Starting phenix.real_space_refine on Sat Aug 23 01:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2g_34437/08_2025/8h2g_34437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2g_34437/08_2025/8h2g_34437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h2g_34437/08_2025/8h2g_34437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2g_34437/08_2025/8h2g_34437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h2g_34437/08_2025/8h2g_34437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2g_34437/08_2025/8h2g_34437.map" } resolution = 3.01 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= -0.000 sd= 0.059 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 64 5.16 5 C 5756 2.51 5 N 1540 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2365 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 9023 At special positions: 0 Unit cell: (88.395, 122.01, 131.97, 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 64 16.00 O 1663 8.00 N 1540 7.00 C 5756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 333.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 13 sheets defined 34.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.098A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 89 removed outlier: 4.013A pdb=" N ARG A 63 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.566A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.604A pdb=" N LYS A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 187 through 218 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 225 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 268 removed outlier: 4.203A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 295 removed outlier: 4.060A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.525A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.132A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.668A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.768A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 352 removed outlier: 4.229A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.520A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.511A pdb=" N THR C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.530A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 9.225A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.335A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.918A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.744A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.703A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.629A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.460A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.525A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.548A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.629A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1215 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: 1.30 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2913 1.35 - 1.47: 2298 1.47 - 1.59: 3917 1.59 - 1.71: 0 1.71 - 1.83: 92 Bond restraints: 9220 Sorted by residual: bond pdb=" C2 NIO A 401 " pdb=" C3 NIO A 401 " ideal model delta sigma weight residual 1.390 1.351 0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C3 NIO A 401 " pdb=" C4 NIO A 401 " ideal model delta sigma weight residual 1.386 1.353 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.49e+00 bond pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG B 32 " pdb=" CD ARG B 32 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 9215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12306 1.95 - 3.89: 136 3.89 - 5.84: 26 5.84 - 7.79: 6 7.79 - 9.73: 2 Bond angle restraints: 12476 Sorted by residual: angle pdb=" C ASP A 97 " pdb=" N ILE A 98 " pdb=" CA ILE A 98 " ideal model delta sigma weight residual 120.24 122.61 -2.37 6.30e-01 2.52e+00 1.41e+01 angle pdb=" C ILE A 98 " pdb=" CA ILE A 98 " pdb=" CB ILE A 98 " ideal model delta sigma weight residual 114.35 110.94 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA TRP A 256 " pdb=" CB TRP A 256 " pdb=" CG TRP A 256 " ideal model delta sigma weight residual 113.60 119.62 -6.02 1.90e+00 2.77e-01 1.01e+01 angle pdb=" CB GLU E 89 " pdb=" CG GLU E 89 " pdb=" CD GLU E 89 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.70e+00 3.46e-01 7.79e+00 angle pdb=" CA LEU A 195 " pdb=" CB LEU A 195 " pdb=" CG LEU A 195 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 ... (remaining 12471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4656 17.92 - 35.83: 625 35.83 - 53.75: 154 53.75 - 71.67: 20 71.67 - 89.58: 8 Dihedral angle restraints: 5463 sinusoidal: 2146 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual -86.00 -156.72 70.72 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA LEU B 268 " pdb=" C LEU B 268 " pdb=" N ASN B 269 " pdb=" CA ASN B 269 " ideal model delta harmonic sigma weight residual 180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.16 32.16 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 887 0.031 - 0.062: 331 0.062 - 0.093: 107 0.093 - 0.124: 63 0.124 - 0.155: 12 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB ILE A 78 " pdb=" CA ILE A 78 " pdb=" CG1 ILE A 78 " pdb=" CG2 ILE A 78 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CG LEU A 195 " pdb=" CB LEU A 195 " pdb=" CD1 LEU A 195 " pdb=" CD2 LEU A 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1397 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASN A 171 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 172 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 200 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 192 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C MET E 192 " -0.029 2.00e-02 2.50e+03 pdb=" O MET E 192 " 0.011 2.00e-02 2.50e+03 pdb=" N SER E 193 " 0.010 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 184 2.68 - 3.23: 8546 3.23 - 3.79: 13875 3.79 - 4.34: 18792 4.34 - 4.90: 32064 Nonbonded interactions: 73461 Sorted by model distance: nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.123 3.040 nonbonded pdb=" CB SER A 298 " pdb=" O GLY B 352 " model vdw 2.153 3.440 nonbonded pdb=" O ASN A 171 " pdb=" ND2 ASN A 171 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.226 3.040 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.246 3.120 ... (remaining 73456 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: 0.400 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.004 0.183 9226 Z= 0.234 Angle : 0.570 9.733 12486 Z= 0.300 Chirality : 0.042 0.155 1400 Planarity : 0.004 0.047 1580 Dihedral : 16.846 89.584 3304 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.61 % Allowed : 29.29 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.07 (0.26), residues: 1131 helix: 1.59 (0.28), residues: 377 sheet: -0.23 (0.34), residues: 264 loop : -0.99 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 32 TYR 0.021 0.001 TYR B 302 PHE 0.021 0.001 PHE A 95 TRP 0.020 0.001 TRP A 93 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9220) covalent geometry : angle 0.56683 (12476) SS BOND : bond 0.00653 ( 5) SS BOND : angle 2.05845 ( 10) hydrogen bonds : bond 0.17411 ( 424) hydrogen bonds : angle 6.93122 ( 1215) Misc. bond : bond 0.18270 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6779 (m) cc_final: 0.6543 (m) REVERT: A 154 ILE cc_start: 0.7938 (mt) cc_final: 0.7725 (mt) outliers start: 6 outliers final: 3 residues processed: 155 average time/residue: 0.0764 time to fit residues: 16.7308 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 131 HIS A 171 ASN A 223 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.199928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161634 restraints weight = 10300.115| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.63 r_work: 0.3413 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9226 Z= 0.249 Angle : 0.705 8.556 12486 Z= 0.366 Chirality : 0.047 0.173 1400 Planarity : 0.006 0.147 1580 Dihedral : 4.932 33.589 1241 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.43 % Allowed : 25.51 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.14 (0.25), residues: 1131 helix: 1.57 (0.28), residues: 372 sheet: -0.45 (0.31), residues: 276 loop : -1.18 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 218 TYR 0.018 0.002 TYR E 190 PHE 0.021 0.002 PHE A 105 TRP 0.023 0.002 TRP A 93 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 9220) covalent geometry : angle 0.70216 (12476) SS BOND : bond 0.01219 ( 5) SS BOND : angle 2.25437 ( 10) hydrogen bonds : bond 0.05360 ( 424) hydrogen bonds : angle 5.24611 ( 1215) Misc. bond : bond 0.00286 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.6655 (OUTLIER) cc_final: 0.6363 (m) REVERT: A 104 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5790 (mt) REVERT: A 112 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7123 (tt0) REVERT: A 187 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6568 (pt0) REVERT: A 234 MET cc_start: 0.6907 (mmm) cc_final: 0.6610 (tpt) REVERT: A 254 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4320 (mt) REVERT: B 285 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7279 (pt) REVERT: C 44 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: C 251 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mtt-85) REVERT: E 89 GLU cc_start: 0.7543 (pp20) cc_final: 0.7195 (pp20) outliers start: 63 outliers final: 33 residues processed: 175 average time/residue: 0.0951 time to fit residues: 23.5342 Evaluate side-chains 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 223 HIS C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.202256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163899 restraints weight = 10275.904| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.68 r_work: 0.3510 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9226 Z= 0.157 Angle : 0.593 7.671 12486 Z= 0.311 Chirality : 0.043 0.158 1400 Planarity : 0.005 0.098 1580 Dihedral : 4.518 22.707 1236 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.12 % Allowed : 24.39 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.01 (0.25), residues: 1131 helix: 1.74 (0.28), residues: 373 sheet: -0.39 (0.31), residues: 267 loop : -1.15 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 218 TYR 0.016 0.002 TYR B 302 PHE 0.014 0.001 PHE A 127 TRP 0.014 0.002 TRP A 93 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9220) covalent geometry : angle 0.59162 (12476) SS BOND : bond 0.00884 ( 5) SS BOND : angle 1.52769 ( 10) hydrogen bonds : bond 0.04582 ( 424) hydrogen bonds : angle 4.90887 ( 1215) Misc. bond : bond 0.00309 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6017 (tmm) cc_final: 0.5690 (tpt) REVERT: A 112 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: A 187 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6725 (pt0) REVERT: A 234 MET cc_start: 0.7109 (mmm) cc_final: 0.6857 (tpt) REVERT: A 272 VAL cc_start: 0.6870 (m) cc_final: 0.6645 (p) REVERT: A 285 MET cc_start: 0.7198 (mtt) cc_final: 0.6047 (tpp) REVERT: B 10 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7333 (ttmp) REVERT: B 255 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7035 (p0) REVERT: C 44 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6801 (mp10) REVERT: C 234 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: E 89 GLU cc_start: 0.7577 (pp20) cc_final: 0.7211 (pp20) outliers start: 60 outliers final: 34 residues processed: 179 average time/residue: 0.0945 time to fit residues: 23.9836 Evaluate side-chains 163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.0030 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 119 ASN 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 = 0.203487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165907 restraints weight = 10476.376| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.70 r_work: 0.3451 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9226 Z= 0.129 Angle : 0.562 8.975 12486 Z= 0.294 Chirality : 0.042 0.160 1400 Planarity : 0.004 0.045 1580 Dihedral : 4.368 22.196 1236 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.92 % Allowed : 25.41 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.05 (0.25), residues: 1131 helix: 1.84 (0.28), residues: 373 sheet: -0.39 (0.31), residues: 263 loop : -1.13 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 218 TYR 0.016 0.001 TYR B 302 PHE 0.017 0.001 PHE A 38 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9220) covalent geometry : angle 0.56089 (12476) SS BOND : bond 0.00698 ( 5) SS BOND : angle 1.21515 ( 10) hydrogen bonds : bond 0.04216 ( 424) hydrogen bonds : angle 4.70941 ( 1215) Misc. bond : bond 0.00174 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: A 187 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6733 (pt0) REVERT: A 234 MET cc_start: 0.7050 (mmm) cc_final: 0.6791 (tpt) REVERT: A 272 VAL cc_start: 0.6903 (m) cc_final: 0.6656 (p) REVERT: B 10 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7169 (mtmm) REVERT: B 249 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7188 (tt) REVERT: C 118 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8337 (p0) REVERT: C 234 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: C 316 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8270 (p) REVERT: E 89 GLU cc_start: 0.7348 (pp20) cc_final: 0.6892 (pp20) outliers start: 58 outliers final: 40 residues processed: 179 average time/residue: 0.0958 time to fit residues: 24.0703 Evaluate side-chains 173 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 27 optimal weight: 0.2980 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.204341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.167093 restraints weight = 10360.314| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.61 r_work: 0.3492 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9226 Z= 0.118 Angle : 0.540 8.339 12486 Z= 0.283 Chirality : 0.042 0.155 1400 Planarity : 0.004 0.043 1580 Dihedral : 4.212 21.656 1236 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.12 % Allowed : 24.90 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.10 (0.25), residues: 1131 helix: 1.82 (0.28), residues: 379 sheet: -0.35 (0.30), residues: 263 loop : -1.09 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 32 TYR 0.016 0.001 TYR B 302 PHE 0.009 0.001 PHE A 127 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9220) covalent geometry : angle 0.53926 (12476) SS BOND : bond 0.00631 ( 5) SS BOND : angle 1.16228 ( 10) hydrogen bonds : bond 0.04021 ( 424) hydrogen bonds : angle 4.55208 ( 1215) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: A 165 LYS cc_start: 0.7385 (tptt) cc_final: 0.5858 (mtpt) REVERT: A 201 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4610 (tp) REVERT: A 222 ARG cc_start: 0.7580 (mpp80) cc_final: 0.7162 (mpp80) REVERT: A 272 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6602 (p) REVERT: A 285 MET cc_start: 0.7228 (mtp) cc_final: 0.6825 (mtt) REVERT: B 10 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7195 (mtmm) REVERT: B 195 HIS cc_start: 0.7725 (t-170) cc_final: 0.7339 (t-170) REVERT: B 249 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7217 (tt) REVERT: C 234 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: D 47 GLU cc_start: 0.6800 (mp0) cc_final: 0.6587 (mt-10) REVERT: E 89 GLU cc_start: 0.7337 (pp20) cc_final: 0.6892 (pp20) REVERT: E 234 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7439 (mm-30) outliers start: 60 outliers final: 43 residues processed: 181 average time/residue: 0.0946 time to fit residues: 24.3480 Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.198275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151824 restraints weight = 10385.929| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.37 r_work: 0.3487 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9226 Z= 0.224 Angle : 0.644 8.839 12486 Z= 0.333 Chirality : 0.046 0.224 1400 Planarity : 0.004 0.048 1580 Dihedral : 4.581 23.583 1236 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 7.65 % Allowed : 24.08 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.15 (0.25), residues: 1131 helix: 1.61 (0.27), residues: 380 sheet: -0.57 (0.29), residues: 274 loop : -1.19 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 218 TYR 0.018 0.002 TYR B 302 PHE 0.021 0.002 PHE A 38 TRP 0.019 0.002 TRP A 93 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 9220) covalent geometry : angle 0.64092 (12476) SS BOND : bond 0.00975 ( 5) SS BOND : angle 2.17375 ( 10) hydrogen bonds : bond 0.04579 ( 424) hydrogen bonds : angle 4.78687 ( 1215) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 137 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: A 165 LYS cc_start: 0.7524 (tptt) cc_final: 0.6148 (mtmm) REVERT: A 187 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6647 (pt0) REVERT: A 272 VAL cc_start: 0.7121 (OUTLIER) cc_final: 0.6790 (p) REVERT: A 285 MET cc_start: 0.7167 (mtp) cc_final: 0.6950 (mtp) REVERT: B 10 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7442 (ttmp) REVERT: B 195 HIS cc_start: 0.7851 (t-170) cc_final: 0.7478 (t-170) REVERT: B 255 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.6980 (p0) REVERT: C 44 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: C 234 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: C 336 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7927 (mp) REVERT: E 234 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7543 (mm-30) outliers start: 75 outliers final: 55 residues processed: 194 average time/residue: 0.0828 time to fit residues: 22.7628 Evaluate side-chains 200 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 136 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.202549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164426 restraints weight = 10341.172| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.73 r_work: 0.3457 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9226 Z= 0.143 Angle : 0.576 8.165 12486 Z= 0.300 Chirality : 0.043 0.212 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.393 24.609 1236 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.84 % Allowed : 25.31 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.01 (0.25), residues: 1131 helix: 1.72 (0.27), residues: 380 sheet: -0.43 (0.30), residues: 267 loop : -1.12 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.017 0.001 TYR B 302 PHE 0.011 0.001 PHE A 232 TRP 0.013 0.001 TRP A 93 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9220) covalent geometry : angle 0.57378 (12476) SS BOND : bond 0.00828 ( 5) SS BOND : angle 1.88564 ( 10) hydrogen bonds : bond 0.04165 ( 424) hydrogen bonds : angle 4.63710 ( 1215) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 187 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6477 (pt0) REVERT: A 272 VAL cc_start: 0.6923 (OUTLIER) cc_final: 0.6586 (p) REVERT: A 285 MET cc_start: 0.6967 (mtp) cc_final: 0.6754 (mtp) REVERT: B 10 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7319 (ttmp) REVERT: B 195 HIS cc_start: 0.7756 (t-170) cc_final: 0.7394 (t-170) REVERT: B 249 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7257 (tt) REVERT: B 255 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.6967 (p0) REVERT: C 44 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: C 234 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: E 234 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7457 (mm-30) outliers start: 67 outliers final: 55 residues processed: 181 average time/residue: 0.0703 time to fit residues: 18.6750 Evaluate side-chains 193 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 129 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164930 restraints weight = 10290.205| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.65 r_work: 0.3465 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9226 Z= 0.138 Angle : 0.577 8.603 12486 Z= 0.299 Chirality : 0.043 0.202 1400 Planarity : 0.004 0.042 1580 Dihedral : 4.337 24.659 1236 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.24 % Allowed : 24.90 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.05 (0.25), residues: 1131 helix: 1.76 (0.27), residues: 380 sheet: -0.40 (0.30), residues: 267 loop : -1.09 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.018 0.001 TYR B 302 PHE 0.024 0.001 PHE A 38 TRP 0.014 0.001 TRP A 93 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9220) covalent geometry : angle 0.57525 (12476) SS BOND : bond 0.00778 ( 5) SS BOND : angle 1.68393 ( 10) hydrogen bonds : bond 0.04092 ( 424) hydrogen bonds : angle 4.58117 ( 1215) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 130 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: A 187 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6679 (pt0) REVERT: A 272 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6612 (p) REVERT: A 285 MET cc_start: 0.6855 (mtp) cc_final: 0.6635 (mtp) REVERT: B 10 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7340 (ttmp) REVERT: B 195 HIS cc_start: 0.7760 (t-170) cc_final: 0.7395 (t-170) REVERT: B 249 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7271 (tt) REVERT: C 44 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: C 234 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: E 18 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7080 (ttm170) REVERT: E 234 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7432 (mm-30) outliers start: 71 outliers final: 58 residues processed: 185 average time/residue: 0.0793 time to fit residues: 21.3148 Evaluate side-chains 195 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 128 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.198340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153168 restraints weight = 10314.140| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.21 r_work: 0.3402 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9226 Z= 0.273 Angle : 0.714 9.312 12486 Z= 0.366 Chirality : 0.049 0.231 1400 Planarity : 0.005 0.055 1580 Dihedral : 4.811 24.138 1236 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.45 % Allowed : 24.69 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1131 helix: 1.50 (0.27), residues: 380 sheet: -0.71 (0.29), residues: 275 loop : -1.26 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 32 TYR 0.025 0.003 TYR B 302 PHE 0.019 0.002 PHE E 212 TRP 0.025 0.002 TRP A 93 HIS 0.006 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 9220) covalent geometry : angle 0.71113 (12476) SS BOND : bond 0.01203 ( 5) SS BOND : angle 2.46445 ( 10) hydrogen bonds : bond 0.04938 ( 424) hydrogen bonds : angle 4.90747 ( 1215) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: A 272 VAL cc_start: 0.7085 (OUTLIER) cc_final: 0.6707 (p) REVERT: B 10 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7404 (ttmp) REVERT: B 255 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.6983 (p0) REVERT: C 44 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6653 (mp10) REVERT: C 234 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: C 336 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7898 (mp) REVERT: D 47 GLU cc_start: 0.7021 (mp0) cc_final: 0.6711 (mt-10) REVERT: E 18 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7295 (tpp80) REVERT: E 234 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7538 (mm-30) outliers start: 73 outliers final: 59 residues processed: 179 average time/residue: 0.0834 time to fit residues: 21.5332 Evaluate side-chains 192 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 23 optimal weight: 0.0670 chunk 106 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157535 restraints weight = 10298.069| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.26 r_work: 0.3476 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9226 Z= 0.131 Angle : 0.585 9.509 12486 Z= 0.301 Chirality : 0.043 0.232 1400 Planarity : 0.004 0.060 1580 Dihedral : 4.405 26.993 1236 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 6.02 % Allowed : 26.33 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.02 (0.25), residues: 1131 helix: 1.71 (0.27), residues: 380 sheet: -0.46 (0.30), residues: 263 loop : -1.11 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 32 TYR 0.021 0.001 TYR B 302 PHE 0.019 0.001 PHE B 334 TRP 0.013 0.002 TRP C 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9220) covalent geometry : angle 0.58350 (12476) SS BOND : bond 0.00708 ( 5) SS BOND : angle 1.60437 ( 10) hydrogen bonds : bond 0.04127 ( 424) hydrogen bonds : angle 4.64707 ( 1215) Misc. bond : bond 0.00053 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 136 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: A 222 ARG cc_start: 0.7549 (mpp80) cc_final: 0.7114 (mpp80) REVERT: A 272 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6461 (p) REVERT: B 32 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7488 (ptp-110) REVERT: B 195 HIS cc_start: 0.7756 (t-170) cc_final: 0.7398 (t-170) REVERT: B 209 LYS cc_start: 0.8339 (pttm) cc_final: 0.7957 (ptpt) REVERT: C 44 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: C 234 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: C 251 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.8003 (mtt-85) REVERT: C 336 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7865 (mp) REVERT: D 47 GLU cc_start: 0.6886 (mp0) cc_final: 0.6559 (mt-10) REVERT: E 234 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7416 (mm-30) outliers start: 59 outliers final: 49 residues processed: 180 average time/residue: 0.0723 time to fit residues: 18.9173 Evaluate side-chains 186 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.0570 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.201061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.155776 restraints weight = 10214.894| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.16 r_work: 0.3503 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9226 Z= 0.172 Angle : 0.625 10.172 12486 Z= 0.320 Chirality : 0.045 0.239 1400 Planarity : 0.004 0.060 1580 Dihedral : 4.523 25.121 1236 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 6.43 % Allowed : 25.61 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: -0.08 (0.25), residues: 1131 helix: 1.65 (0.27), residues: 380 sheet: -0.47 (0.30), residues: 267 loop : -1.16 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 32 TYR 0.025 0.002 TYR B 302 PHE 0.029 0.002 PHE A 38 TRP 0.021 0.002 TRP A 93 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9220) covalent geometry : angle 0.62297 (12476) SS BOND : bond 0.00966 ( 5) SS BOND : angle 1.96492 ( 10) hydrogen bonds : bond 0.04392 ( 424) hydrogen bonds : angle 4.70655 ( 1215) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2485.90 seconds wall clock time: 43 minutes 17.57 seconds (2597.57 seconds total)