60) cc_final: 0.8176 (t60) REVERT: E 65 ASN cc_start: 0.9203 (p0) cc_final: 0.8960 (p0) REVERT: E 76 ARG cc_start: 0.8268 (ptt-90) cc_final: 0.7443 (mpp80) REVERT: E 92 CYS cc_start: 0.8521 (t) cc_final: 0.8230 (t) REVERT: E 111 MET cc_start: 0.8627 (ppp) cc_final: 0.8360 (ppp) REVERT: E 132 SER cc_start: 0.9318 (m) cc_final: 0.9070 (p) REVERT: E 151 CYS cc_start: 0.9175 (m) cc_final: 0.8418 (m) REVERT: E 169 ILE cc_start: 0.9589 (pt) cc_final: 0.9258 (pt) REVERT: E 200 TYR cc_start: 0.9050 (m-80) cc_final: 0.8781 (m-80) REVERT: E 229 ASP cc_start: 0.8566 (p0) cc_final: 0.8353 (p0) REVERT: E 254 GLU cc_start: 0.8766 (pp20) cc_final: 0.8529 (pp20) REVERT: E 257 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8733 (tm-30) REVERT: E 261 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7928 (tm-30) REVERT: E 262 ASN cc_start: 0.9431 (m-40) cc_final: 0.8892 (m-40) outliers start: 4 outliers final: 0 residues processed: 430 average time/residue: 0.2381 time to fit residues: 146.4240 Evaluate side-chains 354 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 126 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.082653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068303 restraints weight = 47554.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.070241 restraints weight = 29685.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071626 restraints weight = 21207.587| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13085 Z= 0.241 Angle : 0.843 7.825 17760 Z= 0.440 Chirality : 0.049 0.190 2005 Planarity : 0.007 0.064 2315 Dihedral : 6.725 79.680 1795 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.19), residues: 1625 helix: -0.92 (0.16), residues: 910 sheet: -1.97 (0.40), residues: 160 loop : -2.80 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 218 HIS 0.004 0.001 HIS E 157 PHE 0.024 0.002 PHE E 306 TYR 0.017 0.002 TYR A 268 ARG 0.007 0.001 ARG B 199 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 773) hydrogen bonds : angle 5.99837 ( 2235) covalent geometry : bond 0.00522 (13085) covalent geometry : angle 0.84267 (17760) *********************** 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 395 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.377 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: 0.9191 (t0) cc_final: 0.8967 (t0) REVERT: A 65 ASN cc_start: 0.9060 (p0) cc_final: 0.8757 (p0) REVERT: A 110 TYR cc_start: 0.8975 (t80) cc_final: 0.8741 (t80) REVERT: A 111 MET cc_start: 0.7826 (ppp) cc_final: 0.7069 (ptm) REVERT: A 163 GLU cc_start: 0.9038 (tp30) cc_final: 0.8836 (tp30) REVERT: A 178 ASP cc_start: 0.8714 (t70) cc_final: 0.8360 (t70) REVERT: A 227 MET cc_start: 0.8698 (tpt) cc_final: 0.8483 (tpp) REVERT: A 282 PHE cc_start: 0.8761 (m-80) cc_final: 0.8528 (m-80) REVERT: A 287 PHE cc_start: 0.8081 (m-10) cc_final: 0.7766 (m-10) REVERT: A 305 ILE cc_start: 0.8983 (mt) cc_final: 0.8747 (mm) REVERT: A 306 PHE cc_start: 0.8251 (p90) cc_final: 0.7882 (p90) REVERT: A 307 CYS cc_start: 0.8887 (m) cc_final: 0.8683 (m) REVERT: B 46 ASN cc_start: 0.9297 (t0) cc_final: 0.8865 (t0) REVERT: B 65 ASN cc_start: 0.9011 (p0) cc_final: 0.8643 (p0) REVERT: B 92 CYS cc_start: 0.8222 (t) cc_final: 0.7756 (m) REVERT: B 157 HIS cc_start: 0.7834 (m170) cc_final: 0.7608 (m-70) REVERT: B 160 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8661 (mt-10) REVERT: B 189 LEU cc_start: 0.9150 (pt) cc_final: 0.8248 (tt) REVERT: B 192 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8670 (tmtt) REVERT: B 200 TYR cc_start: 0.7984 (m-10) cc_final: 0.7592 (m-10) REVERT: B 242 ASP cc_start: 0.9139 (p0) cc_final: 0.8911 (p0) REVERT: B 251 MET cc_start: 0.8183 (mmt) cc_final: 0.7880 (mmt) REVERT: B 268 TYR cc_start: 0.8971 (t80) cc_final: 0.8730 (t80) REVERT: B 278 LEU cc_start: 0.8930 (tt) cc_final: 0.8656 (tt) REVERT: B 282 PHE cc_start: 0.8570 (m-80) cc_final: 0.8211 (m-10) REVERT: C 18 TRP cc_start: 0.8291 (m100) cc_final: 0.7917 (m100) REVERT: C 68 ASP cc_start: 0.8350 (t70) cc_final: 0.7862 (t0) REVERT: C 111 MET cc_start: 0.8108 (ppp) cc_final: 0.7759 (ppp) REVERT: C 123 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8706 (tppp) REVERT: C 157 HIS cc_start: 0.7711 (m170) cc_final: 0.7149 (m-70) REVERT: C 208 TYR cc_start: 0.8900 (m-10) cc_final: 0.8277 (m-10) REVERT: C 229 ASP cc_start: 0.8824 (p0) cc_final: 0.8606 (p0) REVERT: C 232 ASP cc_start: 0.8483 (m-30) cc_final: 0.8233 (m-30) REVERT: C 259 MET cc_start: 0.9007 (mmt) cc_final: 0.8776 (mmp) REVERT: C 270 MET cc_start: 0.8797 (ttt) cc_final: 0.8483 (ttp) REVERT: D 1 MET cc_start: 0.7628 (ppp) cc_final: 0.7163 (ppp) REVERT: D 18 TRP cc_start: 0.9117 (m100) cc_final: 0.8608 (m100) REVERT: D 46 ASN cc_start: 0.9398 (t0) cc_final: 0.9112 (t0) REVERT: D 50 HIS cc_start: 0.7615 (p-80) cc_final: 0.7298 (p90) REVERT: D 76 ARG cc_start: 0.8762 (mtp85) cc_final: 0.6943 (mtp180) REVERT: D 78 ARG cc_start: 0.8814 (ttp-110) cc_final: 0.8129 (ttp-110) REVERT: D 92 CYS cc_start: 0.8808 (t) cc_final: 0.8554 (t) REVERT: D 111 MET cc_start: 0.8291 (ttt) cc_final: 0.6534 (ttt) REVERT: D 123 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8940 (mmmm) REVERT: D 125 LEU cc_start: 0.9475 (mp) cc_final: 0.9273 (mp) REVERT: D 157 HIS cc_start: 0.8225 (m170) cc_final: 0.7873 (m170) REVERT: D 189 LEU cc_start: 0.9415 (pt) cc_final: 0.8710 (tt) REVERT: D 192 LYS cc_start: 0.9463 (tttm) cc_final: 0.9154 (tttt) REVERT: D 194 LEU cc_start: 0.9743 (tp) cc_final: 0.9102 (tp) REVERT: D 244 CYS cc_start: 0.9072 (m) cc_final: 0.8480 (t) REVERT: D 251 MET cc_start: 0.8330 (mmt) cc_final: 0.8032 (mmt) REVERT: D 260 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8698 (tm-30) REVERT: D 278 LEU cc_start: 0.9020 (tt) cc_final: 0.8746 (tt) REVERT: D 282 PHE cc_start: 0.8551 (m-80) cc_final: 0.8050 (m-80) REVERT: E 5 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8903 (ttmm) REVERT: E 65 ASN cc_start: 0.9232 (p0) cc_final: 0.8949 (p0) REVERT: E 111 MET cc_start: 0.8543 (ppp) cc_final: 0.8227 (ppp) REVERT: E 132 SER cc_start: 0.9419 (m) cc_final: 0.9136 (p) REVERT: E 169 ILE cc_start: 0.9697 (pt) cc_final: 0.9303 (pt) REVERT: E 232 ASP cc_start: 0.8804 (m-30) cc_final: 0.7715 (m-30) REVERT: E 234 LEU cc_start: 0.9641 (tp) cc_final: 0.9368 (tp) REVERT: E 236 ARG cc_start: 0.7991 (mpp80) cc_final: 0.7786 (mpt-90) REVERT: E 254 GLU cc_start: 0.8708 (pp20) cc_final: 0.8501 (pp20) REVERT: E 261 GLU cc_start: 0.8655 (tm-30) cc_final: 0.7977 (tm-30) REVERT: E 262 ASN cc_start: 0.9436 (m-40) cc_final: 0.8859 (m-40) REVERT: E 273 MET cc_start: 0.8650 (ttm) cc_final: 0.8428 (ttm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2398 time to fit residues: 135.9651 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 : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 10 ASN E 31 ASN ** E 179 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.086809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072794 restraints weight = 45724.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074873 restraints weight = 28299.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076330 restraints weight = 19957.277| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3754 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= 0.144 Angle : 0.805 9.593 17760 Z= 0.399 Chirality : 0.048 0.235 2005 Planarity : 0.006 0.115 2315 Dihedral : 6.507 78.570 1795 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.20), residues: 1625 helix: -0.20 (0.17), residues: 850 sheet: -1.16 (0.45), residues: 135 loop : -2.67 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 146 HIS 0.003 0.000 HIS B 44 PHE 0.026 0.002 PHE A 306 TYR 0.013 0.002 TYR A 268 ARG 0.008 0.001 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 773) hydrogen bonds : angle 5.61756 ( 2235) covalent geometry : bond 0.00318 (13085) covalent geometry : angle 0.80458 (17760) *********************** 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 427 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 1.636 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 16 PHE cc_start: 0.8001 (p90) cc_final: 0.7593 (p90) REVERT: A 46 ASN cc_start: 0.9232 (t0) cc_final: 0.8934 (t0) REVERT: A 110 TYR cc_start: 0.8773 (t80) cc_final: 0.8379 (t80) REVERT: A 111 MET cc_start: 0.7700 (ppp) cc_final: 0.7459 (ptm) REVERT: A 178 ASP cc_start: 0.8678 (t70) cc_final: 0.8124 (t70) REVERT: A 200 TYR cc_start: 0.8587 (m-80) cc_final: 0.7856 (m-80) REVERT: A 282 PHE cc_start: 0.8589 (m-80) cc_final: 0.8328 (m-80) REVERT: A 305 ILE cc_start: 0.8966 (mt) cc_final: 0.8721 (mm) REVERT: B 1 MET cc_start: 0.4670 (ppp) cc_final: 0.3620 (ppp) REVERT: B 43 LEU cc_start: 0.9089 (tt) cc_final: 0.8694 (mp) REVERT: B 46 ASN cc_start: 0.9211 (t0) cc_final: 0.8724 (t0) REVERT: B 65 ASN cc_start: 0.8941 (p0) cc_final: 0.8601 (p0) REVERT: B 92 CYS cc_start: 0.8168 (t) cc_final: 0.7661 (m) REVERT: B 107 MET cc_start: 0.8571 (tmm) cc_final: 0.7907 (tmm) REVERT: B 160 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8646 (mt-10) REVERT: B 189 LEU cc_start: 0.9003 (pt) cc_final: 0.7961 (tt) REVERT: B 192 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8554 (tttt) REVERT: B 200 TYR cc_start: 0.7580 (m-10) cc_final: 0.6935 (m-10) REVERT: B 219 MET cc_start: 0.8425 (mmm) cc_final: 0.8175 (mmm) REVERT: B 232 ASP cc_start: 0.8649 (m-30) cc_final: 0.8423 (m-30) REVERT: B 273 MET cc_start: 0.9195 (mtp) cc_final: 0.8969 (mtt) REVERT: B 282 PHE cc_start: 0.8549 (m-80) cc_final: 0.8282 (m-10) REVERT: C 18 TRP cc_start: 0.8380 (m100) cc_final: 0.8175 (m100) REVERT: C 46 ASN cc_start: 0.9123 (t0) cc_final: 0.8809 (t0) REVERT: C 68 ASP cc_start: 0.8353 (t70) cc_final: 0.8118 (t0) REVERT: C 123 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8693 (tppp) REVERT: C 157 HIS cc_start: 0.7625 (m170) cc_final: 0.7186 (m-70) REVERT: C 160 GLU cc_start: 0.8589 (pp20) cc_final: 0.8372 (pp20) REVERT: C 163 GLU cc_start: 0.8791 (tp30) cc_final: 0.8513 (tp30) REVERT: C 176 LEU cc_start: 0.9347 (pp) cc_final: 0.9115 (pp) REVERT: C 208 TYR cc_start: 0.8807 (m-10) cc_final: 0.8283 (m-80) REVERT: C 229 ASP cc_start: 0.8859 (p0) cc_final: 0.8628 (p0) REVERT: C 239 ASP cc_start: 0.8693 (p0) cc_final: 0.8026 (p0) REVERT: C 240 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 270 MET cc_start: 0.8827 (ttt) cc_final: 0.8447 (ttp) REVERT: C 326 TRP cc_start: 0.7545 (m100) cc_final: 0.7119 (m100) REVERT: D 1 MET cc_start: 0.7558 (ppp) cc_final: 0.7072 (ppp) REVERT: D 18 TRP cc_start: 0.8982 (m100) cc_final: 0.8629 (m100) REVERT: D 46 ASN cc_start: 0.9376 (t0) cc_final: 0.9055 (t0) REVERT: D 50 HIS cc_start: 0.7968 (p-80) cc_final: 0.7720 (p90) REVERT: D 65 ASN cc_start: 0.9134 (p0) cc_final: 0.8817 (p0) REVERT: D 92 CYS cc_start: 0.8708 (t) cc_final: 0.8477 (t) REVERT: D 111 MET cc_start: 0.8125 (ttt) cc_final: 0.7069 (ttt) REVERT: D 123 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8786 (mmmm) REVERT: D 157 HIS cc_start: 0.8118 (m170) cc_final: 0.7745 (m90) REVERT: D 194 LEU cc_start: 0.9710 (tp) cc_final: 0.9050 (tp) REVERT: D 200 TYR cc_start: 0.8482 (m-10) cc_final: 0.8029 (m-80) REVERT: D 227 MET cc_start: 0.8567 (tpp) cc_final: 0.8083 (tpt) REVERT: D 238 LEU cc_start: 0.9638 (pp) cc_final: 0.9170 (pp) REVERT: D 244 CYS cc_start: 0.9023 (m) cc_final: 0.8460 (t) REVERT: D 278 LEU cc_start: 0.8933 (tt) cc_final: 0.8438 (tt) REVERT: D 282 PHE cc_start: 0.8599 (m-80) cc_final: 0.8046 (m-80) REVERT: E 5 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8795 (ttmm) REVERT: E 18 TRP cc_start: 0.8290 (m-90) cc_final: 0.7875 (m-10) REVERT: E 51 ASP cc_start: 0.8601 (m-30) cc_final: 0.8157 (t0) REVERT: E 65 ASN cc_start: 0.9187 (p0) cc_final: 0.8931 (p0) REVERT: E 111 MET cc_start: 0.8620 (ppp) cc_final: 0.8325 (ppp) REVERT: E 132 SER cc_start: 0.9345 (m) cc_final: 0.9087 (p) REVERT: E 169 ILE cc_start: 0.9652 (pt) cc_final: 0.9307 (pt) REVERT: E 176 LEU cc_start: 0.9433 (pp) cc_final: 0.9168 (pp) REVERT: E 179 GLN cc_start: 0.8363 (mp10) cc_final: 0.7733 (pm20) REVERT: E 197 MET cc_start: 0.8945 (ttm) cc_final: 0.8123 (ttm) REVERT: E 229 ASP cc_start: 0.8512 (p0) cc_final: 0.8248 (p0) REVERT: E 232 ASP cc_start: 0.8702 (m-30) cc_final: 0.8457 (m-30) REVERT: E 234 LEU cc_start: 0.9493 (tp) cc_final: 0.9286 (tp) REVERT: E 261 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8110 (tm-30) REVERT: E 262 ASN cc_start: 0.9359 (m-40) cc_final: 0.8563 (m110) REVERT: E 270 MET cc_start: 0.8690 (tpt) cc_final: 0.8390 (tpt) outliers start: 2 outliers final: 1 residues processed: 427 average time/residue: 0.2353 time to fit residues: 144.1365 Evaluate side-chains 333 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 60 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072977 restraints weight = 46235.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075106 restraints weight = 28223.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076570 restraints weight = 19821.622| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13085 Z= 0.147 Angle : 0.801 9.915 17760 Z= 0.397 Chirality : 0.048 0.202 2005 Planarity : 0.006 0.054 2315 Dihedral : 6.357 77.798 1795 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1625 helix: 0.05 (0.17), residues: 845 sheet: -0.97 (0.45), residues: 135 loop : -2.63 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 218 HIS 0.008 0.001 HIS B 157 PHE 0.040 0.002 PHE C 306 TYR 0.016 0.002 TYR B 110 ARG 0.012 0.001 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 773) hydrogen bonds : angle 5.45416 ( 2235) covalent geometry : bond 0.00334 (13085) covalent geometry : angle 0.80139 (17760) *********************** 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 411 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 2.050 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: 0.8166 (p90) cc_final: 0.7755 (p90) REVERT: A 46 ASN cc_start: 0.9222 (t0) cc_final: 0.8927 (t0) REVERT: A 110 TYR cc_start: 0.8838 (t80) cc_final: 0.8465 (t80) REVERT: A 111 MET cc_start: 0.7566 (ppp) cc_final: 0.6649 (ptm) REVERT: A 169 ILE cc_start: 0.9692 (pt) cc_final: 0.9448 (pt) REVERT: A 178 ASP cc_start: 0.8769 (t70) cc_final: 0.8231 (t70) REVERT: A 200 TYR cc_start: 0.8600 (m-80) cc_final: 0.7761 (m-80) REVERT: A 282 PHE cc_start: 0.8605 (m-80) cc_final: 0.8320 (m-80) REVERT: A 305 ILE cc_start: 0.8907 (mt) cc_final: 0.8683 (mm) REVERT: B 1 MET cc_start: 0.4798 (ppp) cc_final: 0.3790 (ppp) REVERT: B 46 ASN cc_start: 0.9231 (t0) cc_final: 0.8671 (t0) REVERT: B 107 MET cc_start: 0.8503 (tmm) cc_final: 0.8141 (tmm) REVERT: B 160 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8787 (mt-10) REVERT: B 189 LEU cc_start: 0.8912 (pt) cc_final: 0.8664 (pp) REVERT: B 200 TYR cc_start: 0.7435 (m-10) cc_final: 0.7047 (m-10) REVERT: B 232 ASP cc_start: 0.8556 (m-30) cc_final: 0.8329 (m-30) REVERT: B 273 MET cc_start: 0.9193 (mtp) cc_final: 0.8991 (mtt) REVERT: C 46 ASN cc_start: 0.9084 (t0) cc_final: 0.8825 (t0) REVERT: C 68 ASP cc_start: 0.8363 (t70) cc_final: 0.8136 (t0) REVERT: C 123 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8718 (tppp) REVERT: C 157 HIS cc_start: 0.7383 (m170) cc_final: 0.7011 (m-70) REVERT: C 160 GLU cc_start: 0.8558 (pp20) cc_final: 0.8347 (pp20) REVERT: C 208 TYR cc_start: 0.8788 (m-10) cc_final: 0.8317 (m-80) REVERT: C 229 ASP cc_start: 0.8868 (p0) cc_final: 0.8612 (p0) REVERT: C 268 TYR cc_start: 0.8988 (t80) cc_final: 0.8767 (t80) REVERT: C 270 MET cc_start: 0.8816 (ttt) cc_final: 0.8366 (ttp) REVERT: C 287 PHE cc_start: 0.8395 (m-80) cc_final: 0.7987 (m-10) REVERT: D 1 MET cc_start: 0.7483 (ppp) cc_final: 0.6969 (ppp) REVERT: D 18 TRP cc_start: 0.9003 (m100) cc_final: 0.8557 (m100) REVERT: D 46 ASN cc_start: 0.9326 (t0) cc_final: 0.8986 (t0) REVERT: D 76 ARG cc_start: 0.8838 (mtp85) cc_final: 0.8015 (mtp85) REVERT: D 92 CYS cc_start: 0.8648 (t) cc_final: 0.8375 (t) REVERT: D 111 MET cc_start: 0.8142 (ttt) cc_final: 0.7112 (ttt) REVERT: D 178 ASP cc_start: 0.8310 (t70) cc_final: 0.8070 (t70) REVERT: D 189 LEU cc_start: 0.9384 (pp) cc_final: 0.8633 (tt) REVERT: D 194 LEU cc_start: 0.9698 (tp) cc_final: 0.9128 (tp) REVERT: D 200 TYR cc_start: 0.8415 (m-80) cc_final: 0.8070 (m-80) REVERT: D 227 MET cc_start: 0.8682 (tpp) cc_final: 0.8095 (tpt) REVERT: D 244 CYS cc_start: 0.9067 (m) cc_final: 0.8473 (t) REVERT: D 245 ILE cc_start: 0.9436 (pt) cc_final: 0.9165 (pt) REVERT: D 254 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 270 MET cc_start: 0.8979 (ttt) cc_final: 0.8681 (ttt) REVERT: D 278 LEU cc_start: 0.8990 (tt) cc_final: 0.8243 (tt) REVERT: D 282 PHE cc_start: 0.8718 (m-80) cc_final: 0.8381 (m-80) REVERT: E 5 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8768 (ttmm) REVERT: E 51 ASP cc_start: 0.8648 (m-30) cc_final: 0.8267 (t0) REVERT: E 65 ASN cc_start: 0.9114 (p0) cc_final: 0.8906 (p0) REVERT: E 111 MET cc_start: 0.8629 (ppp) cc_final: 0.8233 (ppp) REVERT: E 132 SER cc_start: 0.9377 (m) cc_final: 0.9112 (p) REVERT: E 169 ILE cc_start: 0.9645 (pt) cc_final: 0.9316 (pt) REVERT: E 229 ASP cc_start: 0.8574 (p0) cc_final: 0.8356 (p0) REVERT: E 232 ASP cc_start: 0.8658 (m-30) cc_final: 0.7503 (m-30) REVERT: E 234 LEU cc_start: 0.9432 (tp) cc_final: 0.9164 (tp) REVERT: E 270 MET cc_start: 0.8986 (tpt) cc_final: 0.8665 (tpt) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.2576 time to fit residues: 155.9214 Evaluate side-chains 333 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.085863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.071296 restraints weight = 47837.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073339 restraints weight = 29925.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074718 restraints weight = 21316.282| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4256 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= 0.190 Angle : 0.823 11.406 17760 Z= 0.416 Chirality : 0.049 0.229 2005 Planarity : 0.006 0.057 2315 Dihedral : 6.314 78.115 1795 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1625 helix: 0.27 (0.18), residues: 845 sheet: -1.09 (0.45), residues: 135 loop : -2.54 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 146 HIS 0.010 0.001 HIS B 157 PHE 0.026 0.002 PHE D 306 TYR 0.014 0.002 TYR A 268 ARG 0.008 0.001 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 773) hydrogen bonds : angle 5.38790 ( 2235) covalent geometry : bond 0.00427 (13085) covalent geometry : angle 0.82314 (17760) *********************** 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 397 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.460 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: A 46 ASN cc_start: 0.9229 (t0) cc_final: 0.8943 (t0) REVERT: A 110 TYR cc_start: 0.8876 (t80) cc_final: 0.8492 (t80) REVERT: A 169 ILE cc_start: 0.9651 (pt) cc_final: 0.9404 (pt) REVERT: A 178 ASP cc_start: 0.8745 (t70) cc_final: 0.8254 (t70) REVERT: A 278 LEU cc_start: 0.9137 (pp) cc_final: 0.8935 (pp) REVERT: A 282 PHE cc_start: 0.8606 (m-80) cc_final: 0.8362 (m-80) REVERT: A 305 ILE cc_start: 0.8968 (mt) cc_final: 0.8753 (mm) REVERT: A 326 TRP cc_start: 0.7633 (m100) cc_final: 0.7426 (m100) REVERT: B 1 MET cc_start: 0.4864 (ppp) cc_final: 0.3815 (ppp) REVERT: B 41 CYS cc_start: 0.7682 (m) cc_final: 0.7403 (m) REVERT: B 46 ASN cc_start: 0.9219 (t0) cc_final: 0.8598 (t0) REVERT: B 65 ASN cc_start: 0.8790 (p0) cc_final: 0.8269 (p0) REVERT: B 92 CYS cc_start: 0.8000 (t) cc_final: 0.7761 (t) REVERT: B 107 MET cc_start: 0.8499 (tmm) cc_final: 0.8222 (tmm) REVERT: B 143 CYS cc_start: 0.8050 (p) cc_final: 0.7704 (p) REVERT: B 160 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8789 (mt-10) REVERT: B 189 LEU cc_start: 0.8929 (pt) cc_final: 0.8689 (pp) REVERT: B 200 TYR cc_start: 0.7686 (m-10) cc_final: 0.7028 (m-10) REVERT: B 232 ASP cc_start: 0.8615 (m-30) cc_final: 0.8375 (m-30) REVERT: C 46 ASN cc_start: 0.9107 (t0) cc_final: 0.8868 (t0) REVERT: C 68 ASP cc_start: 0.8345 (t70) cc_final: 0.8099 (t0) REVERT: C 157 HIS cc_start: 0.7668 (m170) cc_final: 0.7135 (m-70) REVERT: C 171 ASP cc_start: 0.9293 (t0) cc_final: 0.9092 (t0) REVERT: C 208 TYR cc_start: 0.8800 (m-10) cc_final: 0.8489 (m-80) REVERT: C 229 ASP cc_start: 0.8845 (p0) cc_final: 0.8620 (p0) REVERT: C 240 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8380 (mm-30) REVERT: C 268 TYR cc_start: 0.9022 (t80) cc_final: 0.8760 (t80) REVERT: C 270 MET cc_start: 0.8864 (ttt) cc_final: 0.8476 (ttp) REVERT: C 326 TRP cc_start: 0.7663 (m100) cc_final: 0.6219 (m100) REVERT: D 1 MET cc_start: 0.7572 (ppp) cc_final: 0.6943 (ppp) REVERT: D 18 TRP cc_start: 0.8964 (m100) cc_final: 0.8532 (m100) REVERT: D 46 ASN cc_start: 0.9371 (t0) cc_final: 0.9054 (t0) REVERT: D 111 MET cc_start: 0.8047 (ttt) cc_final: 0.6851 (ttt) REVERT: D 169 ILE cc_start: 0.9555 (pt) cc_final: 0.9348 (pt) REVERT: D 189 LEU cc_start: 0.9246 (pp) cc_final: 0.8600 (tt) REVERT: D 194 LEU cc_start: 0.9718 (tp) cc_final: 0.9152 (tp) REVERT: D 219 MET cc_start: 0.8294 (mtm) cc_final: 0.7899 (mtm) REVERT: D 244 CYS cc_start: 0.9049 (m) cc_final: 0.8487 (t) REVERT: D 254 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8221 (tm-30) REVERT: D 270 MET cc_start: 0.8965 (ttt) cc_final: 0.8765 (ttt) REVERT: D 278 LEU cc_start: 0.9073 (tt) cc_final: 0.8459 (tt) REVERT: D 282 PHE cc_start: 0.8678 (m-80) cc_final: 0.8360 (m-80) REVERT: D 286 LEU cc_start: 0.8977 (tp) cc_final: 0.8578 (tt) REVERT: D 287 PHE cc_start: 0.8694 (m-80) cc_final: 0.8387 (m-80) REVERT: E 5 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8839 (ttmm) REVERT: E 18 TRP cc_start: 0.8423 (m-90) cc_final: 0.7917 (m-90) REVERT: E 65 ASN cc_start: 0.9133 (p0) cc_final: 0.8897 (p0) REVERT: E 111 MET cc_start: 0.8692 (ppp) cc_final: 0.8298 (ppp) REVERT: E 132 SER cc_start: 0.9414 (m) cc_final: 0.9138 (p) REVERT: E 169 ILE cc_start: 0.9659 (pt) cc_final: 0.9425 (pt) REVERT: E 232 ASP cc_start: 0.8628 (m-30) cc_final: 0.8378 (m-30) REVERT: E 234 LEU cc_start: 0.9443 (tp) cc_final: 0.9197 (tp) REVERT: E 257 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 261 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8053 (tm-30) REVERT: E 270 MET cc_start: 0.8971 (tpt) cc_final: 0.8711 (tpt) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.2307 time to fit residues: 134.3276 Evaluate side-chains 329 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** 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 = 0.3405 r_free = 0.3405 target = 0.084936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070761 restraints weight = 46651.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072776 restraints weight = 29054.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074174 restraints weight = 20569.030| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13085 Z= 0.193 Angle : 0.841 10.916 17760 Z= 0.424 Chirality : 0.049 0.297 2005 Planarity : 0.006 0.052 2315 Dihedral : 6.340 78.677 1795 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1625 helix: 0.35 (0.18), residues: 845 sheet: -1.18 (0.45), residues: 135 loop : -2.48 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 218 HIS 0.009 0.001 HIS B 157 PHE 0.031 0.002 PHE B 306 TYR 0.032 0.002 TYR E 208 ARG 0.012 0.001 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 773) hydrogen bonds : angle 5.42938 ( 2235) covalent geometry : bond 0.00432 (13085) covalent geometry : angle 0.84067 (17760) *********************** 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 391 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.499 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: A 46 ASN cc_start: 0.9229 (t0) cc_final: 0.8945 (t0) REVERT: A 110 TYR cc_start: 0.8909 (t80) cc_final: 0.8503 (t80) REVERT: A 169 ILE cc_start: 0.9658 (pt) cc_final: 0.9411 (pt) REVERT: A 178 ASP cc_start: 0.8735 (t70) cc_final: 0.8235 (t70) REVERT: A 305 ILE cc_start: 0.8991 (mt) cc_final: 0.8777 (mm) REVERT: B 1 MET cc_start: 0.4892 (ppp) cc_final: 0.3845 (ppp) REVERT: B 41 CYS cc_start: 0.7655 (m) cc_final: 0.7323 (m) REVERT: B 46 ASN cc_start: 0.9257 (t0) cc_final: 0.8636 (t0) REVERT: B 65 ASN cc_start: 0.8996 (p0) cc_final: 0.8415 (p0) REVERT: B 92 CYS cc_start: 0.8040 (t) cc_final: 0.7798 (t) REVERT: B 160 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8759 (mt-10) REVERT: B 232 ASP cc_start: 0.8605 (m-30) cc_final: 0.8365 (m-30) REVERT: C 18 TRP cc_start: 0.8364 (m100) cc_final: 0.7954 (m100) REVERT: C 46 ASN cc_start: 0.9116 (t0) cc_final: 0.8865 (t0) REVERT: C 68 ASP cc_start: 0.8366 (t70) cc_final: 0.8146 (t0) REVERT: C 111 MET cc_start: 0.8598 (ptm) cc_final: 0.8249 (ppp) REVERT: C 200 TYR cc_start: 0.8675 (m-80) cc_final: 0.8191 (m-80) REVERT: C 229 ASP cc_start: 0.8868 (p0) cc_final: 0.8588 (p0) REVERT: C 268 TYR cc_start: 0.8998 (t80) cc_final: 0.8754 (t80) REVERT: C 270 MET cc_start: 0.8913 (ttt) cc_final: 0.8512 (ttp) REVERT: C 326 TRP cc_start: 0.7705 (m100) cc_final: 0.6079 (m100) REVERT: D 1 MET cc_start: 0.7559 (ppp) cc_final: 0.6926 (ppp) REVERT: D 18 TRP cc_start: 0.8945 (m100) cc_final: 0.8560 (m100) REVERT: D 46 ASN cc_start: 0.9402 (t0) cc_final: 0.9096 (t0) REVERT: D 65 ASN cc_start: 0.9128 (p0) cc_final: 0.8761 (p0) REVERT: D 76 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8469 (mtp85) REVERT: D 189 LEU cc_start: 0.9402 (pp) cc_final: 0.8764 (tt) REVERT: D 194 LEU cc_start: 0.9732 (tp) cc_final: 0.9227 (tp) REVERT: D 244 CYS cc_start: 0.9053 (m) cc_final: 0.8458 (t) REVERT: D 278 LEU cc_start: 0.9130 (tt) cc_final: 0.8929 (tt) REVERT: D 286 LEU cc_start: 0.8995 (tp) cc_final: 0.8560 (tt) REVERT: D 287 PHE cc_start: 0.8604 (m-80) cc_final: 0.8172 (m-80) REVERT: E 5 LYS cc_start: 0.9251 (ttmm) cc_final: 0.8862 (ttmm) REVERT: E 18 TRP cc_start: 0.8451 (m-90) cc_final: 0.7873 (m-90) REVERT: E 65 ASN cc_start: 0.9119 (p0) cc_final: 0.8859 (p0) REVERT: E 111 MET cc_start: 0.8341 (ppp) cc_final: 0.7981 (ppp) REVERT: E 132 SER cc_start: 0.9428 (m) cc_final: 0.9180 (p) REVERT: E 151 CYS cc_start: 0.9378 (m) cc_final: 0.8821 (m) REVERT: E 169 ILE cc_start: 0.9691 (pt) cc_final: 0.9340 (pt) REVERT: E 197 MET cc_start: 0.9054 (ttm) cc_final: 0.8409 (ttm) REVERT: E 232 ASP cc_start: 0.8599 (m-30) cc_final: 0.7558 (m-30) REVERT: E 234 LEU cc_start: 0.9512 (tp) cc_final: 0.9247 (tp) REVERT: E 257 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8764 (tm-30) REVERT: E 261 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 268 TYR cc_start: 0.8166 (t80) cc_final: 0.7811 (t80) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2422 time to fit residues: 139.0052 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 : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071190 restraints weight = 47124.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073190 restraints weight = 29766.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074610 restraints weight = 21371.913| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13085 Z= 0.168 Angle : 0.844 11.074 17760 Z= 0.420 Chirality : 0.048 0.261 2005 Planarity : 0.005 0.054 2315 Dihedral : 6.323 78.788 1795 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1625 helix: 0.49 (0.18), residues: 845 sheet: -1.19 (0.46), residues: 135 loop : -2.49 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 146 HIS 0.008 0.001 HIS B 157 PHE 0.043 0.003 PHE C 306 TYR 0.019 0.002 TYR D 110 ARG 0.011 0.001 ARG D 184 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 773) hydrogen bonds : angle 5.33775 ( 2235) covalent geometry : bond 0.00383 (13085) covalent geometry : angle 0.84370 (17760) *********************** 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 392 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.387 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 16 PHE cc_start: 0.8229 (p90) cc_final: 0.7743 (p90) REVERT: A 46 ASN cc_start: 0.9204 (t0) cc_final: 0.8938 (t0) REVERT: A 65 ASN cc_start: 0.8946 (p0) cc_final: 0.8695 (p0) REVERT: A 110 TYR cc_start: 0.8870 (t80) cc_final: 0.8467 (t80) REVERT: A 111 MET cc_start: 0.8266 (ptm) cc_final: 0.7387 (ptm) REVERT: A 169 ILE cc_start: 0.9669 (pt) cc_final: 0.9437 (pt) REVERT: A 177 LEU cc_start: 0.9376 (mt) cc_final: 0.8919 (pp) REVERT: A 178 ASP cc_start: 0.8722 (t70) cc_final: 0.8348 (t70) REVERT: A 227 MET cc_start: 0.8890 (mmm) cc_final: 0.8603 (tpp) REVERT: A 278 LEU cc_start: 0.9139 (pp) cc_final: 0.8935 (pp) REVERT: A 282 PHE cc_start: 0.8584 (m-80) cc_final: 0.8366 (m-80) REVERT: A 305 ILE cc_start: 0.8989 (mt) cc_final: 0.8781 (mm) REVERT: B 1 MET cc_start: 0.4939 (ppp) cc_final: 0.3697 (ppp) REVERT: B 41 CYS cc_start: 0.7388 (m) cc_final: 0.7011 (m) REVERT: B 46 ASN cc_start: 0.9249 (t0) cc_final: 0.8613 (t0) REVERT: B 92 CYS cc_start: 0.8130 (t) cc_final: 0.7888 (t) REVERT: B 134 LEU cc_start: 0.9449 (pp) cc_final: 0.9205 (pp) REVERT: B 160 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8738 (mt-10) REVERT: B 197 MET cc_start: 0.9056 (tpp) cc_final: 0.8528 (mmm) REVERT: B 201 MET cc_start: 0.8731 (mmp) cc_final: 0.8225 (mmp) REVERT: B 270 MET cc_start: 0.8947 (ttt) cc_final: 0.8664 (ttt) REVERT: C 46 ASN cc_start: 0.9102 (t0) cc_final: 0.8876 (t0) REVERT: C 68 ASP cc_start: 0.8424 (t70) cc_final: 0.7956 (t0) REVERT: C 227 MET cc_start: 0.9118 (tpp) cc_final: 0.8892 (mmm) REVERT: C 229 ASP cc_start: 0.8811 (p0) cc_final: 0.8515 (p0) REVERT: C 268 TYR cc_start: 0.8948 (t80) cc_final: 0.8698 (t80) REVERT: C 270 MET cc_start: 0.8845 (ttt) cc_final: 0.8444 (ttm) REVERT: C 275 MET cc_start: 0.8479 (mmp) cc_final: 0.8212 (mmp) REVERT: C 326 TRP cc_start: 0.7671 (m100) cc_final: 0.6067 (m100) REVERT: D 1 MET cc_start: 0.7437 (ppp) cc_final: 0.6831 (ppp) REVERT: D 18 TRP cc_start: 0.8855 (m100) cc_final: 0.8614 (m100) REVERT: D 46 ASN cc_start: 0.9399 (t0) cc_final: 0.9092 (t0) REVERT: D 65 ASN cc_start: 0.9136 (p0) cc_final: 0.8763 (p0) REVERT: D 78 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8389 (ttp-110) REVERT: D 92 CYS cc_start: 0.8158 (t) cc_final: 0.7820 (t) REVERT: D 111 MET cc_start: 0.8380 (ttp) cc_final: 0.8077 (tmm) REVERT: D 169 ILE cc_start: 0.9545 (pt) cc_final: 0.9317 (pt) REVERT: D 189 LEU cc_start: 0.9379 (pp) cc_final: 0.8750 (tt) REVERT: D 194 LEU cc_start: 0.9737 (tp) cc_final: 0.9286 (tp) REVERT: D 232 ASP cc_start: 0.8998 (m-30) cc_final: 0.8563 (m-30) REVERT: D 244 CYS cc_start: 0.9044 (m) cc_final: 0.8418 (t) REVERT: D 275 MET cc_start: 0.8772 (mmm) cc_final: 0.8570 (mmm) REVERT: D 278 LEU cc_start: 0.9234 (tt) cc_final: 0.8694 (tt) REVERT: D 286 LEU cc_start: 0.8975 (tp) cc_final: 0.8540 (tt) REVERT: D 287 PHE cc_start: 0.8539 (m-80) cc_final: 0.8183 (m-80) REVERT: E 5 LYS cc_start: 0.9284 (ttmm) cc_final: 0.8876 (ttmm) REVERT: E 18 TRP cc_start: 0.8453 (m-90) cc_final: 0.8165 (m-90) REVERT: E 50 HIS cc_start: 0.8663 (p90) cc_final: 0.8368 (p90) REVERT: E 65 ASN cc_start: 0.9095 (p0) cc_final: 0.8843 (p0) REVERT: E 111 MET cc_start: 0.8366 (ppp) cc_final: 0.8077 (ppp) REVERT: E 132 SER cc_start: 0.9432 (m) cc_final: 0.9195 (p) REVERT: E 151 CYS cc_start: 0.9458 (m) cc_final: 0.8736 (m) REVERT: E 169 ILE cc_start: 0.9712 (pt) cc_final: 0.9357 (pt) REVERT: E 229 ASP cc_start: 0.8805 (p0) cc_final: 0.8537 (p0) REVERT: E 232 ASP cc_start: 0.8739 (m-30) cc_final: 0.8491 (m-30) REVERT: E 257 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8702 (tm-30) REVERT: E 261 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8019 (tm-30) REVERT: E 268 TYR cc_start: 0.8164 (t80) cc_final: 0.7753 (t80) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.2363 time to fit residues: 135.7797 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 : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 89 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.0870 chunk 109 optimal weight: 0.0170 chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073255 restraints weight = 46344.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075346 restraints weight = 29404.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076780 restraints weight = 21137.207| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13085 Z= 0.152 Angle : 0.870 13.789 17760 Z= 0.424 Chirality : 0.048 0.263 2005 Planarity : 0.006 0.072 2315 Dihedral : 6.340 78.568 1795 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1625 helix: 0.43 (0.18), residues: 835 sheet: -1.20 (0.45), residues: 135 loop : -2.50 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 18 HIS 0.007 0.001 HIS B 157 PHE 0.032 0.002 PHE E 161 TYR 0.020 0.002 TYR D 200 ARG 0.012 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 773) hydrogen bonds : angle 5.30957 ( 2235) covalent geometry : bond 0.00345 (13085) covalent geometry : angle 0.87010 (17760) *********************** 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 402 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.394 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: 0.8133 (p90) cc_final: 0.7711 (p90) REVERT: A 46 ASN cc_start: 0.9231 (t0) cc_final: 0.8956 (t0) REVERT: A 65 ASN cc_start: 0.8907 (p0) cc_final: 0.8668 (p0) REVERT: A 110 TYR cc_start: 0.8826 (t80) cc_final: 0.8436 (t80) REVERT: A 111 MET cc_start: 0.8611 (ptm) cc_final: 0.7423 (ptm) REVERT: A 176 LEU cc_start: 0.9482 (pp) cc_final: 0.9260 (pp) REVERT: A 177 LEU cc_start: 0.9354 (mt) cc_final: 0.8959 (pp) REVERT: A 178 ASP cc_start: 0.8697 (t70) cc_final: 0.8383 (t70) REVERT: A 227 MET cc_start: 0.8715 (mmm) cc_final: 0.8471 (tpp) REVERT: A 278 LEU cc_start: 0.9065 (pp) cc_final: 0.8837 (pp) REVERT: A 282 PHE cc_start: 0.8531 (m-80) cc_final: 0.8293 (m-80) REVERT: A 305 ILE cc_start: 0.8986 (mt) cc_final: 0.8771 (mm) REVERT: B 1 MET cc_start: 0.4933 (ppp) cc_final: 0.3690 (ppp) REVERT: B 41 CYS cc_start: 0.7318 (m) cc_final: 0.6835 (m) REVERT: B 46 ASN cc_start: 0.9233 (t0) cc_final: 0.8556 (t0) REVERT: B 65 ASN cc_start: 0.8923 (p0) cc_final: 0.8404 (p0) REVERT: B 76 ARG cc_start: 0.8036 (pmt170) cc_final: 0.7488 (ptt-90) REVERT: B 92 CYS cc_start: 0.8094 (t) cc_final: 0.7857 (t) REVERT: B 107 MET cc_start: 0.8530 (tmm) cc_final: 0.8170 (tmm) REVERT: B 134 LEU cc_start: 0.9385 (pp) cc_final: 0.9066 (pp) REVERT: B 160 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 164 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8616 (tp40) REVERT: B 167 ASP cc_start: 0.8782 (p0) cc_final: 0.8553 (p0) REVERT: B 197 MET cc_start: 0.9108 (tpp) cc_final: 0.8545 (mmm) REVERT: B 200 TYR cc_start: 0.8306 (m-10) cc_final: 0.8070 (m-80) REVERT: B 201 MET cc_start: 0.8742 (mmp) cc_final: 0.8266 (mmp) REVERT: B 229 ASP cc_start: 0.8577 (p0) cc_final: 0.8372 (p0) REVERT: B 232 ASP cc_start: 0.8467 (m-30) cc_final: 0.8210 (m-30) REVERT: B 268 TYR cc_start: 0.9049 (t80) cc_final: 0.8836 (t80) REVERT: B 270 MET cc_start: 0.8822 (ttt) cc_final: 0.8397 (ttt) REVERT: C 68 ASP cc_start: 0.8417 (t70) cc_final: 0.8169 (t0) REVERT: C 200 TYR cc_start: 0.8732 (m-80) cc_final: 0.8196 (m-80) REVERT: C 229 ASP cc_start: 0.8802 (p0) cc_final: 0.8521 (p0) REVERT: C 268 TYR cc_start: 0.8906 (t80) cc_final: 0.8627 (t80) REVERT: C 270 MET cc_start: 0.8811 (ttt) cc_final: 0.8429 (ttm) REVERT: C 275 MET cc_start: 0.8341 (mmp) cc_final: 0.8080 (mmp) REVERT: C 326 TRP cc_start: 0.7707 (m100) cc_final: 0.6258 (m100) REVERT: D 1 MET cc_start: 0.7393 (ppp) cc_final: 0.6771 (ppp) REVERT: D 18 TRP cc_start: 0.8797 (m100) cc_final: 0.8397 (m100) REVERT: D 46 ASN cc_start: 0.9397 (t0) cc_final: 0.9073 (t0) REVERT: D 65 ASN cc_start: 0.9115 (p0) cc_final: 0.8739 (p0) REVERT: D 92 CYS cc_start: 0.8161 (t) cc_final: 0.7855 (t) REVERT: D 111 MET cc_start: 0.8452 (ttp) cc_final: 0.7996 (tmm) REVERT: D 169 ILE cc_start: 0.9506 (pt) cc_final: 0.9266 (pt) REVERT: D 189 LEU cc_start: 0.9383 (pp) cc_final: 0.8668 (tt) REVERT: D 194 LEU cc_start: 0.9713 (tp) cc_final: 0.9324 (tp) REVERT: D 219 MET cc_start: 0.8507 (mtt) cc_final: 0.8094 (mtt) REVERT: D 227 MET cc_start: 0.8418 (mmm) cc_final: 0.8063 (tpp) REVERT: D 232 ASP cc_start: 0.8946 (m-30) cc_final: 0.8552 (m-30) REVERT: D 244 CYS cc_start: 0.9018 (m) cc_final: 0.8400 (t) REVERT: D 278 LEU cc_start: 0.9188 (tt) cc_final: 0.8615 (tt) REVERT: E 5 LYS cc_start: 0.9283 (ttmm) cc_final: 0.8875 (ttmm) REVERT: E 41 CYS cc_start: 0.8062 (m) cc_final: 0.7836 (m) REVERT: E 65 ASN cc_start: 0.9066 (p0) cc_final: 0.8813 (p0) REVERT: E 111 MET cc_start: 0.8415 (ppp) cc_final: 0.8070 (ppp) REVERT: E 132 SER cc_start: 0.9402 (m) cc_final: 0.9161 (p) REVERT: E 169 ILE cc_start: 0.9691 (pt) cc_final: 0.9324 (pt) REVERT: E 229 ASP cc_start: 0.8812 (p0) cc_final: 0.8486 (p0) REVERT: E 232 ASP cc_start: 0.8612 (m-30) cc_final: 0.8323 (m-30) REVERT: E 257 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8607 (tm-30) REVERT: E 261 GLU cc_start: 0.8684 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 268 TYR cc_start: 0.8134 (t80) cc_final: 0.7700 (t80) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2298 time to fit residues: 135.1750 Evaluate side-chains 321 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.086493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071773 restraints weight = 46486.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.073773 restraints weight = 29769.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075145 restraints weight = 21531.557| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5055 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= 0.171 Angle : 0.875 13.047 17760 Z= 0.432 Chirality : 0.049 0.260 2005 Planarity : 0.006 0.054 2315 Dihedral : 6.315 78.728 1795 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1625 helix: 0.25 (0.18), residues: 875 sheet: -1.23 (0.45), residues: 135 loop : -2.48 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 146 HIS 0.008 0.001 HIS B 157 PHE 0.045 0.003 PHE C 306 TYR 0.017 0.002 TYR D 200 ARG 0.010 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 773) hydrogen bonds : angle 5.29016 ( 2235) covalent geometry : bond 0.00391 (13085) covalent geometry : angle 0.87507 (17760) ********************** 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 392 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.554 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: 0.9244 (t0) cc_final: 0.8923 (t0) REVERT: A 65 ASN cc_start: 0.8924 (p0) cc_final: 0.8684 (p0) REVERT: A 110 TYR cc_start: 0.8821 (t80) cc_final: 0.8463 (t80) REVERT: A 111 MET cc_start: 0.8434 (ptm) cc_final: 0.7443 (ptm) REVERT: A 176 LEU cc_start: 0.9487 (pp) cc_final: 0.9263 (pp) REVERT: A 178 ASP cc_start: 0.8701 (t70) cc_final: 0.8298 (t70) REVERT: A 227 MET cc_start: 0.8727 (mmm) cc_final: 0.8470 (tpp) REVERT: A 236 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8020 (mtm180) REVERT: A 273 MET cc_start: 0.8814 (mtp) cc_final: 0.8411 (mtm) REVERT: A 278 LEU cc_start: 0.9152 (pp) cc_final: 0.8889 (pp) REVERT: A 282 PHE cc_start: 0.8513 (m-80) cc_final: 0.8293 (m-80) REVERT: A 305 ILE cc_start: 0.8987 (mt) cc_final: 0.8771 (mm) REVERT: B 1 MET cc_start: 0.4836 (ppp) cc_final: 0.3595 (ppp) REVERT: B 41 CYS cc_start: 0.7181 (m) cc_final: 0.6807 (m) REVERT: B 46 ASN cc_start: 0.9252 (t0) cc_final: 0.8604 (t0) REVERT: B 76 ARG cc_start: 0.7905 (pmt170) cc_final: 0.7470 (ptt-90) REVERT: B 92 CYS cc_start: 0.8136 (t) cc_final: 0.7901 (t) REVERT: B 107 MET cc_start: 0.8523 (tmm) cc_final: 0.8185 (tmm) REVERT: B 134 LEU cc_start: 0.9361 (pp) cc_final: 0.8967 (pp) REVERT: B 164 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8621 (tp40) REVERT: B 167 ASP cc_start: 0.8741 (p0) cc_final: 0.8433 (p0) REVERT: B 229 ASP cc_start: 0.8591 (p0) cc_final: 0.8364 (p0) REVERT: B 232 ASP cc_start: 0.8436 (m-30) cc_final: 0.8125 (m-30) REVERT: B 257 GLN cc_start: 0.9082 (pp30) cc_final: 0.8061 (tm-30) REVERT: B 268 TYR cc_start: 0.9061 (t80) cc_final: 0.8807 (t80) REVERT: B 270 MET cc_start: 0.8851 (ttt) cc_final: 0.8487 (ttt) REVERT: C 68 ASP cc_start: 0.8356 (t70) cc_final: 0.8129 (t0) REVERT: C 111 MET cc_start: 0.8353 (ptm) cc_final: 0.7945 (ppp) REVERT: C 173 GLU cc_start: 0.8701 (pm20) cc_final: 0.8450 (pm20) REVERT: C 200 TYR cc_start: 0.8751 (m-80) cc_final: 0.8174 (m-80) REVERT: C 227 MET cc_start: 0.9043 (tpp) cc_final: 0.8764 (mmm) REVERT: C 229 ASP cc_start: 0.8880 (p0) cc_final: 0.8544 (p0) REVERT: C 268 TYR cc_start: 0.8920 (t80) cc_final: 0.8683 (t80) REVERT: C 270 MET cc_start: 0.8875 (ttt) cc_final: 0.8491 (ttm) REVERT: D 1 MET cc_start: 0.7376 (ppp) cc_final: 0.6742 (ppp) REVERT: D 18 TRP cc_start: 0.8822 (m100) cc_final: 0.8478 (m100) REVERT: D 46 ASN cc_start: 0.9422 (t0) cc_final: 0.9083 (t0) REVERT: D 65 ASN cc_start: 0.8968 (p0) cc_final: 0.8591 (p0) REVERT: D 92 CYS cc_start: 0.8142 (t) cc_final: 0.7845 (t) REVERT: D 111 MET cc_start: 0.8752 (ttp) cc_final: 0.8062 (tmm) REVERT: D 189 LEU cc_start: 0.9352 (pp) cc_final: 0.8714 (tt) REVERT: D 194 LEU cc_start: 0.9686 (tp) cc_final: 0.9131 (tp) REVERT: D 200 TYR cc_start: 0.8259 (m-80) cc_final: 0.7532 (m-80) REVERT: D 201 MET cc_start: 0.8572 (mmt) cc_final: 0.8316 (mmt) REVERT: D 227 MET cc_start: 0.8467 (mmm) cc_final: 0.8247 (tpp) REVERT: D 232 ASP cc_start: 0.8904 (m-30) cc_final: 0.8544 (m-30) REVERT: D 244 CYS cc_start: 0.8959 (m) cc_final: 0.8512 (t) REVERT: D 278 LEU cc_start: 0.9157 (tt) cc_final: 0.8637 (tt) REVERT: E 5 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8852 (ttmm) REVERT: E 18 TRP cc_start: 0.8515 (m-90) cc_final: 0.7896 (m-90) REVERT: E 41 CYS cc_start: 0.8062 (m) cc_final: 0.7861 (m) REVERT: E 111 MET cc_start: 0.8394 (ppp) cc_final: 0.8077 (ppp) REVERT: E 132 SER cc_start: 0.9422 (m) cc_final: 0.9162 (p) REVERT: E 169 ILE cc_start: 0.9680 (pt) cc_final: 0.9308 (pt) REVERT: E 229 ASP cc_start: 0.8753 (p0) cc_final: 0.8463 (p0) REVERT: E 232 ASP cc_start: 0.8656 (m-30) cc_final: 0.8406 (m-30) REVERT: E 257 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8744 (tm-30) REVERT: E 261 GLU cc_start: 0.8742 (tm-30) cc_final: 0.7981 (tm-30) REVERT: E 268 TYR cc_start: 0.8450 (t80) cc_final: 0.7784 (t80) REVERT: E 270 MET cc_start: 0.8839 (tpt) cc_final: 0.8555 (tpp) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.2306 time to fit residues: 132.0547 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 : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.0030 chunk 159 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073767 restraints weight = 46132.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075769 restraints weight = 29722.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077159 restraints weight = 21601.216| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13085 Z= 0.157 Angle : 0.884 13.237 17760 Z= 0.432 Chirality : 0.048 0.246 2005 Planarity : 0.006 0.077 2315 Dihedral : 6.359 78.615 1795 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1625 helix: 0.21 (0.18), residues: 860 sheet: -1.22 (0.45), residues: 135 loop : -2.48 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 218 HIS 0.007 0.001 HIS B 157 PHE 0.025 0.002 PHE D 306 TYR 0.014 0.002 TYR D 200 ARG 0.010 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 773) hydrogen bonds : angle 5.29721 ( 2235) covalent geometry : bond 0.00361 (13085) covalent geometry : angle 0.88430 (17760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.44 seconds wall clock time: 74 minutes 56.66 seconds (4496.66 seconds total)