Starting phenix.real_space_refine on Tue Jul 29 21:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efl_28085/07_2025/8efl_28085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efl_28085/07_2025/8efl_28085.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/8efl_28085/07_2025/8efl_28085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2025/8efl_28085.map" model { file = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2025/8efl_28085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2025/8efl_28085.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 98 5.16 5 Cl 6 4.86 5 C 7645 2.51 5 N 1908 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11750 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'TRANS': 22} Chain: "R" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.69, per 1000 atoms: 0.57 Number of scatterers: 11750 At special positions: 0 Unit cell: (106.029, 116.739, 153.153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 98 16.00 O 2093 8.00 N 1908 7.00 C 7645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 15 sheets defined 49.7% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.730A pdb=" N GLN R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.826A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.031A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.640A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.939A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.597A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.207A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.552A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.845A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.832A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.569A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.306A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'M' and resid 67 through 98 Processing helix chain 'M' and resid 103 through 121 Processing helix chain 'M' and resid 122 through 133 removed outlier: 3.535A pdb=" N GLN M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.689A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.807A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.745A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.587A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 340 removed outlier: 3.745A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'F' and resid 333 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.806A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.298A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.738A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.661A 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: 6.734A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.791A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.740A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.213A 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: 6.398A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.711A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.761A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 703 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1808 1.30 - 1.43: 3148 1.43 - 1.56: 6917 1.56 - 1.69: 9 1.69 - 1.82: 151 Bond restraints: 12033 Sorted by residual: bond pdb=" C03 WH9 R 401 " pdb=" N01 WH9 R 401 " ideal model delta sigma weight residual 1.380 1.316 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C03 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.380 1.316 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C07 WH9 R 401 " pdb=" N02 WH9 R 401 " ideal model delta sigma weight residual 1.391 1.328 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C07 WH9 M 401 " pdb=" N02 WH9 M 401 " ideal model delta sigma weight residual 1.391 1.329 0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C07 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.380 1.322 0.058 2.00e-02 2.50e+03 8.32e+00 ... (remaining 12028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15520 1.77 - 3.54: 704 3.54 - 5.30: 121 5.30 - 7.07: 26 7.07 - 8.84: 8 Bond angle restraints: 16379 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.82 130.69 -5.87 1.78e+00 3.16e-01 1.09e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 116.89 -7.08 2.21e+00 2.05e-01 1.03e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.49 -5.83 1.85e+00 2.92e-01 9.92e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 128.11 -4.64 1.53e+00 4.27e-01 9.18e+00 ... (remaining 16374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 7238 14.15 - 28.29: 298 28.29 - 42.44: 60 42.44 - 56.58: 11 56.58 - 70.73: 2 Dihedral angle restraints: 7609 sinusoidal: 3381 harmonic: 4228 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE B 81 " pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 7606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1699 0.088 - 0.176: 168 0.176 - 0.264: 25 0.264 - 0.352: 8 0.352 - 0.440: 11 Chirality restraints: 1911 Sorted by residual: chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1908 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 236 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 278 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ARG R 278 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG R 278 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 279 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.025 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2204 2.79 - 3.32: 10638 3.32 - 3.84: 19028 3.84 - 4.37: 21433 4.37 - 4.90: 38718 Nonbonded interactions: 92021 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.259 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.304 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.321 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.330 3.040 ... (remaining 92016 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 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'R' } 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: 27.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.005 0.064 12036 Z= 0.250 Angle : 0.868 8.841 16385 Z= 0.463 Chirality : 0.066 0.440 1911 Planarity : 0.006 0.075 1969 Dihedral : 8.532 70.730 4866 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1428 helix: 1.12 (0.17), residues: 664 sheet: 0.57 (0.30), residues: 283 loop : -1.19 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.005 0.001 HIS B 54 PHE 0.026 0.002 PHE A 189 TYR 0.024 0.002 TYR R 108 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.11270 ( 698) hydrogen bonds : angle 5.75249 ( 2040) SS BOND : bond 0.00588 ( 3) SS BOND : angle 1.90709 ( 6) covalent geometry : bond 0.00465 (12033) covalent geometry : angle 0.86737 (16379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.121 Fit side-chains REVERT: R 260 ARG cc_start: 0.7467 (tpt90) cc_final: 0.7009 (tpp80) REVERT: A 44 SER cc_start: 0.7619 (m) cc_final: 0.7127 (p) REVERT: A 309 ASP cc_start: 0.7249 (m-30) cc_final: 0.7039 (m-30) REVERT: B 150 ARG cc_start: 0.8430 (mmt-90) cc_final: 0.8179 (mpt180) REVERT: B 175 GLN cc_start: 0.7608 (mm110) cc_final: 0.7160 (mm110) REVERT: B 189 SER cc_start: 0.8838 (p) cc_final: 0.8480 (t) REVERT: E 167 LEU cc_start: 0.7827 (tp) cc_final: 0.7541 (tp) REVERT: M 266 MET cc_start: 0.5980 (tmt) cc_final: 0.5721 (ttp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2339 time to fit residues: 79.9631 Evaluate side-chains 160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS B 35 ASN B 91 HIS B 155 ASN B 266 HIS B 293 ASN E 77 ASN E 180 GLN M 106 ASN M 330 ASN M 334 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.211821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.187503 restraints weight = 12052.031| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.10 r_work: 0.3731 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12036 Z= 0.119 Angle : 0.489 6.837 16385 Z= 0.259 Chirality : 0.039 0.150 1911 Planarity : 0.004 0.055 1969 Dihedral : 5.990 64.757 2254 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.14 % Allowed : 6.72 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1428 helix: 2.61 (0.18), residues: 671 sheet: 0.57 (0.29), residues: 270 loop : -0.87 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.021 0.001 PHE A 189 TYR 0.019 0.001 TYR E 191 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 698) hydrogen bonds : angle 4.36474 ( 2040) SS BOND : bond 0.00306 ( 3) SS BOND : angle 1.01060 ( 6) covalent geometry : bond 0.00262 (12033) covalent geometry : angle 0.48852 (16379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.260 Fit side-chains REVERT: R 283 MET cc_start: 0.7745 (ttm) cc_final: 0.7383 (mtp) REVERT: R 310 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.5795 (tp) REVERT: A 309 ASP cc_start: 0.7760 (m-30) cc_final: 0.7463 (m-30) REVERT: A 350 ASP cc_start: 0.7788 (t0) cc_final: 0.7448 (m-30) REVERT: B 101 MET cc_start: 0.8969 (mtp) cc_final: 0.8717 (mtp) REVERT: B 161 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8930 (m) REVERT: B 175 GLN cc_start: 0.7784 (mm110) cc_final: 0.7567 (mm-40) REVERT: B 325 MET cc_start: 0.8020 (tpp) cc_final: 0.7669 (mmt) outliers start: 27 outliers final: 15 residues processed: 188 average time/residue: 0.2305 time to fit residues: 64.2079 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN B 75 GLN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.202819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.161663 restraints weight = 12267.548| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.49 r_work: 0.3158 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12036 Z= 0.135 Angle : 0.497 6.494 16385 Z= 0.260 Chirality : 0.039 0.150 1911 Planarity : 0.004 0.047 1969 Dihedral : 6.162 61.407 2254 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.29 % Allowed : 8.70 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.21), residues: 1428 helix: 2.87 (0.18), residues: 669 sheet: 0.51 (0.29), residues: 280 loop : -0.66 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.019 0.001 PHE R 154 TYR 0.012 0.001 TYR E 191 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 698) hydrogen bonds : angle 4.27575 ( 2040) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.30471 ( 6) covalent geometry : bond 0.00313 (12033) covalent geometry : angle 0.49642 (16379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.333 Fit side-chains REVERT: R 283 MET cc_start: 0.8088 (ttm) cc_final: 0.7824 (mtp) REVERT: R 310 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.5957 (tp) REVERT: A 240 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.3149 (mtm) REVERT: A 309 ASP cc_start: 0.7855 (m-30) cc_final: 0.7563 (m-30) REVERT: A 350 ASP cc_start: 0.8329 (t0) cc_final: 0.7671 (m-30) REVERT: B 175 GLN cc_start: 0.7745 (mm110) cc_final: 0.7309 (mm-40) REVERT: B 176 GLN cc_start: 0.8642 (pt0) cc_final: 0.8400 (pt0) REVERT: B 228 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8433 (p0) REVERT: B 262 MET cc_start: 0.7392 (ttm) cc_final: 0.7000 (ttm) REVERT: B 269 ILE cc_start: 0.6829 (mt) cc_final: 0.6533 (tp) REVERT: E 141 MET cc_start: 0.8239 (mmm) cc_final: 0.7698 (tpp) REVERT: M 283 MET cc_start: 0.7918 (tpp) cc_final: 0.7566 (tpp) outliers start: 29 outliers final: 21 residues processed: 169 average time/residue: 0.2215 time to fit residues: 55.2309 Evaluate side-chains 157 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS M 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.201694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.157425 restraints weight = 12341.395| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.84 r_work: 0.3056 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12036 Z= 0.167 Angle : 0.532 7.881 16385 Z= 0.275 Chirality : 0.040 0.155 1911 Planarity : 0.004 0.042 1969 Dihedral : 6.480 59.552 2254 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.93 % Allowed : 8.86 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.21), residues: 1428 helix: 2.84 (0.19), residues: 661 sheet: 0.41 (0.29), residues: 291 loop : -0.66 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS E 233 PHE 0.026 0.002 PHE R 154 TYR 0.019 0.002 TYR R 301 ARG 0.005 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 698) hydrogen bonds : angle 4.40482 ( 2040) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.33769 ( 6) covalent geometry : bond 0.00404 (12033) covalent geometry : angle 0.53129 (16379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.345 Fit side-chains REVERT: R 207 MET cc_start: 0.9125 (mtp) cc_final: 0.8914 (mtm) REVERT: R 310 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6388 (tp) REVERT: A 44 SER cc_start: 0.7758 (m) cc_final: 0.7168 (p) REVERT: A 240 MET cc_start: 0.4302 (OUTLIER) cc_final: 0.3685 (mtm) REVERT: A 309 ASP cc_start: 0.7744 (m-30) cc_final: 0.7503 (m-30) REVERT: A 350 ASP cc_start: 0.8384 (t0) cc_final: 0.7708 (m-30) REVERT: B 101 MET cc_start: 0.9326 (mtp) cc_final: 0.8858 (mtp) REVERT: B 175 GLN cc_start: 0.7863 (mm110) cc_final: 0.7408 (mm110) REVERT: B 176 GLN cc_start: 0.8600 (pt0) cc_final: 0.8306 (pt0) REVERT: B 262 MET cc_start: 0.7586 (ttm) cc_final: 0.7156 (ttm) REVERT: M 283 MET cc_start: 0.8012 (tpp) cc_final: 0.7667 (tpp) outliers start: 37 outliers final: 30 residues processed: 164 average time/residue: 0.2197 time to fit residues: 53.7982 Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.204693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162243 restraints weight = 12271.983| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.97 r_work: 0.3140 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12036 Z= 0.112 Angle : 0.472 6.054 16385 Z= 0.247 Chirality : 0.038 0.144 1911 Planarity : 0.003 0.039 1969 Dihedral : 6.183 56.903 2254 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.37 % Allowed : 10.44 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.22), residues: 1428 helix: 2.95 (0.19), residues: 669 sheet: 0.35 (0.29), residues: 290 loop : -0.56 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.001 PHE R 154 TYR 0.013 0.001 TYR E 94 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 698) hydrogen bonds : angle 4.21735 ( 2040) SS BOND : bond 0.00441 ( 3) SS BOND : angle 1.08106 ( 6) covalent geometry : bond 0.00252 (12033) covalent geometry : angle 0.47145 (16379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.410 Fit side-chains REVERT: R 310 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6913 (tp) REVERT: A 44 SER cc_start: 0.7737 (m) cc_final: 0.7144 (p) REVERT: A 240 MET cc_start: 0.4372 (OUTLIER) cc_final: 0.3757 (mtm) REVERT: A 309 ASP cc_start: 0.7669 (m-30) cc_final: 0.7436 (m-30) REVERT: A 350 ASP cc_start: 0.8249 (t0) cc_final: 0.7693 (m-30) REVERT: B 175 GLN cc_start: 0.7768 (mm110) cc_final: 0.7364 (mm110) REVERT: B 176 GLN cc_start: 0.8527 (pt0) cc_final: 0.8270 (pt0) REVERT: M 257 MET cc_start: 0.8922 (ttt) cc_final: 0.8696 (ttp) REVERT: M 283 MET cc_start: 0.7916 (tpp) cc_final: 0.7518 (tpp) outliers start: 30 outliers final: 24 residues processed: 155 average time/residue: 0.2303 time to fit residues: 52.3920 Evaluate side-chains 157 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.198651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157186 restraints weight = 12192.549| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.68 r_work: 0.3117 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12036 Z= 0.112 Angle : 0.465 5.929 16385 Z= 0.242 Chirality : 0.038 0.140 1911 Planarity : 0.003 0.039 1969 Dihedral : 6.098 59.229 2254 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.85 % Allowed : 10.44 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1428 helix: 3.06 (0.19), residues: 667 sheet: 0.28 (0.29), residues: 292 loop : -0.48 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 PHE 0.014 0.001 PHE R 154 TYR 0.014 0.001 TYR E 94 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 698) hydrogen bonds : angle 4.16981 ( 2040) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.11319 ( 6) covalent geometry : bond 0.00253 (12033) covalent geometry : angle 0.46447 (16379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.214 Fit side-chains REVERT: R 310 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6917 (tp) REVERT: R 333 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7503 (mp) REVERT: A 44 SER cc_start: 0.7745 (m) cc_final: 0.7156 (p) REVERT: A 240 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4111 (mtm) REVERT: A 309 ASP cc_start: 0.7706 (m-30) cc_final: 0.7483 (m-30) REVERT: A 350 ASP cc_start: 0.8332 (t0) cc_final: 0.7780 (m-30) REVERT: B 175 GLN cc_start: 0.7703 (mm110) cc_final: 0.7302 (mm110) REVERT: B 176 GLN cc_start: 0.8535 (pt0) cc_final: 0.8268 (pt0) REVERT: M 283 MET cc_start: 0.7995 (tpp) cc_final: 0.7620 (tpp) outliers start: 36 outliers final: 27 residues processed: 155 average time/residue: 0.2219 time to fit residues: 51.2283 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 87 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.202087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176462 restraints weight = 12218.939| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.14 r_work: 0.3560 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12036 Z= 0.103 Angle : 0.452 6.247 16385 Z= 0.236 Chirality : 0.038 0.138 1911 Planarity : 0.003 0.039 1969 Dihedral : 5.924 57.001 2254 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.77 % Allowed : 10.60 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1428 helix: 3.12 (0.19), residues: 668 sheet: 0.36 (0.29), residues: 283 loop : -0.53 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR E 94 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 698) hydrogen bonds : angle 4.10763 ( 2040) SS BOND : bond 0.00418 ( 3) SS BOND : angle 1.04904 ( 6) covalent geometry : bond 0.00228 (12033) covalent geometry : angle 0.45119 (16379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.302 Fit side-chains REVERT: R 310 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.6409 (tp) REVERT: R 333 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7850 (mp) REVERT: A 44 SER cc_start: 0.8045 (m) cc_final: 0.7376 (p) REVERT: A 240 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.4271 (mtm) REVERT: A 309 ASP cc_start: 0.7894 (m-30) cc_final: 0.7662 (m-30) REVERT: A 350 ASP cc_start: 0.8514 (t0) cc_final: 0.8060 (m-30) REVERT: B 175 GLN cc_start: 0.7884 (mm110) cc_final: 0.7543 (mm110) REVERT: B 176 GLN cc_start: 0.8690 (pt0) cc_final: 0.8449 (pt0) REVERT: E 141 MET cc_start: 0.8141 (mmm) cc_final: 0.6980 (mmm) REVERT: M 283 MET cc_start: 0.8122 (tpp) cc_final: 0.7790 (tpp) outliers start: 35 outliers final: 28 residues processed: 156 average time/residue: 0.2278 time to fit residues: 52.5286 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.204432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.162772 restraints weight = 12396.566| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.10 r_work: 0.3143 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12036 Z= 0.105 Angle : 0.461 6.570 16385 Z= 0.241 Chirality : 0.038 0.137 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.817 55.764 2254 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.85 % Allowed : 10.92 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.22), residues: 1428 helix: 3.16 (0.19), residues: 668 sheet: 0.21 (0.29), residues: 294 loop : -0.48 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR E 94 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 698) hydrogen bonds : angle 4.09808 ( 2040) SS BOND : bond 0.00454 ( 3) SS BOND : angle 1.07590 ( 6) covalent geometry : bond 0.00236 (12033) covalent geometry : angle 0.46111 (16379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 1.655 Fit side-chains REVERT: R 212 TYR cc_start: 0.7781 (m-80) cc_final: 0.7519 (m-80) REVERT: R 310 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.6463 (tp) REVERT: R 333 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 44 SER cc_start: 0.7801 (m) cc_final: 0.7165 (p) REVERT: A 240 MET cc_start: 0.4915 (OUTLIER) cc_final: 0.4230 (mtm) REVERT: A 309 ASP cc_start: 0.7650 (m-30) cc_final: 0.7438 (m-30) REVERT: A 350 ASP cc_start: 0.8241 (t0) cc_final: 0.7733 (m-30) REVERT: B 101 MET cc_start: 0.9224 (mtm) cc_final: 0.8797 (ptp) REVERT: B 175 GLN cc_start: 0.7665 (mm110) cc_final: 0.7258 (mm110) REVERT: B 176 GLN cc_start: 0.8480 (pt0) cc_final: 0.8199 (pt0) REVERT: E 141 MET cc_start: 0.7915 (mmm) cc_final: 0.6795 (mmm) REVERT: M 283 MET cc_start: 0.7858 (tpp) cc_final: 0.7493 (tpp) REVERT: F 354 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7150 (m-80) outliers start: 36 outliers final: 30 residues processed: 156 average time/residue: 0.3283 time to fit residues: 76.6050 Evaluate side-chains 162 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 24 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 53 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 180 GLN M 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.202138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.180721 restraints weight = 12313.874| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 0.94 r_work: 0.3626 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12036 Z= 0.133 Angle : 0.492 6.755 16385 Z= 0.255 Chirality : 0.039 0.146 1911 Planarity : 0.003 0.039 1969 Dihedral : 5.817 56.878 2254 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.77 % Allowed : 11.31 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1428 helix: 3.07 (0.19), residues: 664 sheet: 0.18 (0.29), residues: 294 loop : -0.51 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.016 0.001 TYR E 94 ARG 0.003 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 698) hydrogen bonds : angle 4.21802 ( 2040) SS BOND : bond 0.00470 ( 3) SS BOND : angle 1.11081 ( 6) covalent geometry : bond 0.00313 (12033) covalent geometry : angle 0.49202 (16379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.257 Fit side-chains REVERT: R 310 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7032 (tp) REVERT: A 44 SER cc_start: 0.7917 (m) cc_final: 0.7254 (p) REVERT: A 240 MET cc_start: 0.4915 (OUTLIER) cc_final: 0.4608 (mtm) REVERT: A 350 ASP cc_start: 0.8404 (t0) cc_final: 0.8024 (m-30) REVERT: B 101 MET cc_start: 0.9149 (mtm) cc_final: 0.8671 (ptp) REVERT: B 175 GLN cc_start: 0.7865 (mm110) cc_final: 0.7530 (mm110) REVERT: M 283 MET cc_start: 0.8036 (tpp) cc_final: 0.7721 (tpp) REVERT: F 354 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7555 (m-80) outliers start: 35 outliers final: 32 residues processed: 170 average time/residue: 0.2700 time to fit residues: 69.0928 Evaluate side-chains 167 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 96 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.203480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.165408 restraints weight = 12232.746| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.54 r_work: 0.3394 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12036 Z= 0.114 Angle : 0.480 7.961 16385 Z= 0.249 Chirality : 0.038 0.139 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.633 54.389 2254 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.77 % Allowed : 11.39 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.22), residues: 1428 helix: 3.06 (0.19), residues: 668 sheet: 0.17 (0.29), residues: 294 loop : -0.50 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.001 PHE A 189 TYR 0.015 0.001 TYR R 212 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 698) hydrogen bonds : angle 4.15291 ( 2040) SS BOND : bond 0.00518 ( 3) SS BOND : angle 1.28256 ( 6) covalent geometry : bond 0.00261 (12033) covalent geometry : angle 0.47963 (16379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.492 Fit side-chains REVERT: R 310 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7047 (tp) REVERT: R 333 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 44 SER cc_start: 0.7955 (m) cc_final: 0.7285 (p) REVERT: A 240 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.4559 (mtm) REVERT: A 350 ASP cc_start: 0.8532 (t0) cc_final: 0.8065 (m-30) REVERT: B 101 MET cc_start: 0.9155 (mtm) cc_final: 0.8883 (ptp) REVERT: B 175 GLN cc_start: 0.7920 (mm110) cc_final: 0.7579 (mm110) REVERT: E 141 MET cc_start: 0.8117 (mmm) cc_final: 0.7140 (mmm) REVERT: M 283 MET cc_start: 0.8142 (tpp) cc_final: 0.7824 (tpp) REVERT: F 354 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7702 (m-80) outliers start: 35 outliers final: 29 residues processed: 159 average time/residue: 0.2827 time to fit residues: 67.8516 Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.204292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.182552 restraints weight = 12267.141| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.92 r_work: 0.3643 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12036 Z= 0.111 Angle : 0.474 8.514 16385 Z= 0.245 Chirality : 0.038 0.139 1911 Planarity : 0.003 0.038 1969 Dihedral : 5.515 52.776 2254 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.61 % Allowed : 11.55 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.22), residues: 1428 helix: 3.08 (0.19), residues: 668 sheet: 0.22 (0.30), residues: 294 loop : -0.51 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR E 94 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 698) hydrogen bonds : angle 4.12122 ( 2040) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.07116 ( 6) covalent geometry : bond 0.00252 (12033) covalent geometry : angle 0.47356 (16379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7587.68 seconds wall clock time: 137 minutes 41.01 seconds (8261.01 seconds total)