Starting phenix.real_space_refine on Tue Mar 3 16:43:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6t_25727/03_2026/7t6t_25727_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6t_25727/03_2026/7t6t_25727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6t_25727/03_2026/7t6t_25727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6t_25727/03_2026/7t6t_25727.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6t_25727/03_2026/7t6t_25727_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6t_25727/03_2026/7t6t_25727_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.052 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 53 5.16 5 C 4593 2.51 5 N 1216 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7164 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2327 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 7164 At special positions: 0 Unit cell: (87.78, 104.5, 123.31, 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 53 16.00 O 1302 8.00 N 1216 7.00 C 4593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 270.8 milliseconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 47.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.879A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.979A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.030A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.728A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 23 through 53 removed outlier: 3.701A pdb=" N ILE R 27 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE R 28 " --> pdb=" O PHE R 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 87 removed outlier: 3.717A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR R 75 " --> pdb=" O ASP R 71 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 95 through 129 removed outlier: 4.291A pdb=" N ILE R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 156 removed outlier: 3.992A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 Processing helix chain 'R' and resid 186 through 208 Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 237 through 266 removed outlier: 3.838A pdb=" N ALA R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 272 Processing helix chain 'R' and resid 276 through 302 removed outlier: 3.917A pdb=" N GLY R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE R 281 " --> pdb=" O LYS R 277 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix removed outlier: 3.723A pdb=" N VAL R 302 " --> pdb=" O PRO R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 316 removed outlier: 3.609A pdb=" N LEU R 316 " --> pdb=" O LEU R 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.736A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 removed outlier: 6.394A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.585A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.701A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.854A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.706A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.792A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.807A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 167 through 168 388 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1375 1.32 - 1.45: 1754 1.45 - 1.57: 4101 1.57 - 1.69: 0 1.69 - 1.82: 77 Bond restraints: 7307 Sorted by residual: bond pdb=" C LYS C 20 " pdb=" O LYS C 20 " ideal model delta sigma weight residual 1.236 1.291 -0.055 1.19e-02 7.06e+03 2.11e+01 bond pdb=" CA SER R 255 " pdb=" CB SER R 255 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.33e-02 5.65e+03 1.85e+01 bond pdb=" N SER R 181 " pdb=" CA SER R 181 " ideal model delta sigma weight residual 1.458 1.486 -0.028 7.40e-03 1.83e+04 1.47e+01 bond pdb=" N VAL R 127 " pdb=" CA VAL R 127 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.28e+01 bond pdb=" N VAL R 174 " pdb=" CA VAL R 174 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 ... (remaining 7302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 7649 1.89 - 3.77: 2059 3.77 - 5.66: 148 5.66 - 7.54: 22 7.54 - 9.43: 5 Bond angle restraints: 9883 Sorted by residual: angle pdb=" N PRO R 182 " pdb=" CA PRO R 182 " pdb=" C PRO R 182 " ideal model delta sigma weight residual 113.84 104.41 9.43 1.30e+00 5.92e-01 5.26e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.93 106.05 6.88 1.12e+00 7.97e-01 3.78e+01 angle pdb=" N LEU R 300 " pdb=" CA LEU R 300 " pdb=" CB LEU R 300 " ideal model delta sigma weight residual 110.88 102.71 8.17 1.38e+00 5.25e-01 3.51e+01 angle pdb=" N VAL R 266 " pdb=" CA VAL R 266 " pdb=" C VAL R 266 " ideal model delta sigma weight residual 112.83 107.05 5.78 9.90e-01 1.02e+00 3.41e+01 angle pdb=" N MET R 304 " pdb=" CA MET R 304 " pdb=" C MET R 304 " ideal model delta sigma weight residual 112.92 105.86 7.06 1.23e+00 6.61e-01 3.29e+01 ... (remaining 9878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3909 16.92 - 33.85: 333 33.85 - 50.77: 80 50.77 - 67.69: 13 67.69 - 84.62: 3 Dihedral angle restraints: 4338 sinusoidal: 1709 harmonic: 2629 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual 93.00 177.62 -84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" C PHE R 178 " pdb=" N PHE R 178 " pdb=" CA PHE R 178 " pdb=" CB PHE R 178 " ideal model delta harmonic sigma weight residual -122.60 -112.55 -10.05 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" C GLU R 189 " pdb=" N GLU R 189 " pdb=" CA GLU R 189 " pdb=" CB GLU R 189 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 532 0.070 - 0.140: 398 0.140 - 0.211: 169 0.211 - 0.281: 34 0.281 - 0.351: 4 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA PHE B 235 " pdb=" N PHE B 235 " pdb=" C PHE B 235 " pdb=" CB PHE B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA PHE R 178 " pdb=" N PHE R 178 " pdb=" C PHE R 178 " pdb=" CB PHE R 178 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1134 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME L 1 " 0.057 2.00e-02 2.50e+03 7.27e-02 5.28e+01 pdb=" CA FME L 1 " -0.064 2.00e-02 2.50e+03 pdb=" CN FME L 1 " 0.086 2.00e-02 2.50e+03 pdb=" O1 FME L 1 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 24 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ASN C 24 " 0.079 2.00e-02 2.50e+03 pdb=" O ASN C 24 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE C 25 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 19 " 0.022 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C LEU C 19 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU C 19 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS C 20 " 0.025 2.00e-02 2.50e+03 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 968 2.76 - 3.29: 7499 3.29 - 3.83: 11775 3.83 - 4.36: 15301 4.36 - 4.90: 25450 Nonbonded interactions: 60993 Sorted by model distance: nonbonded pdb=" OD1 ASN B 313 " pdb=" N ARG B 314 " model vdw 2.223 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.339 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.350 3.040 ... (remaining 60988 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.011 0.075 7308 Z= 0.835 Angle : 1.551 9.431 9885 Z= 1.170 Chirality : 0.105 0.351 1137 Planarity : 0.008 0.073 1241 Dihedral : 13.221 78.320 2629 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.16 % Allowed : 5.68 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.27), residues: 893 helix: 1.10 (0.25), residues: 395 sheet: -0.77 (0.38), residues: 178 loop : -0.42 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 201 TYR 0.013 0.002 TYR C 40 PHE 0.013 0.002 PHE R 110 TRP 0.022 0.003 TRP R 132 HIS 0.012 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.01148 ( 7307) covalent geometry : angle 1.55025 ( 9883) SS BOND : bond 0.01070 ( 1) SS BOND : angle 3.49872 ( 2) hydrogen bonds : bond 0.18182 ( 388) hydrogen bonds : angle 7.59724 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 293 time to evaluate : 0.205 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: A 9 ASP cc_start: 0.8017 (p0) cc_final: 0.7780 (p0) REVERT: A 38 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7981 (tt) REVERT: A 251 ASP cc_start: 0.7989 (t0) cc_final: 0.7698 (t0) REVERT: A 252 SER cc_start: 0.8868 (t) cc_final: 0.8665 (t) REVERT: A 262 THR cc_start: 0.9096 (m) cc_final: 0.8781 (p) REVERT: A 276 GLU cc_start: 0.7594 (mp0) cc_final: 0.6581 (mp0) REVERT: A 280 LYS cc_start: 0.8507 (mptt) cc_final: 0.8092 (mptt) REVERT: A 312 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8329 (mmmt) REVERT: A 321 THR cc_start: 0.8481 (m) cc_final: 0.8195 (p) REVERT: B 13 GLN cc_start: 0.8188 (tt0) cc_final: 0.7961 (tt0) REVERT: B 19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7691 (ttp80) REVERT: B 50 THR cc_start: 0.8206 (m) cc_final: 0.8006 (t) REVERT: B 175 GLN cc_start: 0.7949 (pp30) cc_final: 0.7548 (pp30) REVERT: B 176 GLN cc_start: 0.8405 (mt0) cc_final: 0.7794 (mt0) REVERT: B 189 SER cc_start: 0.8737 (p) cc_final: 0.8492 (p) REVERT: B 212 ASP cc_start: 0.7385 (m-30) cc_final: 0.7167 (t0) REVERT: B 225 HIS cc_start: 0.8517 (m-70) cc_final: 0.8284 (m-70) REVERT: B 243 THR cc_start: 0.8572 (m) cc_final: 0.8211 (p) REVERT: B 247 ASP cc_start: 0.8079 (p0) cc_final: 0.7823 (p0) REVERT: B 258 ASP cc_start: 0.7621 (t0) cc_final: 0.7113 (t0) REVERT: B 333 ASP cc_start: 0.7086 (p0) cc_final: 0.6852 (p0) REVERT: C 18 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7706 (tp40) REVERT: R 63 SER cc_start: 0.8003 (m) cc_final: 0.7765 (p) REVERT: R 80 PHE cc_start: 0.8519 (m-80) cc_final: 0.8246 (m-80) REVERT: R 190 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8236 (ttp-170) REVERT: R 207 ILE cc_start: 0.8840 (pt) cc_final: 0.8514 (mm) REVERT: R 265 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (p) REVERT: R 277 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8548 (mmmt) REVERT: R 294 SER cc_start: 0.8550 (m) cc_final: 0.8278 (t) REVERT: R 302 VAL cc_start: 0.8408 (m) cc_final: 0.8039 (t) outliers start: 9 outliers final: 1 residues processed: 295 average time/residue: 0.0952 time to fit residues: 35.9298 Evaluate side-chains 257 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain R residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 311 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS R 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.092490 restraints weight = 12779.741| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.58 r_work: 0.3195 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7308 Z= 0.184 Angle : 0.630 6.838 9885 Z= 0.344 Chirality : 0.046 0.175 1137 Planarity : 0.005 0.050 1241 Dihedral : 5.911 49.238 1006 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.49 % Allowed : 16.28 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.27), residues: 893 helix: 0.81 (0.25), residues: 401 sheet: -0.53 (0.38), residues: 172 loop : -0.96 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 134 TYR 0.015 0.002 TYR B 124 PHE 0.019 0.002 PHE R 178 TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7307) covalent geometry : angle 0.62960 ( 9883) SS BOND : bond 0.01103 ( 1) SS BOND : angle 0.85031 ( 2) hydrogen bonds : bond 0.05099 ( 388) hydrogen bonds : angle 5.39936 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8124 (t0) cc_final: 0.7756 (m-30) REVERT: A 209 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8140 (ttpp) REVERT: A 251 ASP cc_start: 0.8357 (t0) cc_final: 0.8051 (t0) REVERT: A 252 SER cc_start: 0.8817 (t) cc_final: 0.8586 (t) REVERT: A 262 THR cc_start: 0.9251 (m) cc_final: 0.8646 (p) REVERT: A 271 LYS cc_start: 0.8540 (pttp) cc_final: 0.8220 (ptmt) REVERT: A 275 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 279 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8393 (mtpp) REVERT: A 280 LYS cc_start: 0.8754 (mptt) cc_final: 0.7813 (mptt) REVERT: A 312 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8524 (mmmt) REVERT: A 321 THR cc_start: 0.8814 (m) cc_final: 0.8430 (p) REVERT: A 332 VAL cc_start: 0.8773 (t) cc_final: 0.8500 (p) REVERT: B 16 ASN cc_start: 0.8618 (m-40) cc_final: 0.8277 (m-40) REVERT: B 19 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7875 (ttp80) REVERT: B 50 THR cc_start: 0.8721 (m) cc_final: 0.8451 (t) REVERT: B 130 GLU cc_start: 0.5412 (tp30) cc_final: 0.5203 (tp30) REVERT: B 176 GLN cc_start: 0.8790 (mt0) cc_final: 0.8492 (mt0) REVERT: B 186 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7275 (p0) REVERT: B 189 SER cc_start: 0.8840 (p) cc_final: 0.8580 (p) REVERT: B 225 HIS cc_start: 0.8722 (m-70) cc_final: 0.8262 (m-70) REVERT: B 226 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 228 ASP cc_start: 0.7622 (m-30) cc_final: 0.6939 (m-30) REVERT: B 243 THR cc_start: 0.8763 (m) cc_final: 0.8442 (t) REVERT: B 258 ASP cc_start: 0.8081 (t0) cc_final: 0.7486 (t0) REVERT: B 262 MET cc_start: 0.8329 (tpp) cc_final: 0.8096 (tpp) REVERT: B 292 PHE cc_start: 0.8513 (m-10) cc_final: 0.8056 (m-80) REVERT: B 312 ASP cc_start: 0.8277 (t0) cc_final: 0.7901 (t0) REVERT: B 333 ASP cc_start: 0.7703 (p0) cc_final: 0.7488 (p0) REVERT: C 21 MET cc_start: 0.8446 (mmm) cc_final: 0.7706 (mmm) REVERT: R 133 THR cc_start: 0.8840 (t) cc_final: 0.8467 (p) REVERT: R 152 MET cc_start: 0.8296 (mmm) cc_final: 0.8063 (mmm) REVERT: R 197 MET cc_start: 0.8338 (mmp) cc_final: 0.8041 (mmt) REVERT: R 207 ILE cc_start: 0.8879 (pt) cc_final: 0.8567 (mm) REVERT: R 214 MET cc_start: 0.8138 (tpp) cc_final: 0.7923 (tpp) REVERT: R 229 HIS cc_start: 0.8083 (t-170) cc_final: 0.7828 (t70) REVERT: R 231 GLN cc_start: 0.7884 (mm110) cc_final: 0.7570 (mm110) REVERT: R 277 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8611 (mmmt) REVERT: R 294 SER cc_start: 0.8620 (m) cc_final: 0.8213 (t) REVERT: R 302 VAL cc_start: 0.8532 (m) cc_final: 0.8220 (t) outliers start: 27 outliers final: 14 residues processed: 276 average time/residue: 0.1003 time to fit residues: 35.3044 Evaluate side-chains 282 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 241 ASN A 269 ASN B 119 ASN B 220 GLN R 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091995 restraints weight = 12803.654| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.56 r_work: 0.3186 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7308 Z= 0.148 Angle : 0.561 6.837 9885 Z= 0.302 Chirality : 0.044 0.184 1137 Planarity : 0.004 0.048 1241 Dihedral : 5.572 47.507 1003 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.97 % Allowed : 20.16 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 893 helix: 0.89 (0.26), residues: 403 sheet: -0.36 (0.40), residues: 159 loop : -1.19 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.015 0.001 TYR B 124 PHE 0.024 0.002 PHE R 180 TRP 0.019 0.002 TRP B 169 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7307) covalent geometry : angle 0.56101 ( 9883) SS BOND : bond 0.00264 ( 1) SS BOND : angle 1.56660 ( 2) hydrogen bonds : bond 0.04395 ( 388) hydrogen bonds : angle 5.06288 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8134 (mtpp) REVERT: A 251 ASP cc_start: 0.8317 (t0) cc_final: 0.8023 (t0) REVERT: A 257 LYS cc_start: 0.9069 (ptmm) cc_final: 0.8762 (ptmm) REVERT: A 269 ASN cc_start: 0.8605 (m110) cc_final: 0.8333 (m110) REVERT: A 271 LYS cc_start: 0.8717 (pttp) cc_final: 0.8277 (ptmm) REVERT: A 275 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 276 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 279 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8577 (mtmt) REVERT: A 280 LYS cc_start: 0.8786 (mptt) cc_final: 0.8165 (mptt) REVERT: A 285 ILE cc_start: 0.9279 (mm) cc_final: 0.9077 (tt) REVERT: A 312 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8504 (mmmt) REVERT: A 321 THR cc_start: 0.8878 (m) cc_final: 0.8443 (p) REVERT: A 341 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7924 (t0) REVERT: B 10 GLU cc_start: 0.8938 (tp30) cc_final: 0.8652 (tp30) REVERT: B 19 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8051 (ttp80) REVERT: B 145 TYR cc_start: 0.8832 (p90) cc_final: 0.8526 (p90) REVERT: B 176 GLN cc_start: 0.8713 (mt0) cc_final: 0.8416 (mt0) REVERT: B 186 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7198 (p0) REVERT: B 188 MET cc_start: 0.7951 (mmm) cc_final: 0.7474 (mmm) REVERT: B 189 SER cc_start: 0.8874 (p) cc_final: 0.8621 (p) REVERT: B 217 MET cc_start: 0.8473 (ppp) cc_final: 0.7950 (ppp) REVERT: B 225 HIS cc_start: 0.8666 (m-70) cc_final: 0.8273 (m-70) REVERT: B 226 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B 243 THR cc_start: 0.8740 (m) cc_final: 0.8421 (t) REVERT: B 258 ASP cc_start: 0.7946 (t0) cc_final: 0.7077 (t0) REVERT: B 262 MET cc_start: 0.8262 (tpp) cc_final: 0.7824 (tpp) REVERT: B 292 PHE cc_start: 0.8508 (m-10) cc_final: 0.7944 (m-80) REVERT: B 301 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8688 (mmmt) REVERT: B 311 HIS cc_start: 0.7698 (m-70) cc_final: 0.7317 (m-70) REVERT: B 312 ASP cc_start: 0.8319 (t0) cc_final: 0.7836 (t0) REVERT: B 333 ASP cc_start: 0.7807 (p0) cc_final: 0.7527 (p0) REVERT: C 17 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 21 MET cc_start: 0.8229 (mmm) cc_final: 0.7823 (mmm) REVERT: R 39 LEU cc_start: 0.8629 (mm) cc_final: 0.8426 (mm) REVERT: R 143 LYS cc_start: 0.8799 (mttm) cc_final: 0.8580 (mttm) REVERT: R 152 MET cc_start: 0.8384 (mmm) cc_final: 0.8082 (mmm) REVERT: R 161 ILE cc_start: 0.8552 (tt) cc_final: 0.8308 (pt) REVERT: R 190 ARG cc_start: 0.8313 (tmm160) cc_final: 0.8079 (tmm160) REVERT: R 197 MET cc_start: 0.8123 (mmp) cc_final: 0.7782 (mmt) REVERT: R 220 SER cc_start: 0.8211 (m) cc_final: 0.7858 (p) REVERT: R 231 GLN cc_start: 0.7804 (mm110) cc_final: 0.7519 (mm110) REVERT: R 277 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8584 (mmmt) REVERT: R 294 SER cc_start: 0.8639 (m) cc_final: 0.8221 (t) REVERT: R 302 VAL cc_start: 0.8664 (m) cc_final: 0.8281 (t) REVERT: R 309 ARG cc_start: 0.8476 (ttm110) cc_final: 0.7875 (mtm-85) outliers start: 23 outliers final: 9 residues processed: 287 average time/residue: 0.0993 time to fit residues: 36.2145 Evaluate side-chains 277 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 264 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 189 GLU Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 265 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 51 optimal weight: 7.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 213 HIS R 57 HIS R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090608 restraints weight = 12837.266| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.57 r_work: 0.3162 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7308 Z= 0.188 Angle : 0.566 6.693 9885 Z= 0.305 Chirality : 0.044 0.200 1137 Planarity : 0.004 0.048 1241 Dihedral : 5.594 45.746 1003 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.26 % Allowed : 21.83 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 893 helix: 0.86 (0.26), residues: 400 sheet: -0.48 (0.39), residues: 173 loop : -1.16 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.014 0.001 TYR B 124 PHE 0.028 0.002 PHE B 199 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7307) covalent geometry : angle 0.56424 ( 9883) SS BOND : bond 0.00811 ( 1) SS BOND : angle 2.86451 ( 2) hydrogen bonds : bond 0.04293 ( 388) hydrogen bonds : angle 4.98394 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8332 (t0) cc_final: 0.8081 (t0) REVERT: A 257 LYS cc_start: 0.9081 (ptmm) cc_final: 0.8711 (ptmm) REVERT: A 275 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 279 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8591 (mtmt) REVERT: A 280 LYS cc_start: 0.8855 (mptt) cc_final: 0.8312 (mptt) REVERT: A 312 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8520 (mmmt) REVERT: A 321 THR cc_start: 0.8894 (m) cc_final: 0.8451 (p) REVERT: A 341 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7949 (t0) REVERT: B 10 GLU cc_start: 0.8866 (tp30) cc_final: 0.8585 (tp30) REVERT: B 19 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.8099 (ttp80) REVERT: B 145 TYR cc_start: 0.8942 (p90) cc_final: 0.8432 (p90) REVERT: B 176 GLN cc_start: 0.8696 (mt0) cc_final: 0.8421 (mt0) REVERT: B 186 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7160 (p0) REVERT: B 188 MET cc_start: 0.7912 (mmm) cc_final: 0.7316 (mmm) REVERT: B 189 SER cc_start: 0.8883 (p) cc_final: 0.8631 (p) REVERT: B 217 MET cc_start: 0.8469 (ppp) cc_final: 0.7943 (ppp) REVERT: B 225 HIS cc_start: 0.8673 (m-70) cc_final: 0.8339 (m-70) REVERT: B 228 ASP cc_start: 0.7646 (m-30) cc_final: 0.7172 (t0) REVERT: B 243 THR cc_start: 0.8753 (m) cc_final: 0.8077 (p) REVERT: B 258 ASP cc_start: 0.8007 (t0) cc_final: 0.7029 (t0) REVERT: B 292 PHE cc_start: 0.8497 (m-10) cc_final: 0.7905 (m-80) REVERT: B 301 LYS cc_start: 0.9041 (mtpp) cc_final: 0.8721 (mmmt) REVERT: B 312 ASP cc_start: 0.8296 (t0) cc_final: 0.7758 (t0) REVERT: C 20 LYS cc_start: 0.8788 (ttpp) cc_final: 0.7838 (pttm) REVERT: C 21 MET cc_start: 0.8269 (mmm) cc_final: 0.8057 (mmm) REVERT: R 39 LEU cc_start: 0.8698 (mm) cc_final: 0.8489 (mm) REVERT: R 133 THR cc_start: 0.8800 (t) cc_final: 0.8554 (p) REVERT: R 152 MET cc_start: 0.8310 (mmm) cc_final: 0.7989 (mmm) REVERT: R 161 ILE cc_start: 0.8457 (tt) cc_final: 0.8239 (pt) REVERT: R 163 ARG cc_start: 0.8744 (mmp80) cc_final: 0.8481 (mmm160) REVERT: R 195 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8905 (p) REVERT: R 197 MET cc_start: 0.8115 (mmp) cc_final: 0.7802 (mmt) REVERT: R 220 SER cc_start: 0.8239 (m) cc_final: 0.7943 (p) REVERT: R 231 GLN cc_start: 0.7813 (mm110) cc_final: 0.7565 (mm110) REVERT: R 243 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8054 (mm) REVERT: R 277 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8613 (mmmt) REVERT: R 287 SER cc_start: 0.8188 (p) cc_final: 0.7818 (p) REVERT: R 294 SER cc_start: 0.8665 (m) cc_final: 0.8255 (t) REVERT: R 302 VAL cc_start: 0.8661 (m) cc_final: 0.8297 (t) outliers start: 33 outliers final: 23 residues processed: 278 average time/residue: 0.1002 time to fit residues: 35.2706 Evaluate side-chains 285 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 52 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092023 restraints weight = 12803.035| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.58 r_work: 0.3187 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7308 Z= 0.129 Angle : 0.557 7.409 9885 Z= 0.294 Chirality : 0.043 0.159 1137 Planarity : 0.004 0.042 1241 Dihedral : 5.450 49.531 1003 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.01 % Allowed : 22.87 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.28), residues: 893 helix: 0.98 (0.26), residues: 402 sheet: -0.15 (0.41), residues: 159 loop : -1.23 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 27 TYR 0.014 0.001 TYR B 124 PHE 0.024 0.002 PHE R 180 TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7307) covalent geometry : angle 0.55421 ( 9883) SS BOND : bond 0.00050 ( 1) SS BOND : angle 3.90929 ( 2) hydrogen bonds : bond 0.04013 ( 388) hydrogen bonds : angle 4.86822 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8448 (ttm) cc_final: 0.8243 (ttm) REVERT: A 257 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8751 (ptmm) REVERT: A 275 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 279 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8567 (mtmt) REVERT: A 280 LYS cc_start: 0.8884 (mptt) cc_final: 0.8323 (mptt) REVERT: A 296 TYR cc_start: 0.9132 (t80) cc_final: 0.8502 (t80) REVERT: A 312 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8551 (mmmt) REVERT: A 321 THR cc_start: 0.8916 (m) cc_final: 0.8470 (p) REVERT: B 16 ASN cc_start: 0.8605 (m-40) cc_final: 0.8390 (m-40) REVERT: B 19 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.8005 (ttp80) REVERT: B 145 TYR cc_start: 0.8934 (p90) cc_final: 0.8484 (p90) REVERT: B 186 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 188 MET cc_start: 0.7873 (mmm) cc_final: 0.7258 (mmm) REVERT: B 189 SER cc_start: 0.8863 (p) cc_final: 0.8633 (p) REVERT: B 225 HIS cc_start: 0.8627 (m-70) cc_final: 0.8295 (m-70) REVERT: B 228 ASP cc_start: 0.7588 (m-30) cc_final: 0.7048 (t0) REVERT: B 243 THR cc_start: 0.8696 (m) cc_final: 0.8036 (p) REVERT: B 258 ASP cc_start: 0.8032 (t0) cc_final: 0.7130 (t0) REVERT: B 262 MET cc_start: 0.8213 (tpp) cc_final: 0.7974 (tpp) REVERT: B 292 PHE cc_start: 0.8450 (m-10) cc_final: 0.7858 (m-80) REVERT: B 312 ASP cc_start: 0.8182 (t0) cc_final: 0.7757 (t0) REVERT: C 17 GLU cc_start: 0.8693 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 20 LYS cc_start: 0.8713 (ttpp) cc_final: 0.7700 (pttm) REVERT: C 21 MET cc_start: 0.8247 (mmm) cc_final: 0.8035 (mmm) REVERT: R 25 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8298 (mp) REVERT: R 33 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7460 (t80) REVERT: R 39 LEU cc_start: 0.8758 (mm) cc_final: 0.8523 (mm) REVERT: R 77 THR cc_start: 0.8297 (m) cc_final: 0.7939 (p) REVERT: R 133 THR cc_start: 0.8787 (t) cc_final: 0.8501 (p) REVERT: R 152 MET cc_start: 0.8265 (mmm) cc_final: 0.7933 (mmm) REVERT: R 197 MET cc_start: 0.8022 (mmp) cc_final: 0.7737 (mmt) REVERT: R 243 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8092 (mm) REVERT: R 244 SER cc_start: 0.8362 (m) cc_final: 0.8143 (m) REVERT: R 273 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: R 294 SER cc_start: 0.8758 (m) cc_final: 0.8343 (t) REVERT: R 302 VAL cc_start: 0.8692 (m) cc_final: 0.8353 (t) outliers start: 31 outliers final: 16 residues processed: 279 average time/residue: 0.1037 time to fit residues: 36.5907 Evaluate side-chains 282 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 173 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN R 57 HIS R 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.088752 restraints weight = 13048.546| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7308 Z= 0.243 Angle : 0.623 10.164 9885 Z= 0.332 Chirality : 0.046 0.157 1137 Planarity : 0.004 0.043 1241 Dihedral : 5.702 45.568 1003 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.43 % Allowed : 23.13 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.27), residues: 893 helix: 0.83 (0.26), residues: 405 sheet: -0.29 (0.41), residues: 158 loop : -1.35 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.012 0.001 TYR B 59 PHE 0.023 0.002 PHE B 199 TRP 0.018 0.002 TRP B 169 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 7307) covalent geometry : angle 0.61982 ( 9883) SS BOND : bond 0.00723 ( 1) SS BOND : angle 4.58144 ( 2) hydrogen bonds : bond 0.04310 ( 388) hydrogen bonds : angle 4.93096 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6815 (pt0) REVERT: A 257 LYS cc_start: 0.9125 (ptmm) cc_final: 0.8788 (ptmm) REVERT: A 275 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 279 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8567 (mtmt) REVERT: A 280 LYS cc_start: 0.8949 (mptt) cc_final: 0.8474 (mptt) REVERT: A 296 TYR cc_start: 0.9127 (t80) cc_final: 0.8728 (t80) REVERT: A 312 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8671 (mmmt) REVERT: A 321 THR cc_start: 0.9023 (m) cc_final: 0.8604 (p) REVERT: B 19 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8342 (ttp80) REVERT: B 50 THR cc_start: 0.8875 (m) cc_final: 0.8617 (t) REVERT: B 137 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8124 (tpp-160) REVERT: B 145 TYR cc_start: 0.9049 (p90) cc_final: 0.8514 (p90) REVERT: B 156 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8125 (mm110) REVERT: B 186 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7402 (p0) REVERT: B 188 MET cc_start: 0.8136 (mmm) cc_final: 0.7408 (mmm) REVERT: B 189 SER cc_start: 0.8910 (p) cc_final: 0.8631 (p) REVERT: B 243 THR cc_start: 0.8789 (m) cc_final: 0.8086 (p) REVERT: B 258 ASP cc_start: 0.8303 (t0) cc_final: 0.7422 (t0) REVERT: B 262 MET cc_start: 0.8600 (tpp) cc_final: 0.8228 (tpp) REVERT: B 292 PHE cc_start: 0.8674 (m-10) cc_final: 0.8086 (m-80) REVERT: B 301 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8773 (mmmt) REVERT: B 312 ASP cc_start: 0.8432 (t0) cc_final: 0.7987 (t0) REVERT: C 17 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7807 (mm-30) REVERT: C 20 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8081 (pttm) REVERT: C 21 MET cc_start: 0.8624 (mmm) cc_final: 0.8291 (mmm) REVERT: C 52 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (p) REVERT: R 25 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8478 (mp) REVERT: R 39 LEU cc_start: 0.8775 (mm) cc_final: 0.8541 (mm) REVERT: R 106 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7883 (t0) REVERT: R 133 THR cc_start: 0.8898 (t) cc_final: 0.8638 (p) REVERT: R 152 MET cc_start: 0.8523 (mmm) cc_final: 0.8161 (mmm) REVERT: R 197 MET cc_start: 0.8389 (mmp) cc_final: 0.8073 (mmt) REVERT: R 243 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8235 (mm) REVERT: R 244 SER cc_start: 0.8507 (m) cc_final: 0.8305 (m) REVERT: R 273 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: R 287 SER cc_start: 0.8209 (p) cc_final: 0.7850 (p) REVERT: R 294 SER cc_start: 0.8842 (m) cc_final: 0.8434 (t) REVERT: R 302 VAL cc_start: 0.8854 (m) cc_final: 0.8505 (t) REVERT: R 306 GLN cc_start: 0.8789 (tt0) cc_final: 0.8586 (tp40) outliers start: 42 outliers final: 27 residues processed: 278 average time/residue: 0.1040 time to fit residues: 36.3886 Evaluate side-chains 296 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 0.0170 chunk 12 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.0050 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 chunk 18 optimal weight: 0.6980 overall best weight: 0.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.107275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094165 restraints weight = 12934.641| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.59 r_work: 0.3218 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7308 Z= 0.116 Angle : 0.560 11.389 9885 Z= 0.296 Chirality : 0.042 0.170 1137 Planarity : 0.004 0.041 1241 Dihedral : 5.260 46.203 1003 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.88 % Allowed : 25.58 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.28), residues: 893 helix: 0.98 (0.26), residues: 412 sheet: -0.15 (0.40), residues: 165 loop : -1.17 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.012 0.001 TYR B 124 PHE 0.019 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7307) covalent geometry : angle 0.55895 ( 9883) SS BOND : bond 0.00922 ( 1) SS BOND : angle 2.32003 ( 2) hydrogen bonds : bond 0.03813 ( 388) hydrogen bonds : angle 4.70859 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7699 (tt0) REVERT: A 197 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8090 (ttmm) REVERT: A 257 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8781 (ptmm) REVERT: A 275 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 279 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8534 (mtmt) REVERT: A 280 LYS cc_start: 0.8919 (mptt) cc_final: 0.8443 (mptt) REVERT: A 296 TYR cc_start: 0.9128 (t80) cc_final: 0.8674 (t80) REVERT: A 309 ASP cc_start: 0.8010 (m-30) cc_final: 0.7565 (m-30) REVERT: A 312 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8603 (mmmt) REVERT: A 321 THR cc_start: 0.8917 (m) cc_final: 0.8459 (p) REVERT: B 8 ARG cc_start: 0.6934 (mpp-170) cc_final: 0.6664 (mtm-85) REVERT: B 19 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.8015 (ttp80) REVERT: B 145 TYR cc_start: 0.8925 (p90) cc_final: 0.8623 (p90) REVERT: B 156 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7950 (mm110) REVERT: B 188 MET cc_start: 0.7896 (mmm) cc_final: 0.7296 (mmm) REVERT: B 189 SER cc_start: 0.8792 (p) cc_final: 0.8587 (p) REVERT: B 212 ASP cc_start: 0.8091 (t0) cc_final: 0.7726 (m-30) REVERT: B 243 THR cc_start: 0.8732 (m) cc_final: 0.7999 (p) REVERT: B 258 ASP cc_start: 0.8058 (t0) cc_final: 0.7154 (t0) REVERT: B 292 PHE cc_start: 0.8445 (m-10) cc_final: 0.7894 (m-80) REVERT: B 312 ASP cc_start: 0.8081 (t0) cc_final: 0.7726 (t0) REVERT: C 17 GLU cc_start: 0.8723 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 20 LYS cc_start: 0.8786 (ttpp) cc_final: 0.7919 (pttm) REVERT: C 21 MET cc_start: 0.8259 (mmm) cc_final: 0.7989 (mmm) REVERT: R 25 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8272 (mp) REVERT: R 33 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7644 (t80) REVERT: R 39 LEU cc_start: 0.8703 (mm) cc_final: 0.8494 (mm) REVERT: R 82 MET cc_start: 0.8063 (mpp) cc_final: 0.7238 (mpp) REVERT: R 100 PHE cc_start: 0.8323 (t80) cc_final: 0.7970 (t80) REVERT: R 106 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7493 (t0) REVERT: R 133 THR cc_start: 0.8763 (t) cc_final: 0.8465 (p) REVERT: R 152 MET cc_start: 0.8217 (mmm) cc_final: 0.7873 (mmm) REVERT: R 197 MET cc_start: 0.8078 (mmp) cc_final: 0.7822 (mmt) REVERT: R 243 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8083 (mm) REVERT: R 273 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: R 287 SER cc_start: 0.8015 (p) cc_final: 0.7678 (p) REVERT: R 294 SER cc_start: 0.8757 (m) cc_final: 0.8328 (t) REVERT: R 302 VAL cc_start: 0.8750 (m) cc_final: 0.8437 (t) outliers start: 30 outliers final: 16 residues processed: 272 average time/residue: 0.1042 time to fit residues: 35.9689 Evaluate side-chains 276 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 129 HIS Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.091506 restraints weight = 13071.618| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.52 r_work: 0.3173 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7308 Z= 0.150 Angle : 0.582 12.388 9885 Z= 0.306 Chirality : 0.044 0.195 1137 Planarity : 0.004 0.039 1241 Dihedral : 5.282 47.153 1003 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.75 % Allowed : 26.10 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.28), residues: 893 helix: 1.02 (0.26), residues: 405 sheet: -0.06 (0.41), residues: 157 loop : -1.35 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.011 0.001 TYR B 124 PHE 0.019 0.001 PHE B 199 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7307) covalent geometry : angle 0.58046 ( 9883) SS BOND : bond 0.00344 ( 1) SS BOND : angle 2.83904 ( 2) hydrogen bonds : bond 0.03879 ( 388) hydrogen bonds : angle 4.67679 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6668 (pt0) REVERT: A 33 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7552 (tt0) REVERT: A 197 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8071 (ttmm) REVERT: A 257 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8751 (ptmm) REVERT: A 275 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 279 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8603 (mtmt) REVERT: A 280 LYS cc_start: 0.8932 (mptt) cc_final: 0.8443 (mptt) REVERT: A 296 TYR cc_start: 0.9084 (t80) cc_final: 0.8631 (t80) REVERT: A 309 ASP cc_start: 0.7994 (m-30) cc_final: 0.7593 (m-30) REVERT: A 312 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8637 (mmmt) REVERT: A 321 THR cc_start: 0.8933 (m) cc_final: 0.8476 (p) REVERT: B 19 ARG cc_start: 0.8316 (ttp-110) cc_final: 0.8030 (ttp80) REVERT: B 145 TYR cc_start: 0.8938 (p90) cc_final: 0.8467 (p90) REVERT: B 188 MET cc_start: 0.7893 (mmm) cc_final: 0.7253 (mmm) REVERT: B 189 SER cc_start: 0.8810 (p) cc_final: 0.8599 (p) REVERT: B 212 ASP cc_start: 0.8086 (t0) cc_final: 0.7871 (t0) REVERT: B 243 THR cc_start: 0.8692 (m) cc_final: 0.8000 (p) REVERT: B 258 ASP cc_start: 0.7970 (t0) cc_final: 0.7110 (t0) REVERT: B 292 PHE cc_start: 0.8513 (m-10) cc_final: 0.7898 (m-80) REVERT: B 312 ASP cc_start: 0.8074 (t0) cc_final: 0.7673 (t0) REVERT: C 17 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8391 (mm-30) REVERT: C 21 MET cc_start: 0.8333 (mmm) cc_final: 0.7964 (mmm) REVERT: R 25 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8359 (mp) REVERT: R 33 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7654 (t80) REVERT: R 82 MET cc_start: 0.7956 (mpp) cc_final: 0.7013 (mpp) REVERT: R 100 PHE cc_start: 0.8281 (t80) cc_final: 0.7934 (t80) REVERT: R 106 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7492 (t0) REVERT: R 133 THR cc_start: 0.8786 (t) cc_final: 0.8489 (p) REVERT: R 152 MET cc_start: 0.8238 (mmm) cc_final: 0.7881 (mmm) REVERT: R 197 MET cc_start: 0.8054 (mmp) cc_final: 0.7819 (mmt) REVERT: R 220 SER cc_start: 0.8059 (m) cc_final: 0.7787 (p) REVERT: R 243 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8037 (mm) REVERT: R 273 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: R 287 SER cc_start: 0.8126 (p) cc_final: 0.7755 (p) REVERT: R 294 SER cc_start: 0.8747 (m) cc_final: 0.8334 (t) REVERT: R 302 VAL cc_start: 0.8782 (m) cc_final: 0.8478 (t) outliers start: 29 outliers final: 19 residues processed: 264 average time/residue: 0.1055 time to fit residues: 35.0626 Evaluate side-chains 275 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 129 HIS Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 273 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN C 18 GLN R 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.091140 restraints weight = 13055.471| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.50 r_work: 0.3171 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7308 Z= 0.163 Angle : 0.610 13.237 9885 Z= 0.317 Chirality : 0.044 0.192 1137 Planarity : 0.004 0.038 1241 Dihedral : 5.354 46.796 1003 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.62 % Allowed : 26.23 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.28), residues: 893 helix: 1.00 (0.26), residues: 405 sheet: -0.16 (0.41), residues: 158 loop : -1.41 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 309 TYR 0.011 0.001 TYR B 124 PHE 0.035 0.002 PHE R 74 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7307) covalent geometry : angle 0.60893 ( 9883) SS BOND : bond 0.00351 ( 1) SS BOND : angle 2.91065 ( 2) hydrogen bonds : bond 0.03879 ( 388) hydrogen bonds : angle 4.67969 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7621 (tm-30) cc_final: 0.6718 (pt0) REVERT: A 33 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7872 (tt0) REVERT: A 197 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8238 (ttmm) REVERT: A 204 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8333 (tp40) REVERT: A 205 ARG cc_start: 0.7988 (mmt-90) cc_final: 0.7747 (mmt-90) REVERT: A 257 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8815 (ptmm) REVERT: A 275 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 279 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8593 (mtmt) REVERT: A 280 LYS cc_start: 0.8955 (mptt) cc_final: 0.8451 (mptt) REVERT: A 296 TYR cc_start: 0.9101 (t80) cc_final: 0.8642 (t80) REVERT: A 309 ASP cc_start: 0.8143 (m-30) cc_final: 0.7814 (m-30) REVERT: A 312 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8677 (mmmt) REVERT: A 321 THR cc_start: 0.9032 (m) cc_final: 0.8590 (p) REVERT: B 8 ARG cc_start: 0.7336 (mtt90) cc_final: 0.7120 (mtm-85) REVERT: B 19 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8233 (ttp80) REVERT: B 145 TYR cc_start: 0.9037 (p90) cc_final: 0.8548 (p90) REVERT: B 188 MET cc_start: 0.8142 (mmm) cc_final: 0.7481 (mmm) REVERT: B 189 SER cc_start: 0.8915 (p) cc_final: 0.8702 (p) REVERT: B 212 ASP cc_start: 0.8371 (t0) cc_final: 0.8114 (t0) REVERT: B 243 THR cc_start: 0.8778 (m) cc_final: 0.8107 (p) REVERT: B 258 ASP cc_start: 0.8346 (t0) cc_final: 0.7487 (t0) REVERT: B 262 MET cc_start: 0.8365 (tpp) cc_final: 0.8153 (mmm) REVERT: B 292 PHE cc_start: 0.8619 (m-10) cc_final: 0.8025 (m-80) REVERT: B 312 ASP cc_start: 0.8339 (t0) cc_final: 0.7948 (t0) REVERT: C 17 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8535 (mm-30) REVERT: C 21 MET cc_start: 0.8619 (mmm) cc_final: 0.8195 (mmm) REVERT: R 25 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8413 (mp) REVERT: R 33 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7684 (t80) REVERT: R 82 MET cc_start: 0.8244 (mpp) cc_final: 0.7413 (mpp) REVERT: R 100 PHE cc_start: 0.8327 (t80) cc_final: 0.7976 (t80) REVERT: R 106 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7784 (t0) REVERT: R 133 THR cc_start: 0.8884 (t) cc_final: 0.8600 (p) REVERT: R 152 MET cc_start: 0.8411 (mmm) cc_final: 0.8071 (mmm) REVERT: R 197 MET cc_start: 0.8311 (mmp) cc_final: 0.8085 (mmt) REVERT: R 220 SER cc_start: 0.8215 (m) cc_final: 0.7974 (p) REVERT: R 243 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8200 (mm) REVERT: R 244 SER cc_start: 0.8499 (m) cc_final: 0.8277 (m) REVERT: R 273 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: R 287 SER cc_start: 0.8160 (p) cc_final: 0.7781 (p) REVERT: R 294 SER cc_start: 0.8810 (m) cc_final: 0.8442 (t) REVERT: R 302 VAL cc_start: 0.8832 (m) cc_final: 0.8518 (t) REVERT: R 309 ARG cc_start: 0.8701 (ttm110) cc_final: 0.7862 (mtm110) outliers start: 28 outliers final: 22 residues processed: 265 average time/residue: 0.1132 time to fit residues: 37.7011 Evaluate side-chains 280 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 129 HIS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 273 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 57 HIS ** R 258 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 = 0.3500 r_free = 0.3500 target = 0.103627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.090970 restraints weight = 13051.627| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.48 r_work: 0.3171 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7308 Z= 0.162 Angle : 0.608 13.154 9885 Z= 0.318 Chirality : 0.044 0.186 1137 Planarity : 0.004 0.037 1241 Dihedral : 5.398 46.881 1003 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.75 % Allowed : 25.84 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.28), residues: 893 helix: 1.00 (0.26), residues: 405 sheet: -0.19 (0.40), residues: 158 loop : -1.43 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 309 TYR 0.011 0.001 TYR B 124 PHE 0.033 0.002 PHE R 74 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7307) covalent geometry : angle 0.60669 ( 9883) SS BOND : bond 0.00325 ( 1) SS BOND : angle 2.88017 ( 2) hydrogen bonds : bond 0.03894 ( 388) hydrogen bonds : angle 4.66742 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6753 (pt0) REVERT: A 33 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7857 (tt0) REVERT: A 197 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8259 (ttmm) REVERT: A 252 SER cc_start: 0.8903 (t) cc_final: 0.8421 (p) REVERT: A 257 LYS cc_start: 0.9111 (ptmm) cc_final: 0.8799 (ptmm) REVERT: A 275 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8194 (mm-30) REVERT: A 279 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: A 280 LYS cc_start: 0.8961 (mptt) cc_final: 0.8449 (mptt) REVERT: A 296 TYR cc_start: 0.9107 (t80) cc_final: 0.8724 (t80) REVERT: A 309 ASP cc_start: 0.8142 (m-30) cc_final: 0.7871 (m-30) REVERT: A 312 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8641 (mmmt) REVERT: A 321 THR cc_start: 0.9029 (m) cc_final: 0.8592 (p) REVERT: B 8 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7079 (mtm-85) REVERT: B 19 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8249 (ttp80) REVERT: B 145 TYR cc_start: 0.9036 (p90) cc_final: 0.8631 (p90) REVERT: B 189 SER cc_start: 0.8952 (p) cc_final: 0.8717 (p) REVERT: B 212 ASP cc_start: 0.8385 (t0) cc_final: 0.8127 (t0) REVERT: B 243 THR cc_start: 0.8767 (m) cc_final: 0.8095 (p) REVERT: B 258 ASP cc_start: 0.8396 (t0) cc_final: 0.7544 (t0) REVERT: B 292 PHE cc_start: 0.8624 (m-10) cc_final: 0.8057 (m-80) REVERT: B 312 ASP cc_start: 0.8329 (t0) cc_final: 0.7967 (t0) REVERT: C 17 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8576 (mm-30) REVERT: C 21 MET cc_start: 0.8610 (mmm) cc_final: 0.8179 (mmm) REVERT: R 25 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8490 (mp) REVERT: R 33 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7725 (t80) REVERT: R 82 MET cc_start: 0.8247 (mpp) cc_final: 0.7505 (mpp) REVERT: R 100 PHE cc_start: 0.8320 (t80) cc_final: 0.7956 (t80) REVERT: R 106 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7778 (t0) REVERT: R 133 THR cc_start: 0.8891 (t) cc_final: 0.8605 (p) REVERT: R 152 MET cc_start: 0.8423 (mmm) cc_final: 0.8084 (mmm) REVERT: R 197 MET cc_start: 0.8306 (mmp) cc_final: 0.8077 (mmt) REVERT: R 220 SER cc_start: 0.8197 (m) cc_final: 0.7969 (p) REVERT: R 243 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8184 (mm) REVERT: R 244 SER cc_start: 0.8480 (m) cc_final: 0.8252 (m) REVERT: R 273 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: R 277 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8539 (mmmt) REVERT: R 287 SER cc_start: 0.8223 (p) cc_final: 0.7842 (p) REVERT: R 294 SER cc_start: 0.8818 (m) cc_final: 0.8444 (t) REVERT: R 302 VAL cc_start: 0.8844 (m) cc_final: 0.8580 (t) outliers start: 29 outliers final: 23 residues processed: 273 average time/residue: 0.1109 time to fit residues: 38.3071 Evaluate side-chains 287 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 33 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 129 HIS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 304 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.0470 chunk 81 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN R 57 HIS ** R 258 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 = 0.3520 r_free = 0.3520 target = 0.105204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092403 restraints weight = 12921.572| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.54 r_work: 0.3192 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7308 Z= 0.129 Angle : 0.591 12.960 9885 Z= 0.309 Chirality : 0.044 0.173 1137 Planarity : 0.004 0.036 1241 Dihedral : 5.275 47.692 1003 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.88 % Allowed : 26.36 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.28), residues: 893 helix: 1.05 (0.27), residues: 406 sheet: -0.07 (0.41), residues: 155 loop : -1.41 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 309 TYR 0.010 0.001 TYR B 124 PHE 0.032 0.001 PHE R 74 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.000 HIS R 90 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7307) covalent geometry : angle 0.59014 ( 9883) SS BOND : bond 0.00271 ( 1) SS BOND : angle 2.33472 ( 2) hydrogen bonds : bond 0.03743 ( 388) hydrogen bonds : angle 4.59180 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.03 seconds wall clock time: 32 minutes 13.79 seconds (1933.79 seconds total)