Starting phenix.real_space_refine on Thu Sep 18 15:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhl_44549/09_2025/9bhl_44549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhl_44549/09_2025/9bhl_44549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bhl_44549/09_2025/9bhl_44549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhl_44549/09_2025/9bhl_44549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bhl_44549/09_2025/9bhl_44549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhl_44549/09_2025/9bhl_44549.map" } resolution = 2.8 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= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3251 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4905 2.51 5 N 1327 2.21 5 O 1432 1.98 5 H 7571 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15287 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3954 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 4461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4461 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 295} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1900 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4972 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 291} Time building chain proxies: 3.13, per 1000 atoms: 0.20 Number of scatterers: 15287 At special positions: 0 Unit cell: (82.665, 101.035, 136.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1432 8.00 N 1327 7.00 C 4905 6.00 H 7571 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 5 " - pdb=" SG CYS R 160 " distance=2.03 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 469.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 13 sheets defined 41.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 removed outlier: 3.637A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.591A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 279 removed outlier: 3.931A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 4.076A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.926A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.033A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.820A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.549A pdb=" N ALA N 56 " --> pdb=" O GLN N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 6 through 45 removed outlier: 4.139A pdb=" N HIS R 10 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP R 11 " --> pdb=" O GLU R 7 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR R 15 " --> pdb=" O ASP R 11 " (cutoff:3.500A) Proline residue: R 18 - end of helix removed outlier: 3.822A pdb=" N PHE R 23 " --> pdb=" O ILE R 19 " (cutoff:3.500A) Proline residue: R 30 - end of helix removed outlier: 3.602A pdb=" N LYS R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 75 removed outlier: 3.904A pdb=" N TYR R 52 " --> pdb=" O GLU R 48 " (cutoff:3.500A) Proline residue: R 68 - end of helix Processing helix chain 'R' and resid 83 through 118 removed outlier: 3.729A pdb=" N CYS R 87 " --> pdb=" O SER R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 147 Processing helix chain 'R' and resid 147 through 152 removed outlier: 3.716A pdb=" N TRP R 151 " --> pdb=" O ALA R 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 147 through 152' Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.540A pdb=" N PHE R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 213 Processing helix chain 'R' and resid 217 through 256 Proline residue: R 241 - end of helix removed outlier: 3.847A pdb=" N HIS R 254 " --> pdb=" O CYS R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 280 removed outlier: 4.010A pdb=" N TYR R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR R 270 " --> pdb=" O LYS R 266 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 292 removed outlier: 4.248A pdb=" N VAL R 284 " --> pdb=" O SER R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 296 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.211A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.550A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.781A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.447A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.703A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.741A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.227A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 317 removed outlier: 3.861A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 328 removed outlier: 4.226A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.824A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.598A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 59 removed outlier: 3.760A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 155 through 160 360 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7546 1.03 - 1.23: 129 1.23 - 1.43: 3299 1.43 - 1.62: 4412 1.62 - 1.82: 71 Bond restraints: 15457 Sorted by residual: bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N THR A 9 " pdb=" H THR A 9 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" CA SER B 191 " pdb=" C SER B 191 " ideal model delta sigma weight residual 1.533 1.521 0.012 9.60e-03 1.09e+04 1.49e+00 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.467 -0.007 7.50e-03 1.78e+04 9.47e-01 bond pdb=" C TRP B 63 " pdb=" N GLY B 64 " ideal model delta sigma weight residual 1.336 1.326 0.010 1.01e-02 9.80e+03 9.36e-01 ... (remaining 15452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 26402 1.20 - 2.40: 1262 2.40 - 3.60: 90 3.60 - 4.80: 17 4.80 - 6.00: 3 Bond angle restraints: 27774 Sorted by residual: angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 113.53 109.90 3.63 9.80e-01 1.04e+00 1.37e+01 angle pdb=" C ALA B 92 " pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 122.59 120.63 1.96 7.20e-01 1.93e+00 7.40e+00 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 110.62 113.28 -2.66 1.02e+00 9.61e-01 6.81e+00 angle pdb=" C CYS R 238 " pdb=" N PHE R 239 " pdb=" CA PHE R 239 " ideal model delta sigma weight residual 122.53 118.06 4.47 1.92e+00 2.71e-01 5.41e+00 angle pdb=" CA TYR N 117 " pdb=" C TYR N 117 " pdb=" N ARG N 118 " ideal model delta sigma weight residual 114.60 117.55 -2.95 1.30e+00 5.92e-01 5.13e+00 ... (remaining 27769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 6510 17.11 - 34.21: 566 34.21 - 51.32: 163 51.32 - 68.43: 43 68.43 - 85.53: 21 Dihedral angle restraints: 7303 sinusoidal: 3877 harmonic: 3426 Sorted by residual: dihedral pdb=" CA SER B 227 " pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta harmonic sigma weight residual -180.00 -148.24 -31.76 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA ASP B 228 " pdb=" C ASP B 228 " pdb=" N ILE B 229 " pdb=" CA ILE B 229 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 129.99 -36.99 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 7300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 833 0.035 - 0.070: 251 0.070 - 0.106: 79 0.106 - 0.141: 30 0.141 - 0.176: 1 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CB ILE B 229 " pdb=" CA ILE B 229 " pdb=" CG1 ILE B 229 " pdb=" CG2 ILE B 229 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1191 not shown) Planarity restraints: 2297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 264 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C SER R 264 " 0.028 2.00e-02 2.50e+03 pdb=" O SER R 264 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY R 265 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 98 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C PHE R 98 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE R 98 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR R 99 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 288 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C ILE R 288 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE R 288 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU R 289 " -0.008 2.00e-02 2.50e+03 ... (remaining 2294 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 595 2.15 - 2.76: 29334 2.76 - 3.37: 43379 3.37 - 3.99: 54157 3.99 - 4.60: 85550 Nonbonded interactions: 213015 Sorted by model distance: nonbonded pdb=" OE1 GLU R 48 " pdb=" H GLU R 48 " model vdw 1.537 2.450 nonbonded pdb=" OD1 ASN B 295 " pdb="HH11 ARG B 304 " model vdw 1.552 2.450 nonbonded pdb=" OD1 ASN R 213 " pdb=" HG1 THR R 216 " model vdw 1.582 2.450 nonbonded pdb=" O GLN B 75 " pdb=" HG SER B 98 " model vdw 1.594 2.450 nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.614 2.450 ... (remaining 213010 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.430 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3924 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 : 0.003 0.032 7890 Z= 0.163 Angle : 0.609 5.996 10696 Z= 0.362 Chirality : 0.040 0.176 1194 Planarity : 0.003 0.034 1357 Dihedral : 14.813 85.534 2833 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.12 % Allowed : 12.49 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.22 (0.27), residues: 959 helix: 1.40 (0.28), residues: 332 sheet: -1.19 (0.34), residues: 208 loop : -0.77 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 298 TYR 0.016 0.002 TYR N 60 PHE 0.015 0.001 PHE B 241 TRP 0.012 0.002 TRP B 99 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7886) covalent geometry : angle 0.60922 (10688) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.76634 ( 8) hydrogen bonds : bond 0.20226 ( 360) hydrogen bonds : angle 7.35431 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.5145 (mt0) cc_final: 0.4730 (tp-100) REVERT: A 352 SER cc_start: 0.6831 (t) cc_final: 0.6483 (p) REVERT: A 356 ARG cc_start: 0.6887 (mtp85) cc_final: 0.5816 (ptt90) REVERT: A 360 TYR cc_start: 0.6480 (m-80) cc_final: 0.5848 (m-80) REVERT: B 45 MET cc_start: 0.3258 (mtp) cc_final: 0.3011 (ptp) REVERT: B 277 SER cc_start: 0.4318 (t) cc_final: 0.4089 (p) REVERT: N 83 MET cc_start: 0.1901 (mpp) cc_final: 0.1689 (mtt) REVERT: R 121 LYS cc_start: 0.6116 (mttt) cc_final: 0.5654 (mptt) REVERT: R 123 PHE cc_start: 0.4802 (t80) cc_final: 0.3855 (m-80) REVERT: R 133 MET cc_start: 0.5557 (mtp) cc_final: 0.5307 (mtp) REVERT: R 149 MET cc_start: 0.5792 (ptm) cc_final: 0.5102 (ptp) REVERT: R 204 ARG cc_start: 0.5483 (tpt170) cc_final: 0.4754 (mtt90) REVERT: R 271 MET cc_start: 0.2498 (mtm) cc_final: 0.2133 (mtp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 1.0796 time to fit residues: 167.6833 Evaluate side-chains 95 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 88 ASN N 74 ASN R 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.266094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.238752 restraints weight = 26424.799| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 1.86 r_work: 0.4537 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4445 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7890 Z= 0.147 Angle : 0.594 5.778 10696 Z= 0.328 Chirality : 0.041 0.153 1194 Planarity : 0.004 0.039 1357 Dihedral : 5.646 33.443 1064 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 15.22 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.41 (0.27), residues: 959 helix: 1.31 (0.27), residues: 341 sheet: -1.46 (0.33), residues: 209 loop : -0.90 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.018 0.002 TYR N 60 PHE 0.015 0.001 PHE A 212 TRP 0.009 0.002 TRP B 99 HIS 0.015 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7886) covalent geometry : angle 0.59367 (10688) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.18085 ( 8) hydrogen bonds : bond 0.05760 ( 360) hydrogen bonds : angle 5.78079 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6419 (mt0) cc_final: 0.6100 (tp-100) REVERT: A 356 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6832 (ptt90) REVERT: A 360 TYR cc_start: 0.6872 (m-80) cc_final: 0.6281 (m-80) REVERT: R 123 PHE cc_start: 0.5491 (t80) cc_final: 0.5071 (m-80) REVERT: R 133 MET cc_start: 0.6259 (mtp) cc_final: 0.5999 (mtp) REVERT: R 149 MET cc_start: 0.5941 (ptm) cc_final: 0.5427 (ptp) REVERT: R 172 ASP cc_start: 0.6990 (p0) cc_final: 0.6728 (t0) REVERT: R 204 ARG cc_start: 0.5749 (tpt170) cc_final: 0.5384 (mtt90) REVERT: R 271 MET cc_start: 0.3499 (mtm) cc_final: 0.3129 (mtp) outliers start: 25 outliers final: 13 residues processed: 118 average time/residue: 1.1127 time to fit residues: 140.6382 Evaluate side-chains 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 97 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 10.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 176 GLN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.258891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.229522 restraints weight = 26335.554| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 1.87 r_work: 0.4467 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4375 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7890 Z= 0.182 Angle : 0.638 8.059 10696 Z= 0.350 Chirality : 0.042 0.157 1194 Planarity : 0.005 0.034 1357 Dihedral : 5.973 35.917 1064 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.04 % Allowed : 14.86 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.73 (0.26), residues: 959 helix: 1.05 (0.27), residues: 344 sheet: -1.56 (0.34), residues: 202 loop : -1.16 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 304 TYR 0.016 0.002 TYR R 171 PHE 0.018 0.002 PHE A 273 TRP 0.014 0.002 TRP B 99 HIS 0.014 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7886) covalent geometry : angle 0.63762 (10688) SS BOND : bond 0.00362 ( 4) SS BOND : angle 1.17590 ( 8) hydrogen bonds : bond 0.05817 ( 360) hydrogen bonds : angle 5.58697 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6284 (tm-30) cc_final: 0.5892 (mp10) REVERT: A 31 GLN cc_start: 0.6521 (mt0) cc_final: 0.6111 (tp-100) REVERT: A 60 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.1333 (ppp) REVERT: A 356 ARG cc_start: 0.7235 (mtp85) cc_final: 0.6994 (ptt90) REVERT: B 75 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: B 96 ARG cc_start: 0.6892 (ttm-80) cc_final: 0.6413 (mtm-85) REVERT: B 142 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8100 (m-70) REVERT: N 83 MET cc_start: 0.4335 (mpp) cc_final: 0.4000 (mtt) REVERT: R 65 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6225 (tm) REVERT: R 72 ASP cc_start: 0.6818 (t0) cc_final: 0.6571 (t70) REVERT: R 123 PHE cc_start: 0.5750 (t80) cc_final: 0.5210 (m-80) REVERT: R 133 MET cc_start: 0.6121 (mtp) cc_final: 0.5841 (mtp) REVERT: R 149 MET cc_start: 0.5993 (ptm) cc_final: 0.5563 (ptp) REVERT: R 154 GLU cc_start: 0.5632 (pp20) cc_final: 0.5403 (pp20) REVERT: R 172 ASP cc_start: 0.7057 (p0) cc_final: 0.6786 (t0) REVERT: R 204 ARG cc_start: 0.5731 (tpt170) cc_final: 0.5276 (mtt90) REVERT: R 271 MET cc_start: 0.3509 (mtm) cc_final: 0.3160 (mtp) outliers start: 34 outliers final: 21 residues processed: 128 average time/residue: 1.0643 time to fit residues: 145.6325 Evaluate side-chains 122 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.261788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.235986 restraints weight = 26138.020| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 1.76 r_work: 0.4493 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4399 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7890 Z= 0.129 Angle : 0.565 7.357 10696 Z= 0.309 Chirality : 0.041 0.146 1194 Planarity : 0.004 0.032 1357 Dihedral : 5.593 33.076 1064 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.69 % Allowed : 16.53 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.54 (0.27), residues: 959 helix: 1.19 (0.27), residues: 347 sheet: -1.45 (0.35), residues: 197 loop : -1.07 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.015 0.001 TYR R 171 PHE 0.016 0.001 PHE A 273 TRP 0.011 0.001 TRP N 47 HIS 0.011 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7886) covalent geometry : angle 0.56408 (10688) SS BOND : bond 0.01194 ( 4) SS BOND : angle 1.53672 ( 8) hydrogen bonds : bond 0.04936 ( 360) hydrogen bonds : angle 5.30374 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6096 (tm-30) cc_final: 0.5866 (mp10) REVERT: A 31 GLN cc_start: 0.6540 (mt0) cc_final: 0.6121 (tp-100) REVERT: A 209 GLU cc_start: 0.6224 (mt-10) cc_final: 0.6009 (mt-10) REVERT: B 142 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: B 171 ILE cc_start: 0.5930 (mm) cc_final: 0.5701 (mm) REVERT: N 83 MET cc_start: 0.4371 (mpp) cc_final: 0.4101 (mtt) REVERT: R 65 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5270 (mm) REVERT: R 72 ASP cc_start: 0.6797 (t0) cc_final: 0.6533 (t70) REVERT: R 123 PHE cc_start: 0.5656 (t80) cc_final: 0.5219 (m-80) REVERT: R 128 ARG cc_start: 0.6457 (ttm110) cc_final: 0.6155 (mtm110) REVERT: R 133 MET cc_start: 0.6182 (mtp) cc_final: 0.5906 (mtp) REVERT: R 149 MET cc_start: 0.5916 (ptm) cc_final: 0.5564 (ptp) REVERT: R 204 ARG cc_start: 0.5701 (tpt170) cc_final: 0.5278 (mtt90) REVERT: R 271 MET cc_start: 0.3473 (mtm) cc_final: 0.3008 (mmt) outliers start: 31 outliers final: 17 residues processed: 122 average time/residue: 1.0436 time to fit residues: 136.5085 Evaluate side-chains 112 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 97 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.254198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.227158 restraints weight = 26063.792| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 1.81 r_work: 0.4427 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4331 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 7890 Z= 0.207 Angle : 0.682 10.011 10696 Z= 0.370 Chirality : 0.044 0.167 1194 Planarity : 0.005 0.052 1357 Dihedral : 6.168 36.603 1064 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.40 % Allowed : 16.53 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.03 (0.26), residues: 959 helix: 0.80 (0.26), residues: 339 sheet: -1.64 (0.35), residues: 200 loop : -1.36 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.016 0.002 TYR A 391 PHE 0.018 0.002 PHE A 273 TRP 0.018 0.002 TRP B 99 HIS 0.006 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7886) covalent geometry : angle 0.68098 (10688) SS BOND : bond 0.00528 ( 4) SS BOND : angle 1.49243 ( 8) hydrogen bonds : bond 0.05997 ( 360) hydrogen bonds : angle 5.54060 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6225 (tm-30) cc_final: 0.5849 (mm110) REVERT: A 31 GLN cc_start: 0.6613 (mt0) cc_final: 0.6176 (tp-100) REVERT: A 356 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6976 (ptt90) REVERT: B 96 ARG cc_start: 0.6854 (ttm-80) cc_final: 0.6160 (mtm-85) REVERT: B 142 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8077 (m-70) REVERT: B 229 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6668 (mm) REVERT: B 243 THR cc_start: 0.4035 (OUTLIER) cc_final: 0.3729 (m) REVERT: N 83 MET cc_start: 0.4565 (mpp) cc_final: 0.4196 (mtt) REVERT: R 65 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6203 (tm) REVERT: R 72 ASP cc_start: 0.6769 (t0) cc_final: 0.6522 (t70) REVERT: R 123 PHE cc_start: 0.5614 (t80) cc_final: 0.5141 (m-80) REVERT: R 124 PHE cc_start: 0.5276 (t80) cc_final: 0.4386 (p90) REVERT: R 128 ARG cc_start: 0.6659 (ttm110) cc_final: 0.6340 (mtm110) REVERT: R 133 MET cc_start: 0.6193 (mtp) cc_final: 0.5843 (mtp) REVERT: R 149 MET cc_start: 0.5950 (ptm) cc_final: 0.5657 (ptp) REVERT: R 271 MET cc_start: 0.3339 (mtm) cc_final: 0.2933 (mmt) outliers start: 37 outliers final: 22 residues processed: 122 average time/residue: 0.9849 time to fit residues: 128.8196 Evaluate side-chains 109 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 27 PHE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 137 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 43 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.264458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.237347 restraints weight = 26220.438| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 1.87 r_work: 0.4526 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4431 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7890 Z= 0.129 Angle : 0.576 8.063 10696 Z= 0.312 Chirality : 0.040 0.145 1194 Planarity : 0.004 0.036 1357 Dihedral : 5.680 33.121 1064 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.80 % Allowed : 17.36 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.82 (0.26), residues: 959 helix: 1.08 (0.27), residues: 339 sheet: -1.62 (0.33), residues: 215 loop : -1.26 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.011 0.001 TYR R 171 PHE 0.018 0.001 PHE A 273 TRP 0.013 0.002 TRP B 99 HIS 0.002 0.001 HIS R 14 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7886) covalent geometry : angle 0.57509 (10688) SS BOND : bond 0.00276 ( 4) SS BOND : angle 1.16959 ( 8) hydrogen bonds : bond 0.04968 ( 360) hydrogen bonds : angle 5.26943 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6131 (tm-30) cc_final: 0.5903 (mp10) REVERT: A 31 GLN cc_start: 0.6557 (mt0) cc_final: 0.6272 (tp-100) REVERT: A 60 MET cc_start: 0.3035 (OUTLIER) cc_final: 0.1330 (ppp) REVERT: A 356 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6744 (ptt90) REVERT: B 142 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.7997 (m-70) REVERT: N 83 MET cc_start: 0.4519 (mpp) cc_final: 0.4148 (mtt) REVERT: R 65 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5390 (mm) REVERT: R 72 ASP cc_start: 0.6703 (t0) cc_final: 0.6463 (t70) REVERT: R 123 PHE cc_start: 0.5638 (t80) cc_final: 0.5344 (m-80) REVERT: R 124 PHE cc_start: 0.5225 (t80) cc_final: 0.4469 (p90) REVERT: R 128 ARG cc_start: 0.6585 (ttm110) cc_final: 0.6347 (mtt90) REVERT: R 133 MET cc_start: 0.6117 (mtp) cc_final: 0.5782 (mtp) REVERT: R 149 MET cc_start: 0.5795 (ptm) cc_final: 0.5525 (ptp) REVERT: R 271 MET cc_start: 0.3443 (mtm) cc_final: 0.3017 (mmt) outliers start: 32 outliers final: 17 residues processed: 110 average time/residue: 0.8673 time to fit residues: 102.6538 Evaluate side-chains 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 97 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.265922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.239436 restraints weight = 25951.120| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 1.78 r_work: 0.4537 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4446 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7890 Z= 0.120 Angle : 0.552 7.329 10696 Z= 0.296 Chirality : 0.040 0.139 1194 Planarity : 0.003 0.033 1357 Dihedral : 5.409 31.943 1064 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.92 % Allowed : 17.48 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.61 (0.27), residues: 959 helix: 1.28 (0.27), residues: 344 sheet: -1.59 (0.33), residues: 215 loop : -1.14 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.010 0.001 TYR N 60 PHE 0.019 0.001 PHE A 273 TRP 0.012 0.001 TRP N 47 HIS 0.002 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7886) covalent geometry : angle 0.55126 (10688) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.21947 ( 8) hydrogen bonds : bond 0.04609 ( 360) hydrogen bonds : angle 5.07671 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6510 (mt0) cc_final: 0.6252 (tp-100) REVERT: B 142 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7889 (m-70) REVERT: B 214 ARG cc_start: 0.7073 (mmt180) cc_final: 0.6824 (mpt90) REVERT: N 83 MET cc_start: 0.4361 (mpp) cc_final: 0.4123 (mtt) REVERT: R 65 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.6047 (tm) REVERT: R 72 ASP cc_start: 0.6808 (t0) cc_final: 0.6516 (t70) REVERT: R 123 PHE cc_start: 0.5586 (t80) cc_final: 0.5348 (m-80) REVERT: R 124 PHE cc_start: 0.5217 (t80) cc_final: 0.4485 (p90) REVERT: R 133 MET cc_start: 0.6147 (mtp) cc_final: 0.5773 (mtp) REVERT: R 138 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5825 (tt) REVERT: R 149 MET cc_start: 0.5775 (ptm) cc_final: 0.5511 (ptp) REVERT: R 271 MET cc_start: 0.3362 (mtm) cc_final: 0.2997 (mmt) outliers start: 33 outliers final: 17 residues processed: 116 average time/residue: 0.8084 time to fit residues: 101.9574 Evaluate side-chains 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 231 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.262665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.235709 restraints weight = 26045.841| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 1.76 r_work: 0.4508 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4419 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7890 Z= 0.154 Angle : 0.604 10.663 10696 Z= 0.324 Chirality : 0.041 0.145 1194 Planarity : 0.004 0.075 1357 Dihedral : 5.690 34.472 1064 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.26 % Rotamer: Outliers : 2.85 % Allowed : 18.91 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.78 (0.27), residues: 959 helix: 1.14 (0.27), residues: 339 sheet: -1.63 (0.34), residues: 210 loop : -1.25 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 128 TYR 0.012 0.001 TYR A 391 PHE 0.020 0.002 PHE A 273 TRP 0.013 0.002 TRP B 99 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7886) covalent geometry : angle 0.60376 (10688) SS BOND : bond 0.00329 ( 4) SS BOND : angle 1.22031 ( 8) hydrogen bonds : bond 0.05084 ( 360) hydrogen bonds : angle 5.19685 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6558 (mt0) cc_final: 0.6223 (tp-100) REVERT: A 356 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6651 (ptt90) REVERT: B 142 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.7943 (m-70) REVERT: B 214 ARG cc_start: 0.7101 (mmt180) cc_final: 0.6758 (mpt90) REVERT: N 83 MET cc_start: 0.4335 (mpp) cc_final: 0.4030 (mtt) REVERT: R 65 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5369 (mm) REVERT: R 72 ASP cc_start: 0.6762 (t0) cc_final: 0.6483 (t70) REVERT: R 123 PHE cc_start: 0.5543 (t80) cc_final: 0.5279 (m-80) REVERT: R 124 PHE cc_start: 0.5362 (t80) cc_final: 0.4568 (p90) REVERT: R 138 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5862 (tt) REVERT: R 149 MET cc_start: 0.5765 (ptm) cc_final: 0.5528 (ptp) REVERT: R 271 MET cc_start: 0.3312 (mtm) cc_final: 0.2979 (mmm) REVERT: R 301 MET cc_start: 0.5810 (tmt) cc_final: 0.4169 (tpt) outliers start: 24 outliers final: 15 residues processed: 105 average time/residue: 0.9858 time to fit residues: 111.5111 Evaluate side-chains 99 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 231 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.264089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.237559 restraints weight = 26017.453| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 1.77 r_work: 0.4524 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7890 Z= 0.128 Angle : 0.562 9.120 10696 Z= 0.301 Chirality : 0.040 0.140 1194 Planarity : 0.003 0.034 1357 Dihedral : 5.500 35.303 1064 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 2.73 % Allowed : 19.14 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.66 (0.27), residues: 959 helix: 1.23 (0.27), residues: 341 sheet: -1.61 (0.33), residues: 215 loop : -1.14 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.009 0.001 TYR N 60 PHE 0.022 0.001 PHE A 273 TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7886) covalent geometry : angle 0.56122 (10688) SS BOND : bond 0.00336 ( 4) SS BOND : angle 1.10973 ( 8) hydrogen bonds : bond 0.04697 ( 360) hydrogen bonds : angle 5.09424 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6574 (mt0) cc_final: 0.6252 (tp-100) REVERT: A 60 MET cc_start: 0.3032 (OUTLIER) cc_final: 0.1302 (ppp) REVERT: B 142 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.7881 (m-70) REVERT: B 214 ARG cc_start: 0.7098 (mmt180) cc_final: 0.6759 (mpt90) REVERT: N 83 MET cc_start: 0.4372 (mpp) cc_final: 0.4100 (mtt) REVERT: R 65 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5321 (mm) REVERT: R 72 ASP cc_start: 0.6753 (t0) cc_final: 0.6472 (t70) REVERT: R 124 PHE cc_start: 0.5336 (t80) cc_final: 0.4546 (p90) REVERT: R 138 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5823 (tt) REVERT: R 149 MET cc_start: 0.5675 (ptm) cc_final: 0.5444 (ptp) REVERT: R 271 MET cc_start: 0.3362 (mtm) cc_final: 0.2972 (mmm) REVERT: R 301 MET cc_start: 0.5869 (tmt) cc_final: 0.4299 (tpt) outliers start: 23 outliers final: 15 residues processed: 101 average time/residue: 0.9692 time to fit residues: 105.8816 Evaluate side-chains 97 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 231 ILE Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.263263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.238680 restraints weight = 26198.858| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 1.64 r_work: 0.4542 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4455 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7890 Z= 0.115 Angle : 0.541 9.156 10696 Z= 0.289 Chirality : 0.040 0.139 1194 Planarity : 0.003 0.032 1357 Dihedral : 5.294 34.296 1064 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 2.14 % Allowed : 19.62 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.53 (0.27), residues: 959 helix: 1.26 (0.27), residues: 347 sheet: -1.55 (0.33), residues: 215 loop : -1.01 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.016 0.001 TYR R 174 PHE 0.015 0.001 PHE A 340 TRP 0.013 0.001 TRP A 281 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7886) covalent geometry : angle 0.54072 (10688) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.02413 ( 8) hydrogen bonds : bond 0.04393 ( 360) hydrogen bonds : angle 4.97841 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.2927 (OUTLIER) cc_final: 0.1244 (ppp) REVERT: B 46 ARG cc_start: 0.6031 (mtp-110) cc_final: 0.5746 (ptt90) REVERT: B 142 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.7809 (m-70) REVERT: B 214 ARG cc_start: 0.7052 (mmt180) cc_final: 0.6708 (mpt90) REVERT: R 72 ASP cc_start: 0.6760 (t0) cc_final: 0.6504 (t70) REVERT: R 124 PHE cc_start: 0.5372 (t80) cc_final: 0.4622 (p90) REVERT: R 133 MET cc_start: 0.6123 (mtp) cc_final: 0.5836 (mtp) REVERT: R 138 ILE cc_start: 0.5969 (OUTLIER) cc_final: 0.5755 (tt) REVERT: R 149 MET cc_start: 0.5693 (ptm) cc_final: 0.5474 (ptp) REVERT: R 204 ARG cc_start: 0.6226 (tpt90) cc_final: 0.5187 (mtt90) REVERT: R 271 MET cc_start: 0.3387 (mtm) cc_final: 0.3001 (mmm) REVERT: R 301 MET cc_start: 0.5870 (tmt) cc_final: 0.4307 (tpt) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 1.0119 time to fit residues: 110.8103 Evaluate side-chains 98 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 58 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.266312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.240416 restraints weight = 25866.904| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 1.76 r_work: 0.4545 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4457 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7890 Z= 0.110 Angle : 0.532 8.941 10696 Z= 0.285 Chirality : 0.040 0.137 1194 Planarity : 0.003 0.032 1357 Dihedral : 5.203 34.749 1064 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 1.90 % Allowed : 20.21 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.49 (0.27), residues: 959 helix: 1.33 (0.27), residues: 347 sheet: -1.55 (0.33), residues: 215 loop : -1.03 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.009 0.001 TYR N 60 PHE 0.015 0.001 PHE A 340 TRP 0.012 0.001 TRP A 281 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7886) covalent geometry : angle 0.53180 (10688) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.01252 ( 8) hydrogen bonds : bond 0.04268 ( 360) hydrogen bonds : angle 4.91234 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5691.45 seconds wall clock time: 97 minutes 2.55 seconds (5822.55 seconds total)