Starting phenix.real_space_refine on Thu May 15 06:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5n9y_3605/05_2025/5n9y_3605.cif Found real_map, /net/cci-nas-00/data/ceres_data/5n9y_3605/05_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_3605/05_2025/5n9y_3605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5n9y_3605/05_2025/5n9y_3605.map" model { file = "/net/cci-nas-00/data/ceres_data/5n9y_3605/05_2025/5n9y_3605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5n9y_3605/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.99, per 1000 atoms: 0.62 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: 2.87 Conformation dependent library (CDL) restraints added in 1.6 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: 1.24 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: 3.87 Time building geometry restraints manager: 3.40 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: 0.250 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.880 Find NCS groups from input model: 0.410 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- 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 : 1.331 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: 0.2656 time to fit residues: 158.6846 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 : 1.544 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.085354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.071528 restraints weight = 46291.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073624 restraints weight = 28382.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075071 restraints weight = 19808.265| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2543 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= 0.178 Angle : 0.834 11.208 17760 Z= 0.427 Chirality : 0.048 0.206 2005 Planarity : 0.008 0.096 2315 Dihedral : 7.037 82.946 1795 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.48 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: -3.18 (0.18), residues: 1625 helix: -1.44 (0.16), residues: 850 sheet: -1.58 (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 0.04274 ( 773) hydrogen bonds : angle 6.55623 ( 2235) covalent geometry : bond 0.00384 (13085) covalent geometry : angle 0.83411 (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 : 1.441 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: 0.9233 (t0) cc_final: 0.8863 (t0) REVERT: A 65 ASN cc_start: 0.9059 (p0) cc_final: 0.8806 (p0) REVERT: A 105 VAL cc_start: 0.9074 (t) cc_final: 0.8278 (t) REVERT: A 110 TYR cc_start: 0.8882 (t80) cc_final: 0.8610 (t80) REVERT: A 111 MET cc_start: 0.7643 (ppp) cc_final: 0.6896 (ptm) REVERT: A 169 ILE cc_start: 0.9683 (pt) cc_final: 0.9427 (pt) REVERT: A 178 ASP cc_start: 0.8539 (t70) cc_final: 0.8014 (t70) REVERT: A 197 MET cc_start: 0.8912 (mtp) cc_final: 0.7462 (mtp) REVERT: A 273 MET cc_start: 0.8884 (ttm) cc_final: 0.7853 (mtp) REVERT: A 287 PHE cc_start: 0.7947 (m-10) cc_final: 0.7699 (m-10) REVERT: A 305 ILE cc_start: 0.8978 (mt) cc_final: 0.8723 (mm) REVERT: B 46 ASN cc_start: 0.9280 (t0) cc_final: 0.8956 (t0) REVERT: B 65 ASN cc_start: 0.9145 (p0) cc_final: 0.8869 (p0) REVERT: B 92 CYS cc_start: 0.8186 (t) cc_final: 0.7707 (m) REVERT: B 151 CYS cc_start: 0.9334 (m) cc_final: 0.8895 (m) REVERT: B 157 HIS cc_start: 0.7855 (m170) cc_final: 0.7155 (m-70) REVERT: B 160 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8605 (pt0) REVERT: B 189 LEU cc_start: 0.9038 (pt) cc_final: 0.7948 (tt) REVERT: B 192 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8540 (tmtt) REVERT: B 253 ASP cc_start: 0.8706 (t70) cc_final: 0.8478 (t70) REVERT: B 278 LEU cc_start: 0.8966 (tt) cc_final: 0.8764 (tt) REVERT: B 282 PHE cc_start: 0.8658 (m-80) cc_final: 0.8329 (m-10) REVERT: C 18 TRP cc_start: 0.8242 (m100) cc_final: 0.7369 (m100) REVERT: C 68 ASP cc_start: 0.8246 (t70) cc_final: 0.7809 (t0) REVERT: C 107 MET cc_start: 0.8967 (tmm) cc_final: 0.8765 (tmm) REVERT: C 111 MET cc_start: 0.8114 (ppp) cc_final: 0.7809 (ppp) REVERT: C 123 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8668 (tppp) REVERT: C 157 HIS cc_start: 0.7399 (m170) cc_final: 0.6738 (m-70) REVERT: C 160 GLU cc_start: 0.8704 (pp20) cc_final: 0.8417 (pp20) REVERT: C 200 TYR cc_start: 0.8435 (m-80) cc_final: 0.8053 (m-80) REVERT: C 208 TYR cc_start: 0.9007 (m-10) cc_final: 0.8756 (m-10) REVERT: C 229 ASP cc_start: 0.8839 (p0) cc_final: 0.8631 (p0) REVERT: C 232 ASP cc_start: 0.8433 (m-30) cc_final: 0.8141 (m-30) REVERT: C 259 MET cc_start: 0.9018 (mmt) cc_final: 0.8755 (mmp) REVERT: C 326 TRP cc_start: 0.7620 (m100) cc_final: 0.6802 (m100) REVERT: D 1 MET cc_start: 0.7648 (ppp) cc_final: 0.7189 (ppp) REVERT: D 18 TRP cc_start: 0.9107 (m100) cc_final: 0.8260 (m100) REVERT: D 41 CYS cc_start: 0.7881 (p) cc_final: 0.6796 (p) REVERT: D 46 ASN cc_start: 0.9372 (t0) cc_final: 0.9032 (t0) REVERT: D 76 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8134 (mmm-85) REVERT: D 78 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8278 (ttp-110) REVERT: D 92 CYS cc_start: 0.8689 (t) cc_final: 0.8346 (t) REVERT: D 111 MET cc_start: 0.8213 (ttt) cc_final: 0.6455 (ttt) REVERT: D 123 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8860 (mmmm) REVERT: D 125 LEU cc_start: 0.9461 (mp) cc_final: 0.9243 (mp) REVERT: D 157 HIS cc_start: 0.8144 (m170) cc_final: 0.7790 (m170) REVERT: D 169 ILE cc_start: 0.9520 (pt) cc_final: 0.9212 (pt) REVERT: D 189 LEU cc_start: 0.9388 (pt) cc_final: 0.8455 (tt) REVERT: D 194 LEU cc_start: 0.9610 (tp) cc_final: 0.8941 (tp) REVERT: D 200 TYR cc_start: 0.8304 (m-80) cc_final: 0.8070 (m-10) REVERT: D 227 MET cc_start: 0.8727 (tpt) cc_final: 0.8364 (tpp) REVERT: D 244 CYS cc_start: 0.8942 (m) cc_final: 0.8456 (t) REVERT: D 260 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8608 (tm-30) REVERT: D 282 PHE cc_start: 0.8497 (m-80) cc_final: 0.8257 (m-80) REVERT: E 5 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8852 (ttmm) REVERT: E 16 PHE cc_start: 0.8033 (m-10) cc_final: 0.7794 (m-10) REVERT: E 41 CYS cc_start: 0.8049 (m) cc_final: 0.7840 (m) REVERT: E 42 TRP cc_start: 0.9114 (t60) cc_final: 0.8172 (t60) REVERT: E 65 ASN cc_start: 0.9206 (p0) cc_final: 0.8962 (p0) REVERT: E 76 ARG cc_start: 0.8271 (ptt-90) cc_final: 0.7446 (mpp80) REVERT: E 92 CYS cc_start: 0.8525 (t) cc_final: 0.8229 (t) REVERT: E 111 MET cc_start: 0.8633 (ppp) cc_final: 0.8362 (ppp) REVERT: E 132 SER cc_start: 0.9319 (m) cc_final: 0.9070 (p) REVERT: E 151 CYS cc_start: 0.9182 (m) cc_final: 0.8418 (m) REVERT: E 169 ILE cc_start: 0.9587 (pt) cc_final: 0.9256 (pt) REVERT: E 200 TYR cc_start: 0.9054 (m-80) cc_final: 0.8786 (m-80) REVERT: E 229 ASP cc_start: 0.8565 (p0) cc_final: 0.8344 (p0) REVERT: E 254 GLU cc_start: 0.8766 (pp20) cc_final: 0.8529 (pp20) REVERT: E 257 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8736 (tm-30) REVERT: E 261 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 262 ASN cc_start: 0.9434 (m-40) cc_final: 0.8895 (m-40) outliers start: 4 outliers final: 0 residues processed: 430 average time/residue: 0.2321 time to fit residues: 142.7793 Evaluate side-chains 355 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 157 HIS A 193 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.080098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.066208 restraints weight = 48319.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.068086 restraints weight = 29986.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.069402 restraints weight = 21303.045| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 13085 Z= 0.342 Angle : 0.927 8.325 17760 Z= 0.492 Chirality : 0.051 0.196 2005 Planarity : 0.007 0.067 2315 Dihedral : 6.897 79.606 1795 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.14 % Allowed : 6.86 % Favored : 93.00 % 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: -2.67 (0.19), residues: 1625 helix: -0.97 (0.16), residues: 910 sheet: -2.11 (0.39), residues: 160 loop : -2.86 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 218 HIS 0.005 0.001 HIS E 157 PHE 0.022 0.003 PHE E 306 TYR 0.020 0.003 TYR A 268 ARG 0.009 0.001 ARG B 199 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 773) hydrogen bonds : angle 6.18311 ( 2235) covalent geometry : bond 0.00722 (13085) covalent geometry : angle 0.92730 (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 376 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 1.381 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 65 ASN cc_start: 0.9125 (p0) cc_final: 0.8785 (p0) REVERT: A 107 MET cc_start: 0.9041 (tmm) cc_final: 0.8836 (tmm) REVERT: A 111 MET cc_start: 0.7911 (ppp) cc_final: 0.7123 (ptm) REVERT: A 157 HIS cc_start: 0.8195 (m90) cc_final: 0.7707 (m-70) REVERT: A 178 ASP cc_start: 0.8601 (t70) cc_final: 0.8362 (t70) REVERT: A 242 ASP cc_start: 0.9155 (p0) cc_final: 0.8935 (p0) REVERT: A 278 LEU cc_start: 0.9117 (pp) cc_final: 0.8910 (pp) REVERT: A 282 PHE cc_start: 0.8805 (m-80) cc_final: 0.8587 (m-80) REVERT: A 305 ILE cc_start: 0.9037 (mt) cc_final: 0.8803 (mm) REVERT: A 307 CYS cc_start: 0.8920 (m) cc_final: 0.8708 (m) REVERT: B 46 ASN cc_start: 0.9327 (t0) cc_final: 0.8987 (t0) REVERT: B 92 CYS cc_start: 0.8286 (t) cc_final: 0.7795 (m) REVERT: B 94 ASN cc_start: 0.6958 (t0) cc_final: 0.6755 (t0) REVERT: B 157 HIS cc_start: 0.7870 (m170) cc_final: 0.7614 (m-70) REVERT: B 160 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8636 (mt-10) REVERT: B 189 LEU cc_start: 0.9184 (pt) cc_final: 0.8380 (tt) REVERT: B 192 LYS cc_start: 0.9216 (ttmm) cc_final: 0.8848 (tmtt) REVERT: B 208 TYR cc_start: 0.8901 (m-80) cc_final: 0.8574 (m-80) REVERT: B 268 TYR cc_start: 0.9003 (t80) cc_final: 0.8777 (t80) REVERT: B 278 LEU cc_start: 0.9085 (tt) cc_final: 0.8650 (tt) REVERT: B 282 PHE cc_start: 0.8578 (m-80) cc_final: 0.8193 (m-10) REVERT: C 46 ASN cc_start: 0.9117 (t0) cc_final: 0.8915 (t0) REVERT: C 123 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8690 (tppp) REVERT: C 157 HIS cc_start: 0.7964 (m170) cc_final: 0.7322 (m-70) REVERT: C 160 GLU cc_start: 0.8715 (pp20) cc_final: 0.8475 (pp20) REVERT: C 208 TYR cc_start: 0.8930 (m-10) cc_final: 0.8527 (m-10) REVERT: C 229 ASP cc_start: 0.8866 (p0) cc_final: 0.8656 (p0) REVERT: C 232 ASP cc_start: 0.8447 (m-30) cc_final: 0.8053 (m-30) REVERT: C 259 MET cc_start: 0.9021 (mmt) cc_final: 0.8779 (mmp) REVERT: C 270 MET cc_start: 0.8782 (ttt) cc_final: 0.8341 (ttp) REVERT: D 1 MET cc_start: 0.7670 (ppp) cc_final: 0.7211 (ppp) REVERT: D 18 TRP cc_start: 0.9183 (m100) cc_final: 0.8736 (m100) REVERT: D 46 ASN cc_start: 0.9372 (t0) cc_final: 0.9121 (t0) REVERT: D 92 CYS cc_start: 0.8735 (t) cc_final: 0.8463 (t) REVERT: D 123 LYS cc_start: 0.9185 (mtpp) cc_final: 0.8794 (mtpp) REVERT: D 169 ILE cc_start: 0.9641 (pt) cc_final: 0.9423 (pt) REVERT: D 189 LEU cc_start: 0.9451 (pt) cc_final: 0.8761 (tt) REVERT: D 192 LYS cc_start: 0.9519 (tttm) cc_final: 0.9253 (tttt) REVERT: D 194 LEU cc_start: 0.9766 (tp) cc_final: 0.9194 (tp) REVERT: D 244 CYS cc_start: 0.9115 (m) cc_final: 0.8547 (t) REVERT: D 251 MET cc_start: 0.8375 (mmt) cc_final: 0.8075 (mmt) REVERT: D 278 LEU cc_start: 0.9152 (tt) cc_final: 0.8884 (tt) REVERT: D 282 PHE cc_start: 0.8522 (m-80) cc_final: 0.8043 (m-80) REVERT: E 5 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8765 (ttmm) REVERT: E 65 ASN cc_start: 0.9252 (p0) cc_final: 0.8960 (p0) REVERT: E 68 ASP cc_start: 0.8063 (t70) cc_final: 0.7794 (t70) REVERT: E 111 MET cc_start: 0.8602 (ppp) cc_final: 0.8251 (ppp) REVERT: E 132 SER cc_start: 0.9462 (m) cc_final: 0.9184 (p) REVERT: E 169 ILE cc_start: 0.9678 (pt) cc_final: 0.9261 (pt) REVERT: E 234 LEU cc_start: 0.9663 (tp) cc_final: 0.9426 (tp) REVERT: E 261 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8037 (tm-30) REVERT: E 262 ASN cc_start: 0.9454 (m-40) cc_final: 0.8883 (m-40) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.2334 time to fit residues: 125.9594 Evaluate side-chains 307 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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: 4.9990 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 204 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** E 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.084655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070268 restraints weight = 46149.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072301 restraints weight = 28793.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073702 restraints weight = 20486.825| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13085 Z= 0.151 Angle : 0.823 10.260 17760 Z= 0.409 Chirality : 0.048 0.243 2005 Planarity : 0.007 0.109 2315 Dihedral : 6.607 78.543 1795 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % 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: -1.91 (0.19), residues: 1625 helix: -0.22 (0.17), residues: 850 sheet: -1.35 (0.44), residues: 135 loop : -2.69 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 218 HIS 0.005 0.001 HIS D 157 PHE 0.025 0.002 PHE A 306 TYR 0.017 0.002 TYR A 268 ARG 0.008 0.001 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 773) hydrogen bonds : angle 5.68871 ( 2235) covalent geometry : bond 0.00336 (13085) covalent geometry : angle 0.82271 (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 419 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 1.385 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: 0.9223 (t0) cc_final: 0.8926 (t0) REVERT: A 65 ASN cc_start: 0.9025 (p0) cc_final: 0.8743 (p0) REVERT: A 110 TYR cc_start: 0.8943 (t80) cc_final: 0.8659 (t80) REVERT: A 111 MET cc_start: 0.7806 (ppp) cc_final: 0.6830 (ptm) REVERT: A 163 GLU cc_start: 0.8936 (tp30) cc_final: 0.8718 (tp30) REVERT: A 178 ASP cc_start: 0.8690 (t70) cc_final: 0.8171 (t70) REVERT: A 282 PHE cc_start: 0.8617 (m-80) cc_final: 0.8386 (m-80) REVERT: A 287 PHE cc_start: 0.7828 (m-10) cc_final: 0.7580 (m-10) REVERT: A 305 ILE cc_start: 0.8988 (mt) cc_final: 0.8747 (mm) REVERT: A 306 PHE cc_start: 0.8105 (p90) cc_final: 0.7786 (p90) REVERT: B 1 MET cc_start: 0.5006 (ppp) cc_final: 0.3947 (ppp) REVERT: B 43 LEU cc_start: 0.8948 (tt) cc_final: 0.8597 (mp) REVERT: B 46 ASN cc_start: 0.9273 (t0) cc_final: 0.8811 (t0) REVERT: B 65 ASN cc_start: 0.8776 (p0) cc_final: 0.8196 (p0) REVERT: B 92 CYS cc_start: 0.8159 (t) cc_final: 0.7679 (m) REVERT: B 107 MET cc_start: 0.8536 (tmm) cc_final: 0.8240 (tmm) REVERT: B 160 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8570 (mt-10) REVERT: B 189 LEU cc_start: 0.9075 (pt) cc_final: 0.8070 (tt) REVERT: B 192 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8672 (tmtt) REVERT: B 200 TYR cc_start: 0.7657 (m-10) cc_final: 0.7016 (m-10) REVERT: B 232 ASP cc_start: 0.8629 (m-30) cc_final: 0.8429 (m-30) REVERT: B 273 MET cc_start: 0.9203 (mtp) cc_final: 0.8978 (mtt) REVERT: B 278 LEU cc_start: 0.8799 (tt) cc_final: 0.8529 (tt) REVERT: B 282 PHE cc_start: 0.8519 (m-80) cc_final: 0.8156 (m-10) REVERT: C 46 ASN cc_start: 0.9122 (t0) cc_final: 0.8824 (t0) REVERT: C 68 ASP cc_start: 0.8388 (t70) cc_final: 0.7922 (t0) REVERT: C 123 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8643 (tppp) REVERT: C 157 HIS cc_start: 0.7790 (m170) cc_final: 0.7229 (m90) REVERT: C 176 LEU cc_start: 0.9340 (pp) cc_final: 0.9121 (pp) REVERT: C 200 TYR cc_start: 0.8592 (m-80) cc_final: 0.7096 (m-80) REVERT: C 208 TYR cc_start: 0.8869 (m-10) cc_final: 0.8442 (m-10) REVERT: C 229 ASP cc_start: 0.8844 (p0) cc_final: 0.8627 (p0) REVERT: C 240 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 270 MET cc_start: 0.8796 (ttt) cc_final: 0.8329 (ttp) REVERT: C 326 TRP cc_start: 0.7577 (m100) cc_final: 0.7024 (m100) REVERT: D 1 MET cc_start: 0.7606 (ppp) cc_final: 0.7111 (ppp) REVERT: D 18 TRP cc_start: 0.8979 (m100) cc_final: 0.8655 (m100) REVERT: D 46 ASN cc_start: 0.9381 (t0) cc_final: 0.9095 (t0) REVERT: D 76 ARG cc_start: 0.8558 (mtp85) cc_final: 0.7142 (mmm-85) REVERT: D 78 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.8000 (ttp-110) REVERT: D 92 CYS cc_start: 0.8704 (t) cc_final: 0.8396 (t) REVERT: D 111 MET cc_start: 0.7917 (ttt) cc_final: 0.6799 (tmm) REVERT: D 123 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8879 (mmmm) REVERT: D 194 LEU cc_start: 0.9722 (tp) cc_final: 0.9138 (tp) REVERT: D 200 TYR cc_start: 0.8614 (m-80) cc_final: 0.8001 (m-80) REVERT: D 244 CYS cc_start: 0.9018 (m) cc_final: 0.8540 (t) REVERT: D 275 MET cc_start: 0.9072 (mmm) cc_final: 0.8811 (mmm) REVERT: D 278 LEU cc_start: 0.8995 (tt) cc_final: 0.8236 (tt) REVERT: D 282 PHE cc_start: 0.8635 (m-80) cc_final: 0.8065 (m-80) REVERT: E 5 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8776 (ttmm) REVERT: E 51 ASP cc_start: 0.8599 (m-30) cc_final: 0.8197 (t0) REVERT: E 65 ASN cc_start: 0.9186 (p0) cc_final: 0.8901 (p0) REVERT: E 111 MET cc_start: 0.8638 (ppp) cc_final: 0.8291 (ppp) REVERT: E 132 SER cc_start: 0.9384 (m) cc_final: 0.9115 (p) REVERT: E 169 ILE cc_start: 0.9667 (pt) cc_final: 0.9207 (pt) REVERT: E 179 GLN cc_start: 0.8146 (mp10) cc_final: 0.7330 (mp10) REVERT: E 197 MET cc_start: 0.8912 (ttm) cc_final: 0.8103 (ttm) REVERT: E 232 ASP cc_start: 0.8654 (m-30) cc_final: 0.8205 (m-30) REVERT: E 234 LEU cc_start: 0.9544 (tp) cc_final: 0.9312 (tp) REVERT: E 261 GLU cc_start: 0.8621 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 262 ASN cc_start: 0.9373 (m-40) cc_final: 0.8778 (m-40) REVERT: E 270 MET cc_start: 0.8761 (tpt) cc_final: 0.8494 (tpt) outliers start: 1 outliers final: 1 residues processed: 419 average time/residue: 0.2451 time to fit residues: 149.7247 Evaluate side-chains 325 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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: 4.9990 chunk 138 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071557 restraints weight = 46430.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073596 restraints weight = 28881.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075020 restraints weight = 20503.607| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13085 Z= 0.149 Angle : 0.820 10.658 17760 Z= 0.407 Chirality : 0.048 0.210 2005 Planarity : 0.006 0.057 2315 Dihedral : 6.412 77.695 1795 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -1.69 (0.20), residues: 1625 helix: -0.02 (0.17), residues: 845 sheet: -1.27 (0.43), residues: 135 loop : -2.61 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 18 HIS 0.008 0.001 HIS B 157 PHE 0.041 0.002 PHE C 306 TYR 0.015 0.002 TYR B 110 ARG 0.009 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 773) hydrogen bonds : angle 5.57260 ( 2235) covalent geometry : bond 0.00335 (13085) covalent geometry : angle 0.82002 (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 410 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8123 (p90) cc_final: 0.7689 (p90) REVERT: A 46 ASN cc_start: 0.9222 (t0) cc_final: 0.8937 (t0) REVERT: A 65 ASN cc_start: 0.9029 (p0) cc_final: 0.8708 (p0) REVERT: A 110 TYR cc_start: 0.8848 (t80) cc_final: 0.8558 (t80) REVERT: A 111 MET cc_start: 0.7648 (ppp) cc_final: 0.6564 (ptm) REVERT: A 169 ILE cc_start: 0.9683 (pt) cc_final: 0.9444 (pt) REVERT: A 178 ASP cc_start: 0.8729 (t70) cc_final: 0.8228 (t70) REVERT: A 282 PHE cc_start: 0.8604 (m-80) cc_final: 0.8351 (m-80) REVERT: A 305 ILE cc_start: 0.8989 (mt) cc_final: 0.8741 (mm) REVERT: A 306 PHE cc_start: 0.8130 (p90) cc_final: 0.7869 (p90) REVERT: A 307 CYS cc_start: 0.8844 (m) cc_final: 0.8632 (m) REVERT: A 326 TRP cc_start: 0.7452 (m100) cc_final: 0.7060 (m100) REVERT: B 1 MET cc_start: 0.4806 (ppp) cc_final: 0.3815 (ppp) REVERT: B 46 ASN cc_start: 0.9238 (t0) cc_final: 0.8820 (t0) REVERT: B 65 ASN cc_start: 0.8932 (p0) cc_final: 0.8359 (p0) REVERT: B 111 MET cc_start: 0.8260 (tpt) cc_final: 0.7912 (tpt) REVERT: B 160 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8779 (mt-10) REVERT: B 189 LEU cc_start: 0.8974 (pt) cc_final: 0.8003 (tp) REVERT: B 192 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8568 (tttt) REVERT: B 200 TYR cc_start: 0.7481 (m-10) cc_final: 0.7001 (m-10) REVERT: B 232 ASP cc_start: 0.8550 (m-30) cc_final: 0.8335 (m-30) REVERT: C 46 ASN cc_start: 0.9124 (t0) cc_final: 0.8806 (t0) REVERT: C 68 ASP cc_start: 0.8456 (t70) cc_final: 0.8003 (t0) REVERT: C 111 MET cc_start: 0.8444 (ptm) cc_final: 0.8099 (ppp) REVERT: C 123 LYS cc_start: 0.9030 (mtpp) cc_final: 0.8708 (tppp) REVERT: C 176 LEU cc_start: 0.9380 (pp) cc_final: 0.8968 (pp) REVERT: C 208 TYR cc_start: 0.8806 (m-10) cc_final: 0.8278 (m-80) REVERT: C 229 ASP cc_start: 0.8893 (p0) cc_final: 0.8673 (p0) REVERT: C 270 MET cc_start: 0.8838 (ttt) cc_final: 0.8508 (ttp) REVERT: D 1 MET cc_start: 0.7558 (ppp) cc_final: 0.6977 (ppp) REVERT: D 18 TRP cc_start: 0.8973 (m100) cc_final: 0.8515 (m100) REVERT: D 46 ASN cc_start: 0.9376 (t0) cc_final: 0.9073 (t0) REVERT: D 65 ASN cc_start: 0.9142 (p0) cc_final: 0.8930 (p0) REVERT: D 76 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8576 (mtm-85) REVERT: D 78 ARG cc_start: 0.8778 (ttp-110) cc_final: 0.8556 (ttp-110) REVERT: D 92 CYS cc_start: 0.8631 (t) cc_final: 0.8331 (t) REVERT: D 111 MET cc_start: 0.7889 (ttt) cc_final: 0.7173 (ttt) REVERT: D 123 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8841 (mmmm) REVERT: D 169 ILE cc_start: 0.9535 (pt) cc_final: 0.9322 (pt) REVERT: D 194 LEU cc_start: 0.9707 (tp) cc_final: 0.9156 (tp) REVERT: D 200 TYR cc_start: 0.8727 (m-80) cc_final: 0.7996 (m-80) REVERT: D 244 CYS cc_start: 0.9096 (m) cc_final: 0.8463 (t) REVERT: D 254 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 278 LEU cc_start: 0.8975 (tt) cc_final: 0.8470 (tt) REVERT: D 282 PHE cc_start: 0.8655 (m-80) cc_final: 0.8370 (m-80) REVERT: E 5 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8789 (ttmm) REVERT: E 18 TRP cc_start: 0.8339 (m-90) cc_final: 0.7829 (m-90) REVERT: E 51 ASP cc_start: 0.8666 (m-30) cc_final: 0.8084 (t0) REVERT: E 65 ASN cc_start: 0.9131 (p0) cc_final: 0.8877 (p0) REVERT: E 70 LEU cc_start: 0.9633 (tp) cc_final: 0.9400 (tt) REVERT: E 76 ARG cc_start: 0.8236 (mtm180) cc_final: 0.7978 (ptt180) REVERT: E 111 MET cc_start: 0.8635 (ppp) cc_final: 0.8273 (ppp) REVERT: E 132 SER cc_start: 0.9362 (m) cc_final: 0.9068 (p) REVERT: E 169 ILE cc_start: 0.9682 (pt) cc_final: 0.9257 (pt) REVERT: E 179 GLN cc_start: 0.8386 (mp10) cc_final: 0.7638 (mp10) REVERT: E 232 ASP cc_start: 0.8634 (m-30) cc_final: 0.8425 (m-30) REVERT: E 234 LEU cc_start: 0.9451 (tp) cc_final: 0.9210 (tp) REVERT: E 261 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 262 ASN cc_start: 0.9309 (m-40) cc_final: 0.8769 (m-40) REVERT: E 270 MET cc_start: 0.9070 (tpt) cc_final: 0.8779 (tpt) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.2248 time to fit residues: 133.0033 Evaluate side-chains 343 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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: 0.7980 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** 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 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064340 restraints weight = 48204.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066467 restraints weight = 30023.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067935 restraints weight = 21173.048| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13085 Z= 0.165 Angle : 0.816 10.240 17760 Z= 0.410 Chirality : 0.049 0.227 2005 Planarity : 0.006 0.057 2315 Dihedral : 6.309 78.123 1795 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % 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: -1.52 (0.20), residues: 1625 helix: 0.15 (0.17), residues: 845 sheet: -1.31 (0.43), residues: 135 loop : -2.53 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 218 HIS 0.013 0.001 HIS E 50 PHE 0.029 0.002 PHE D 306 TYR 0.014 0.002 TYR D 110 ARG 0.011 0.000 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 773) hydrogen bonds : angle 5.48410 ( 2235) covalent geometry : bond 0.00374 (13085) covalent geometry : angle 0.81618 (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 399 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.509 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: 0.9240 (t0) cc_final: 0.8934 (t0) REVERT: A 65 ASN cc_start: 0.9116 (p0) cc_final: 0.8773 (p0) REVERT: A 110 TYR cc_start: 0.8833 (t80) cc_final: 0.8506 (t80) REVERT: A 111 MET cc_start: 0.7563 (ppp) cc_final: 0.6589 (ptm) REVERT: A 169 ILE cc_start: 0.9646 (pt) cc_final: 0.9387 (pt) REVERT: A 178 ASP cc_start: 0.8689 (t70) cc_final: 0.8215 (t70) REVERT: A 200 TYR cc_start: 0.8564 (m-80) cc_final: 0.7847 (m-80) REVERT: A 282 PHE cc_start: 0.8693 (m-80) cc_final: 0.8473 (m-80) REVERT: A 305 ILE cc_start: 0.8934 (mt) cc_final: 0.8705 (mm) REVERT: B 1 MET cc_start: 0.4852 (ppp) cc_final: 0.3838 (ppp) REVERT: B 46 ASN cc_start: 0.9279 (t0) cc_final: 0.8696 (t0) REVERT: B 92 CYS cc_start: 0.8075 (t) cc_final: 0.7818 (t) REVERT: B 107 MET cc_start: 0.8676 (tmm) cc_final: 0.8264 (tmm) REVERT: B 111 MET cc_start: 0.8163 (tpt) cc_final: 0.7961 (tpt) REVERT: B 160 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 192 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8651 (tttt) REVERT: B 200 TYR cc_start: 0.7666 (m-10) cc_final: 0.7003 (m-10) REVERT: B 232 ASP cc_start: 0.8555 (m-30) cc_final: 0.8315 (m-30) REVERT: B 251 MET cc_start: 0.8053 (mmt) cc_final: 0.7672 (mmt) REVERT: B 259 MET cc_start: 0.8640 (ttm) cc_final: 0.8388 (ttp) REVERT: C 46 ASN cc_start: 0.9110 (t0) cc_final: 0.8859 (t0) REVERT: C 68 ASP cc_start: 0.8316 (t70) cc_final: 0.7852 (t0) REVERT: C 111 MET cc_start: 0.8421 (ptm) cc_final: 0.8053 (ppp) REVERT: C 123 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8684 (tppp) REVERT: C 163 GLU cc_start: 0.8779 (tp30) cc_final: 0.8560 (tp30) REVERT: C 197 MET cc_start: 0.8952 (tpp) cc_final: 0.8595 (tpp) REVERT: C 200 TYR cc_start: 0.8729 (m-80) cc_final: 0.8207 (m-80) REVERT: C 208 TYR cc_start: 0.8821 (m-10) cc_final: 0.8471 (m-80) REVERT: C 229 ASP cc_start: 0.8820 (p0) cc_final: 0.8551 (p0) REVERT: C 250 VAL cc_start: 0.9410 (m) cc_final: 0.9206 (m) REVERT: C 268 TYR cc_start: 0.9010 (t80) cc_final: 0.8759 (t80) REVERT: C 270 MET cc_start: 0.8893 (ttt) cc_final: 0.8456 (ttp) REVERT: C 275 MET cc_start: 0.8180 (mmp) cc_final: 0.7895 (mmp) REVERT: C 326 TRP cc_start: 0.7725 (m100) cc_final: 0.6282 (m100) REVERT: D 1 MET cc_start: 0.7578 (ppp) cc_final: 0.6943 (ppp) REVERT: D 18 TRP cc_start: 0.8882 (m100) cc_final: 0.8392 (m100) REVERT: D 46 ASN cc_start: 0.9363 (t0) cc_final: 0.9059 (t0) REVERT: D 76 ARG cc_start: 0.8813 (mtp85) cc_final: 0.7969 (mtp85) REVERT: D 78 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8563 (ttp-110) REVERT: D 92 CYS cc_start: 0.8586 (t) cc_final: 0.8324 (t) REVERT: D 123 LYS cc_start: 0.9149 (mtpp) cc_final: 0.8841 (mmmm) REVERT: D 194 LEU cc_start: 0.9725 (tp) cc_final: 0.9146 (tp) REVERT: D 244 CYS cc_start: 0.9029 (m) cc_final: 0.8484 (t) REVERT: D 278 LEU cc_start: 0.8999 (tt) cc_final: 0.8557 (tt) REVERT: D 282 PHE cc_start: 0.8617 (m-80) cc_final: 0.8410 (m-80) REVERT: E 5 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8876 (ttmm) REVERT: E 18 TRP cc_start: 0.8384 (m-90) cc_final: 0.7822 (m-90) REVERT: E 65 ASN cc_start: 0.9105 (p0) cc_final: 0.8840 (p0) REVERT: E 111 MET cc_start: 0.8295 (ppp) cc_final: 0.7987 (ppp) REVERT: E 132 SER cc_start: 0.9371 (m) cc_final: 0.9087 (p) REVERT: E 151 CYS cc_start: 0.9147 (m) cc_final: 0.8806 (m) REVERT: E 169 ILE cc_start: 0.9664 (pt) cc_final: 0.9241 (pt) REVERT: E 179 GLN cc_start: 0.8294 (mp10) cc_final: 0.7708 (mp10) REVERT: E 208 TYR cc_start: 0.8507 (m-10) cc_final: 0.7861 (m-80) REVERT: E 232 ASP cc_start: 0.8570 (m-30) cc_final: 0.7385 (m-30) REVERT: E 234 LEU cc_start: 0.9440 (tp) cc_final: 0.9182 (tp) REVERT: E 261 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 262 ASN cc_start: 0.9335 (m-40) cc_final: 0.8812 (m-40) REVERT: E 270 MET cc_start: 0.9029 (tpt) cc_final: 0.8776 (tpt) REVERT: E 273 MET cc_start: 0.8604 (ttm) cc_final: 0.8243 (ttm) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2241 time to fit residues: 130.3918 Evaluate side-chains 335 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 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 64 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070733 restraints weight = 46843.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072728 restraints weight = 28998.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074112 restraints weight = 20483.050| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 0.053 13085 Z= 0.197 Angle : 0.832 10.680 17760 Z= 0.422 Chirality : 0.049 0.198 2005 Planarity : 0.006 0.094 2315 Dihedral : 6.271 78.662 1795 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -1.38 (0.20), residues: 1625 helix: 0.30 (0.18), residues: 845 sheet: -1.34 (0.44), residues: 135 loop : -2.51 (0.22), residues: 645 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 0.033 0.003 PHE B 306 TYR 0.017 0.002 TYR E 208 ARG 0.013 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 773) hydrogen bonds : angle 5.47104 ( 2235) covalent geometry : bond 0.00441 (13085) covalent geometry : angle 0.83196 (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 396 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9241 (t0) cc_final: 0.8952 (t0) REVERT: A 65 ASN cc_start: 0.9060 (p0) cc_final: 0.8741 (p0) REVERT: A 110 TYR cc_start: 0.8850 (t80) cc_final: 0.8496 (t80) REVERT: A 169 ILE cc_start: 0.9657 (pt) cc_final: 0.9393 (pt) REVERT: A 176 LEU cc_start: 0.9431 (pp) cc_final: 0.9217 (pp) REVERT: A 177 LEU cc_start: 0.9388 (mt) cc_final: 0.8980 (pp) REVERT: A 178 ASP cc_start: 0.8656 (t70) cc_final: 0.8290 (t70) REVERT: A 305 ILE cc_start: 0.9048 (mt) cc_final: 0.8816 (mm) REVERT: A 326 TRP cc_start: 0.7345 (m100) cc_final: 0.6975 (m100) REVERT: B 1 MET cc_start: 0.4956 (ppp) cc_final: 0.3692 (ppp) REVERT: B 41 CYS cc_start: 0.7956 (m) cc_final: 0.7653 (m) REVERT: B 46 ASN cc_start: 0.9248 (t0) cc_final: 0.8561 (t0) REVERT: B 92 CYS cc_start: 0.8089 (t) cc_final: 0.7834 (t) REVERT: B 107 MET cc_start: 0.8647 (tmm) cc_final: 0.8293 (tmm) REVERT: B 134 LEU cc_start: 0.9427 (pp) cc_final: 0.9139 (pp) REVERT: B 160 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 192 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8729 (tttt) REVERT: B 197 MET cc_start: 0.9204 (tpp) cc_final: 0.8817 (tpp) REVERT: B 200 TYR cc_start: 0.8217 (m-10) cc_final: 0.8000 (m-80) REVERT: C 46 ASN cc_start: 0.9130 (t0) cc_final: 0.8862 (t0) REVERT: C 68 ASP cc_start: 0.8412 (t70) cc_final: 0.8156 (t0) REVERT: C 100 ARG cc_start: 0.8284 (mmp-170) cc_final: 0.7338 (mmp80) REVERT: C 123 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8628 (tppp) REVERT: C 197 MET cc_start: 0.8889 (tpp) cc_final: 0.8651 (tpp) REVERT: C 200 TYR cc_start: 0.8699 (m-80) cc_final: 0.8293 (m-80) REVERT: C 208 TYR cc_start: 0.8981 (m-10) cc_final: 0.8713 (m-80) REVERT: C 229 ASP cc_start: 0.8896 (p0) cc_final: 0.8664 (p0) REVERT: C 240 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8413 (mm-30) REVERT: C 268 TYR cc_start: 0.9064 (t80) cc_final: 0.8788 (t80) REVERT: C 270 MET cc_start: 0.8923 (ttt) cc_final: 0.8535 (ttp) REVERT: C 275 MET cc_start: 0.8457 (mmp) cc_final: 0.8192 (mmp) REVERT: C 326 TRP cc_start: 0.7684 (m100) cc_final: 0.6073 (m100) REVERT: D 1 MET cc_start: 0.7443 (ppp) cc_final: 0.6850 (ppp) REVERT: D 18 TRP cc_start: 0.8909 (m100) cc_final: 0.8461 (m100) REVERT: D 46 ASN cc_start: 0.9354 (t0) cc_final: 0.9051 (t0) REVERT: D 78 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8223 (ttp-110) REVERT: D 92 CYS cc_start: 0.8613 (t) cc_final: 0.8259 (t) REVERT: D 111 MET cc_start: 0.8306 (ttp) cc_final: 0.8001 (tmm) REVERT: D 123 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8787 (mmmm) REVERT: D 194 LEU cc_start: 0.9753 (tp) cc_final: 0.9216 (tp) REVERT: D 200 TYR cc_start: 0.8215 (m-80) cc_final: 0.7845 (m-80) REVERT: D 239 ASP cc_start: 0.9225 (t0) cc_final: 0.8949 (t70) REVERT: D 244 CYS cc_start: 0.9023 (m) cc_final: 0.8333 (t) REVERT: D 278 LEU cc_start: 0.9123 (tt) cc_final: 0.8913 (tt) REVERT: E 5 LYS cc_start: 0.9256 (ttmm) cc_final: 0.8854 (ttmm) REVERT: E 18 TRP cc_start: 0.8488 (m-90) cc_final: 0.7834 (m-90) REVERT: E 65 ASN cc_start: 0.9113 (p0) cc_final: 0.8859 (p0) REVERT: E 111 MET cc_start: 0.8417 (ppp) cc_final: 0.8097 (ppp) REVERT: E 132 SER cc_start: 0.9416 (m) cc_final: 0.9147 (p) REVERT: E 151 CYS cc_start: 0.9320 (m) cc_final: 0.8909 (m) REVERT: E 169 ILE cc_start: 0.9631 (pt) cc_final: 0.9124 (pt) REVERT: E 197 MET cc_start: 0.8906 (ttm) cc_final: 0.8151 (ttm) REVERT: E 232 ASP cc_start: 0.8580 (m-30) cc_final: 0.8306 (m-30) REVERT: E 234 LEU cc_start: 0.9427 (tp) cc_final: 0.9211 (tp) REVERT: E 257 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8787 (tm-30) REVERT: E 261 GLU cc_start: 0.8736 (tm-30) cc_final: 0.7969 (tm-30) REVERT: E 262 ASN cc_start: 0.9324 (m-40) cc_final: 0.8782 (m-40) REVERT: E 268 TYR cc_start: 0.8043 (t80) cc_final: 0.7729 (t80) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2417 time to fit residues: 141.6931 Evaluate side-chains 336 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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: 0.9990 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.087241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072404 restraints weight = 46871.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074482 restraints weight = 29301.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075946 restraints weight = 20800.006| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4754 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= 0.148 Angle : 0.843 12.151 17760 Z= 0.414 Chirality : 0.049 0.297 2005 Planarity : 0.006 0.063 2315 Dihedral : 6.220 78.528 1795 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1625 helix: 0.35 (0.18), residues: 845 sheet: -1.62 (0.40), residues: 160 loop : -2.41 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 18 HIS 0.007 0.001 HIS B 157 PHE 0.044 0.002 PHE C 306 TYR 0.014 0.001 TYR A 268 ARG 0.017 0.001 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 773) hydrogen bonds : angle 5.37130 ( 2235) covalent geometry : bond 0.00340 (13085) covalent geometry : angle 0.84268 (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 418 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9236 (t0) cc_final: 0.8947 (t0) REVERT: A 65 ASN cc_start: 0.9050 (p0) cc_final: 0.8736 (p0) REVERT: A 110 TYR cc_start: 0.8734 (t80) cc_final: 0.8361 (t80) REVERT: A 169 ILE cc_start: 0.9667 (pt) cc_final: 0.9438 (pt) REVERT: A 177 LEU cc_start: 0.9412 (mt) cc_final: 0.8971 (pp) REVERT: A 200 TYR cc_start: 0.8418 (m-80) cc_final: 0.7771 (m-80) REVERT: A 305 ILE cc_start: 0.9045 (mt) cc_final: 0.8816 (mm) REVERT: A 326 TRP cc_start: 0.7316 (m100) cc_final: 0.6952 (m100) REVERT: B 1 MET cc_start: 0.4925 (ppp) cc_final: 0.3688 (ppp) REVERT: B 41 CYS cc_start: 0.7914 (m) cc_final: 0.7559 (m) REVERT: B 46 ASN cc_start: 0.9163 (t0) cc_final: 0.8466 (t0) REVERT: B 65 ASN cc_start: 0.8878 (p0) cc_final: 0.8342 (p0) REVERT: B 92 CYS cc_start: 0.7973 (t) cc_final: 0.7724 (m) REVERT: B 107 MET cc_start: 0.8561 (tmm) cc_final: 0.8351 (tmm) REVERT: B 134 LEU cc_start: 0.9372 (pp) cc_final: 0.9040 (pp) REVERT: B 160 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8769 (mt-10) REVERT: B 192 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8598 (tttm) REVERT: B 232 ASP cc_start: 0.8477 (m-30) cc_final: 0.8227 (m-30) REVERT: B 259 MET cc_start: 0.8581 (ttm) cc_final: 0.8334 (ttp) REVERT: C 46 ASN cc_start: 0.9111 (t0) cc_final: 0.8841 (t0) REVERT: C 68 ASP cc_start: 0.8442 (t70) cc_final: 0.8026 (t0) REVERT: C 151 CYS cc_start: 0.9202 (m) cc_final: 0.8938 (m) REVERT: C 200 TYR cc_start: 0.8732 (m-80) cc_final: 0.8182 (m-80) REVERT: C 228 GLN cc_start: 0.9311 (tp40) cc_final: 0.8759 (tp40) REVERT: C 268 TYR cc_start: 0.8982 (t80) cc_final: 0.8732 (t80) REVERT: C 270 MET cc_start: 0.8925 (ttt) cc_final: 0.8562 (ttp) REVERT: C 275 MET cc_start: 0.8418 (mmp) cc_final: 0.8214 (mmp) REVERT: C 326 TRP cc_start: 0.7733 (m100) cc_final: 0.6276 (m100) REVERT: D 1 MET cc_start: 0.7428 (ppp) cc_final: 0.6778 (ppp) REVERT: D 18 TRP cc_start: 0.8863 (m100) cc_final: 0.8356 (m100) REVERT: D 46 ASN cc_start: 0.9349 (t0) cc_final: 0.9036 (t0) REVERT: D 65 ASN cc_start: 0.9093 (p0) cc_final: 0.8675 (p0) REVERT: D 78 ARG cc_start: 0.8783 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: D 92 CYS cc_start: 0.8483 (t) cc_final: 0.8220 (t) REVERT: D 111 MET cc_start: 0.8404 (ttp) cc_final: 0.7575 (tmm) REVERT: D 123 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8828 (mmmm) REVERT: D 169 ILE cc_start: 0.9504 (pt) cc_final: 0.9272 (pt) REVERT: D 194 LEU cc_start: 0.9751 (tp) cc_final: 0.9289 (tp) REVERT: D 200 TYR cc_start: 0.8512 (m-80) cc_final: 0.7851 (m-80) REVERT: D 244 CYS cc_start: 0.8986 (m) cc_final: 0.8289 (t) REVERT: D 278 LEU cc_start: 0.9102 (tt) cc_final: 0.8717 (tt) REVERT: D 282 PHE cc_start: 0.8642 (m-80) cc_final: 0.8410 (m-80) REVERT: E 5 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8874 (ttmm) REVERT: E 18 TRP cc_start: 0.8362 (m-90) cc_final: 0.8068 (m100) REVERT: E 65 ASN cc_start: 0.9092 (p0) cc_final: 0.8857 (p0) REVERT: E 92 CYS cc_start: 0.7809 (t) cc_final: 0.7525 (t) REVERT: E 100 ARG cc_start: 0.7652 (mmp-170) cc_final: 0.7409 (mmm160) REVERT: E 111 MET cc_start: 0.8442 (ppp) cc_final: 0.8087 (ppp) REVERT: E 132 SER cc_start: 0.9417 (m) cc_final: 0.9176 (p) REVERT: E 151 CYS cc_start: 0.9416 (m) cc_final: 0.8334 (m) REVERT: E 169 ILE cc_start: 0.9675 (pt) cc_final: 0.9256 (pt) REVERT: E 180 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8740 (tp-100) REVERT: E 232 ASP cc_start: 0.8547 (m-30) cc_final: 0.8247 (m-30) REVERT: E 234 LEU cc_start: 0.9401 (tp) cc_final: 0.9130 (tp) REVERT: E 261 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8057 (tm-30) REVERT: E 262 ASN cc_start: 0.9332 (m-40) cc_final: 0.8763 (m-40) REVERT: E 268 TYR cc_start: 0.8023 (t80) cc_final: 0.7666 (t80) REVERT: E 273 MET cc_start: 0.8501 (ttm) cc_final: 0.8256 (ttm) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.2196 time to fit residues: 133.2036 Evaluate side-chains 332 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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: 3.9990 chunk 158 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071400 restraints weight = 47226.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073353 restraints weight = 30469.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.074737 restraints weight = 22160.974| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13085 Z= 0.172 Angle : 0.855 12.020 17760 Z= 0.428 Chirality : 0.049 0.267 2005 Planarity : 0.006 0.081 2315 Dihedral : 6.257 78.697 1795 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -1.42 (0.20), residues: 1625 helix: 0.17 (0.18), residues: 875 sheet: -1.63 (0.41), residues: 160 loop : -2.41 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 146 HIS 0.008 0.001 HIS B 157 PHE 0.035 0.003 PHE B 306 TYR 0.015 0.002 TYR D 110 ARG 0.018 0.001 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 773) hydrogen bonds : angle 5.39451 ( 2235) covalent geometry : bond 0.00391 (13085) covalent geometry : angle 0.85474 (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 401 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.418 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: 0.9249 (t0) cc_final: 0.8966 (t0) REVERT: A 65 ASN cc_start: 0.9086 (p0) cc_final: 0.8739 (p0) REVERT: A 110 TYR cc_start: 0.8751 (t80) cc_final: 0.8340 (t80) REVERT: A 169 ILE cc_start: 0.9707 (pt) cc_final: 0.9456 (pt) REVERT: A 177 LEU cc_start: 0.9378 (mt) cc_final: 0.8960 (pp) REVERT: A 178 ASP cc_start: 0.8404 (t70) cc_final: 0.8085 (t70) REVERT: A 200 TYR cc_start: 0.8519 (m-80) cc_final: 0.7736 (m-80) REVERT: A 305 ILE cc_start: 0.8991 (mt) cc_final: 0.8768 (mm) REVERT: A 326 TRP cc_start: 0.7345 (m100) cc_final: 0.7011 (m100) REVERT: B 1 MET cc_start: 0.4953 (ppp) cc_final: 0.3684 (ppp) REVERT: B 41 CYS cc_start: 0.7866 (m) cc_final: 0.7410 (m) REVERT: B 46 ASN cc_start: 0.9246 (t0) cc_final: 0.8618 (t0) REVERT: B 65 ASN cc_start: 0.8911 (p0) cc_final: 0.8309 (p0) REVERT: B 92 CYS cc_start: 0.8117 (t) cc_final: 0.7718 (m) REVERT: B 134 LEU cc_start: 0.9399 (pp) cc_final: 0.9057 (pp) REVERT: B 160 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 192 LYS cc_start: 0.9111 (ttmm) cc_final: 0.8782 (tmtt) REVERT: B 200 TYR cc_start: 0.8590 (m-10) cc_final: 0.8383 (m-80) REVERT: B 229 ASP cc_start: 0.8624 (p0) cc_final: 0.8407 (p0) REVERT: B 253 ASP cc_start: 0.8546 (t70) cc_final: 0.8343 (t70) REVERT: B 257 GLN cc_start: 0.8854 (pp30) cc_final: 0.8116 (tm-30) REVERT: B 268 TYR cc_start: 0.9044 (t80) cc_final: 0.8839 (t80) REVERT: B 275 MET cc_start: 0.8676 (tpp) cc_final: 0.7961 (tpp) REVERT: C 46 ASN cc_start: 0.9112 (t0) cc_final: 0.8887 (t0) REVERT: C 68 ASP cc_start: 0.8432 (t70) cc_final: 0.8026 (t0) REVERT: C 163 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8757 (tp30) REVERT: C 200 TYR cc_start: 0.8767 (m-80) cc_final: 0.8204 (m-80) REVERT: C 232 ASP cc_start: 0.8359 (m-30) cc_final: 0.8139 (m-30) REVERT: C 268 TYR cc_start: 0.8978 (t80) cc_final: 0.8733 (t80) REVERT: C 270 MET cc_start: 0.8850 (ttt) cc_final: 0.8561 (ttp) REVERT: C 275 MET cc_start: 0.8421 (mmp) cc_final: 0.8134 (mmp) REVERT: C 326 TRP cc_start: 0.7718 (m100) cc_final: 0.6263 (m100) REVERT: D 1 MET cc_start: 0.7343 (ppp) cc_final: 0.6712 (ppp) REVERT: D 18 TRP cc_start: 0.8799 (m100) cc_final: 0.8565 (m100) REVERT: D 46 ASN cc_start: 0.9364 (t0) cc_final: 0.9060 (t0) REVERT: D 65 ASN cc_start: 0.8953 (p0) cc_final: 0.8586 (p0) REVERT: D 78 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8334 (ttp-110) REVERT: D 92 CYS cc_start: 0.8439 (t) cc_final: 0.8169 (t) REVERT: D 111 MET cc_start: 0.8793 (ttp) cc_final: 0.8149 (tmm) REVERT: D 123 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8871 (mmmm) REVERT: D 169 ILE cc_start: 0.9577 (pt) cc_final: 0.8917 (pt) REVERT: D 189 LEU cc_start: 0.9235 (pp) cc_final: 0.8550 (tt) REVERT: D 200 TYR cc_start: 0.8414 (m-80) cc_final: 0.7876 (m-80) REVERT: D 244 CYS cc_start: 0.8927 (m) cc_final: 0.8658 (t) REVERT: D 278 LEU cc_start: 0.9184 (tt) cc_final: 0.8770 (tt) REVERT: D 287 PHE cc_start: 0.8254 (m-80) cc_final: 0.8040 (m-10) REVERT: E 5 LYS cc_start: 0.9289 (ttmm) cc_final: 0.8896 (ttmm) REVERT: E 18 TRP cc_start: 0.8312 (m-90) cc_final: 0.7991 (m100) REVERT: E 100 ARG cc_start: 0.7737 (mmp-170) cc_final: 0.7165 (mmm160) REVERT: E 111 MET cc_start: 0.8386 (ppp) cc_final: 0.8052 (ppp) REVERT: E 132 SER cc_start: 0.9412 (m) cc_final: 0.9170 (p) REVERT: E 151 CYS cc_start: 0.9332 (m) cc_final: 0.8812 (m) REVERT: E 169 ILE cc_start: 0.9689 (pt) cc_final: 0.9249 (pt) REVERT: E 177 LEU cc_start: 0.9194 (mt) cc_final: 0.8916 (mt) REVERT: E 232 ASP cc_start: 0.8562 (m-30) cc_final: 0.8251 (m-30) REVERT: E 261 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8007 (tm-30) REVERT: E 262 ASN cc_start: 0.9179 (m-40) cc_final: 0.8644 (m-40) REVERT: E 268 TYR cc_start: 0.8110 (t80) cc_final: 0.7632 (t80) REVERT: E 270 MET cc_start: 0.9089 (tpt) cc_final: 0.8820 (tpt) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2238 time to fit residues: 131.7765 Evaluate side-chains 324 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1742 > 50: distance: 44 - 179: 10.960 distance: 55 - 163: 14.101 distance: 58 - 160: 14.423 distance: 73 - 151: 5.111 distance: 76 - 148: 8.176 distance: 101 - 105: 17.524 distance: 105 - 106: 18.971 distance: 106 - 107: 14.402 distance: 106 - 109: 15.774 distance: 107 - 108: 25.757 distance: 107 - 116: 11.485 distance: 109 - 110: 12.862 distance: 110 - 111: 7.067 distance: 111 - 112: 10.184 distance: 112 - 113: 3.385 distance: 113 - 114: 7.185 distance: 113 - 115: 8.877 distance: 116 - 117: 7.100 distance: 116 - 122: 14.008 distance: 117 - 118: 9.586 distance: 117 - 120: 7.632 distance: 118 - 119: 19.388 distance: 118 - 123: 10.127 distance: 120 - 121: 13.180 distance: 121 - 122: 11.950 distance: 123 - 124: 33.831 distance: 124 - 125: 41.588 distance: 124 - 127: 33.615 distance: 125 - 126: 18.525 distance: 125 - 131: 41.913 distance: 127 - 128: 9.908 distance: 128 - 129: 10.190 distance: 128 - 130: 17.610 distance: 131 - 132: 53.174 distance: 132 - 133: 21.449 distance: 132 - 135: 34.628 distance: 133 - 134: 9.913 distance: 133 - 140: 7.233 distance: 135 - 136: 26.125 distance: 136 - 137: 25.102 distance: 137 - 138: 10.428 distance: 137 - 139: 17.266 distance: 140 - 141: 3.782 distance: 141 - 142: 10.823 distance: 141 - 144: 10.560 distance: 142 - 143: 28.387 distance: 142 - 148: 6.463 distance: 144 - 145: 13.973 distance: 145 - 146: 15.833 distance: 145 - 147: 11.166 distance: 148 - 149: 8.093 distance: 149 - 150: 7.782 distance: 150 - 151: 8.741 distance: 150 - 155: 6.241 distance: 152 - 153: 5.554 distance: 152 - 154: 12.341 distance: 155 - 156: 7.546 distance: 156 - 157: 14.641 distance: 156 - 159: 14.084 distance: 157 - 158: 12.679 distance: 157 - 160: 16.754 distance: 160 - 161: 4.006 distance: 161 - 162: 11.448 distance: 161 - 164: 5.217 distance: 162 - 163: 5.108 distance: 162 - 168: 6.061 distance: 164 - 165: 8.347 distance: 165 - 166: 17.032 distance: 166 - 167: 4.312 distance: 168 - 169: 10.520 distance: 168 - 208: 8.501 distance: 169 - 170: 12.586 distance: 169 - 172: 11.170 distance: 170 - 171: 3.413 distance: 170 - 179: 8.554 distance: 171 - 205: 6.633 distance: 172 - 173: 9.210 distance: 173 - 174: 7.133 distance: 174 - 175: 5.870 distance: 175 - 176: 5.692 distance: 176 - 177: 4.085 distance: 176 - 178: 5.655 distance: 179 - 180: 3.799 distance: 180 - 181: 7.531 distance: 181 - 186: 3.461 distance: 183 - 184: 14.110 distance: 183 - 185: 13.043