Starting phenix.real_space_refine on Mon Jun 16 00:12:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhl_44549/06_2025/9bhl_44549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhl_44549/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhl_44549/06_2025/9bhl_44549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhl_44549/06_2025/9bhl_44549.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhl_44549/06_2025/9bhl_44549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhl_44549/06_2025/9bhl_44549.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.114 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 2, 'ARG: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: 8.21, per 1000 atoms: 0.54 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: 4.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.38 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: 5.63 Time building geometry restraints manager: 5.12 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.290 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.750 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (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 TRP 0.012 0.002 TRP B 99 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 241 TYR 0.016 0.002 TYR N 60 ARG 0.004 0.001 ARG R 298 Details of bonding type rmsd hydrogen bonds : bond 0.20226 ( 360) hydrogen bonds : angle 7.35431 ( 1035) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.76634 ( 8) covalent geometry : bond 0.00315 ( 7886) covalent geometry : angle 0.60922 (10688) *********************** 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 : 1.105 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: 0.5145 (mt0) cc_final: 0.4730 (tp-100) REVERT: A 352 SER cc_start: 0.6831 (t) cc_final: 0.6482 (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: 0.5849 (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: 0.1687 (mtt) 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: 1.9589 time to fit residues: 305.9501 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 : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 = 0.4815 r_free = 0.4815 target = 0.265133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.237512 restraints weight = 26297.381| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 1.85 r_work: 0.4529 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4434 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7890 Z= 0.152 Angle : 0.604 6.079 10696 Z= 0.333 Chirality : 0.042 0.154 1194 Planarity : 0.004 0.041 1357 Dihedral : 5.720 34.236 1064 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.21 % Allowed : 14.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 959 helix: 1.27 (0.27), residues: 341 sheet: -1.41 (0.34), residues: 204 loop : -0.96 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 99 HIS 0.017 0.001 HIS R 212 PHE 0.016 0.001 PHE A 212 TYR 0.019 0.002 TYR N 60 ARG 0.006 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05680 ( 360) hydrogen bonds : angle 5.78316 ( 1035) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.21691 ( 8) covalent geometry : bond 0.00326 ( 7886) covalent geometry : angle 0.60339 (10688) *********************** 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 130 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 1.197 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: 0.6436 (mt0) cc_final: 0.6088 (tp-100) REVERT: A 60 MET cc_start: 0.2806 (OUTLIER) cc_final: 0.1192 (ppp) REVERT: A 271 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5404 (m110) REVERT: A 356 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6828 (ptt90) REVERT: A 360 TYR cc_start: 0.6907 (m-80) cc_final: 0.6352 (m-80) REVERT: B 142 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.7831 (m-70) REVERT: R 123 PHE cc_start: 0.5526 (t80) cc_final: 0.5067 (m-80) REVERT: R 133 MET cc_start: 0.6220 (mtp) cc_final: 0.5959 (mtp) REVERT: R 149 MET cc_start: 0.5915 (ptm) cc_final: 0.5405 (ptp) REVERT: R 172 ASP cc_start: 0.7036 (p0) cc_final: 0.6761 (t0) REVERT: R 204 ARG cc_start: 0.5764 (tpt170) cc_final: 0.5375 (mtt90) REVERT: R 271 MET cc_start: 0.3478 (mtm) cc_final: 0.3105 (mtp) outliers start: 27 outliers final: 14 residues processed: 123 average time/residue: 2.0216 time to fit residues: 268.4206 Evaluate side-chains 114 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN 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 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 21 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.263331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.235099 restraints weight = 26370.125| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 1.85 r_work: 0.4511 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4413 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.2673 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= 0.140 Angle : 0.569 6.977 10696 Z= 0.313 Chirality : 0.041 0.155 1194 Planarity : 0.004 0.045 1357 Dihedral : 5.595 33.639 1064 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.80 % Allowed : 15.46 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 959 helix: 1.25 (0.27), residues: 341 sheet: -1.48 (0.34), residues: 202 loop : -1.04 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 47 HIS 0.014 0.001 HIS R 212 PHE 0.014 0.001 PHE A 212 TYR 0.016 0.002 TYR R 171 ARG 0.005 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 360) hydrogen bonds : angle 5.43006 ( 1035) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.09888 ( 8) covalent geometry : bond 0.00305 ( 7886) covalent geometry : angle 0.56866 (10688) *********************** 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 136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6226 (tm-30) cc_final: 0.5907 (mm110) REVERT: A 31 GLN cc_start: 0.6511 (mt0) cc_final: 0.6117 (tp-100) REVERT: A 356 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6943 (ptt90) REVERT: B 96 ARG cc_start: 0.6888 (ttm-80) cc_final: 0.6385 (mtm-85) REVERT: B 142 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.7940 (m-70) REVERT: R 65 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6168 (tm) REVERT: R 72 ASP cc_start: 0.6814 (t0) cc_final: 0.6541 (t70) REVERT: R 123 PHE cc_start: 0.5618 (t80) cc_final: 0.5191 (m-80) REVERT: R 133 MET cc_start: 0.6117 (mtp) cc_final: 0.5901 (mtp) REVERT: R 138 ILE cc_start: 0.5765 (OUTLIER) cc_final: 0.5513 (tt) REVERT: R 149 MET cc_start: 0.5965 (ptm) cc_final: 0.5536 (ptp) REVERT: R 172 ASP cc_start: 0.7054 (p0) cc_final: 0.6806 (t0) REVERT: R 204 ARG cc_start: 0.5746 (tpt170) cc_final: 0.5389 (mtt90) REVERT: R 271 MET cc_start: 0.3528 (mtm) cc_final: 0.3180 (mtp) outliers start: 32 outliers final: 23 residues processed: 125 average time/residue: 2.0066 time to fit residues: 269.9835 Evaluate side-chains 120 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 273 PHE 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 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 138 ILE Chi-restraints excluded: chain R residue 301 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.0570 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 overall best weight: 1.4702 ------------------------------------------------------------------------------- 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** B 176 GLN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.257387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.230420 restraints weight = 26254.548| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 1.81 r_work: 0.4455 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4362 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7890 Z= 0.191 Angle : 0.647 8.529 10696 Z= 0.354 Chirality : 0.043 0.148 1194 Planarity : 0.005 0.057 1357 Dihedral : 5.976 35.933 1064 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.16 % Allowed : 16.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 959 helix: 1.01 (0.27), residues: 340 sheet: -1.31 (0.36), residues: 197 loop : -1.31 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.011 0.001 HIS R 212 PHE 0.017 0.002 PHE B 241 TYR 0.015 0.002 TYR R 171 ARG 0.008 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05739 ( 360) hydrogen bonds : angle 5.52157 ( 1035) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.55566 ( 8) covalent geometry : bond 0.00430 ( 7886) covalent geometry : angle 0.64536 (10688) *********************** 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 132 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6265 (tm-30) cc_final: 0.5935 (mp10) REVERT: A 31 GLN cc_start: 0.6601 (mt0) cc_final: 0.6181 (tp-100) REVERT: A 271 ASN cc_start: 0.5659 (OUTLIER) cc_final: 0.5456 (m110) REVERT: A 314 GLU cc_start: 0.4975 (mm-30) cc_final: 0.4770 (mm-30) REVERT: A 356 ARG cc_start: 0.7221 (mtp85) cc_final: 0.6998 (ptt90) REVERT: B 96 ARG cc_start: 0.6923 (ttm-80) cc_final: 0.6445 (mtm-85) REVERT: B 171 ILE cc_start: 0.6012 (mm) cc_final: 0.5749 (mm) REVERT: B 186 ASP cc_start: 0.7325 (m-30) cc_final: 0.7103 (m-30) REVERT: R 65 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6112 (tm) REVERT: R 72 ASP cc_start: 0.6848 (t0) cc_final: 0.6586 (t70) REVERT: R 123 PHE cc_start: 0.5778 (t80) cc_final: 0.5212 (m-80) REVERT: R 133 MET cc_start: 0.6251 (mtp) cc_final: 0.5926 (mtp) REVERT: R 138 ILE cc_start: 0.5981 (OUTLIER) cc_final: 0.5762 (tt) REVERT: R 149 MET cc_start: 0.5924 (ptm) cc_final: 0.5563 (ptp) REVERT: R 204 ARG cc_start: 0.5719 (tpt170) cc_final: 0.5311 (mtt90) REVERT: R 271 MET cc_start: 0.3381 (mtm) cc_final: 0.2913 (mmt) outliers start: 35 outliers final: 19 residues processed: 123 average time/residue: 1.9107 time to fit residues: 253.1630 Evaluate side-chains 112 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 153 ASP 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 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 138 ILE Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.254778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.227646 restraints weight = 26177.283| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.80 r_work: 0.4434 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4337 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7890 Z= 0.196 Angle : 0.665 10.200 10696 Z= 0.360 Chirality : 0.043 0.154 1194 Planarity : 0.005 0.040 1357 Dihedral : 6.112 36.100 1064 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.64 % Allowed : 16.65 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.26), residues: 959 helix: 0.85 (0.27), residues: 342 sheet: -1.69 (0.34), residues: 216 loop : -1.36 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.008 0.001 HIS R 212 PHE 0.015 0.002 PHE R 104 TYR 0.018 0.002 TYR R 171 ARG 0.007 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05901 ( 360) hydrogen bonds : angle 5.51997 ( 1035) SS BOND : bond 0.00415 ( 4) SS BOND : angle 1.52000 ( 8) covalent geometry : bond 0.00438 ( 7886) covalent geometry : angle 0.66367 (10688) *********************** 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 132 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6224 (tm-30) cc_final: 0.5848 (mm110) REVERT: A 31 GLN cc_start: 0.6563 (mt0) cc_final: 0.6153 (tp-100) REVERT: A 314 GLU cc_start: 0.5210 (mm-30) cc_final: 0.4963 (mm-30) REVERT: A 356 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6957 (ptt90) REVERT: A 360 TYR cc_start: 0.6992 (m-80) cc_final: 0.5896 (m-80) REVERT: B 96 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6455 (mtm-85) REVERT: B 142 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8047 (m-70) REVERT: B 229 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6713 (mm) REVERT: B 243 THR cc_start: 0.4093 (OUTLIER) cc_final: 0.3840 (m) REVERT: B 284 LEU cc_start: 0.3949 (OUTLIER) cc_final: 0.3722 (pp) REVERT: R 65 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.5519 (mm) REVERT: R 72 ASP cc_start: 0.6786 (t0) cc_final: 0.6528 (t70) REVERT: R 123 PHE cc_start: 0.5708 (t80) cc_final: 0.5215 (m-80) REVERT: R 128 ARG cc_start: 0.6604 (ttm110) cc_final: 0.6319 (mtm110) REVERT: R 133 MET cc_start: 0.6223 (mtp) cc_final: 0.5937 (mtp) REVERT: R 149 MET cc_start: 0.5938 (ptm) cc_final: 0.5655 (ptp) REVERT: R 271 MET cc_start: 0.3414 (mtm) cc_final: 0.2974 (mmt) outliers start: 39 outliers final: 19 residues processed: 124 average time/residue: 2.0329 time to fit residues: 271.9949 Evaluate side-chains 109 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 239 ASN 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 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 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 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 Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.260993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.234018 restraints weight = 26077.734| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 1.76 r_work: 0.4497 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4409 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7890 Z= 0.172 Angle : 0.628 8.780 10696 Z= 0.340 Chirality : 0.042 0.145 1194 Planarity : 0.004 0.038 1357 Dihedral : 5.995 35.067 1064 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.99 % Allowed : 16.65 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.26), residues: 959 helix: 0.89 (0.27), residues: 339 sheet: -1.70 (0.33), residues: 215 loop : -1.38 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.002 PHE R 104 TYR 0.020 0.002 TYR R 171 ARG 0.006 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05532 ( 360) hydrogen bonds : angle 5.42927 ( 1035) SS BOND : bond 0.00392 ( 4) SS BOND : angle 1.37291 ( 8) covalent geometry : bond 0.00381 ( 7886) covalent geometry : angle 0.62710 (10688) *********************** 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 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6184 (tm-30) cc_final: 0.5948 (mp10) REVERT: A 31 GLN cc_start: 0.6513 (mt0) cc_final: 0.6232 (tp-100) REVERT: A 60 MET cc_start: 0.3185 (OUTLIER) cc_final: 0.1468 (ppp) REVERT: A 271 ASN cc_start: 0.5670 (OUTLIER) cc_final: 0.5449 (m110) REVERT: A 360 TYR cc_start: 0.6888 (m-80) cc_final: 0.5852 (m-80) REVERT: B 96 ARG cc_start: 0.6861 (ttm-80) cc_final: 0.6513 (ttm-80) REVERT: B 142 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.7975 (m-70) REVERT: B 214 ARG cc_start: 0.7101 (mmt180) cc_final: 0.6706 (mpt90) REVERT: B 229 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6674 (mm) REVERT: R 37 CYS cc_start: 0.7544 (p) cc_final: 0.7280 (p) REVERT: R 65 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5447 (mm) REVERT: R 72 ASP cc_start: 0.6762 (t0) cc_final: 0.6521 (t70) REVERT: R 123 PHE cc_start: 0.5542 (t80) cc_final: 0.5329 (m-80) REVERT: R 124 PHE cc_start: 0.5434 (t80) cc_final: 0.4597 (p90) REVERT: R 133 MET cc_start: 0.6126 (mtp) cc_final: 0.5782 (mtp) REVERT: R 149 MET cc_start: 0.5873 (ptm) cc_final: 0.5590 (ptp) REVERT: R 271 MET cc_start: 0.3540 (mtm) cc_final: 0.3102 (mmt) outliers start: 42 outliers final: 24 residues processed: 131 average time/residue: 2.2071 time to fit residues: 314.0617 Evaluate side-chains 117 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS 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 275 SER 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 81 LEU 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 Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** A 29 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 = 0.4723 r_free = 0.4723 target = 0.252470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.221593 restraints weight = 26092.564| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 1.92 r_work: 0.4406 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4312 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7890 Z= 0.196 Angle : 0.657 9.090 10696 Z= 0.356 Chirality : 0.043 0.153 1194 Planarity : 0.005 0.057 1357 Dihedral : 6.223 40.795 1064 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 4.99 % Allowed : 17.72 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 959 helix: 0.81 (0.27), residues: 340 sheet: -1.75 (0.34), residues: 212 loop : -1.47 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.002 PHE R 104 TYR 0.016 0.002 TYR R 171 ARG 0.010 0.001 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.05820 ( 360) hydrogen bonds : angle 5.51985 ( 1035) SS BOND : bond 0.00406 ( 4) SS BOND : angle 1.33011 ( 8) covalent geometry : bond 0.00437 ( 7886) covalent geometry : angle 0.65643 (10688) *********************** 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 130 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5922 (mt-10) REVERT: A 29 GLN cc_start: 0.6167 (tm-30) cc_final: 0.5848 (mp10) REVERT: A 31 GLN cc_start: 0.6665 (mt0) cc_final: 0.6094 (tp-100) REVERT: A 271 ASN cc_start: 0.5462 (OUTLIER) cc_final: 0.5234 (m110) REVERT: A 360 TYR cc_start: 0.7019 (m-80) cc_final: 0.5991 (m-80) REVERT: B 46 ARG cc_start: 0.6164 (mtp-110) cc_final: 0.5875 (ptt90) REVERT: B 96 ARG cc_start: 0.6958 (ttm-80) cc_final: 0.6642 (ttm-80) REVERT: B 142 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.7929 (m-70) REVERT: B 214 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6687 (mpt90) REVERT: B 229 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6710 (mm) REVERT: B 262 MET cc_start: 0.5755 (ppp) cc_final: 0.5315 (ppp) REVERT: R 65 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5471 (mm) REVERT: R 72 ASP cc_start: 0.6777 (t0) cc_final: 0.6505 (t70) REVERT: R 123 PHE cc_start: 0.5470 (t80) cc_final: 0.5144 (m-80) REVERT: R 124 PHE cc_start: 0.5442 (t80) cc_final: 0.4495 (p90) REVERT: R 128 ARG cc_start: 0.6621 (ttm110) cc_final: 0.6368 (mtt90) REVERT: R 133 MET cc_start: 0.6190 (mtp) cc_final: 0.5836 (mtp) REVERT: R 149 MET cc_start: 0.5923 (ptm) cc_final: 0.5647 (ptp) REVERT: R 271 MET cc_start: 0.3396 (mtm) cc_final: 0.2963 (mmt) outliers start: 42 outliers final: 29 residues processed: 122 average time/residue: 2.5766 time to fit residues: 346.8499 Evaluate side-chains 120 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain A residue 310 ASP 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 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 GLN 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 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 329 THR 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 72 ARG Chi-restraints excluded: chain N residue 81 LEU 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 Chi-restraints excluded: chain R residue 143 THR 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 89 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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** ** A 29 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 = 0.4733 r_free = 0.4733 target = 0.254264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.224496 restraints weight = 25861.525| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 1.88 r_work: 0.4435 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4338 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7890 Z= 0.142 Angle : 0.589 7.697 10696 Z= 0.319 Chirality : 0.041 0.144 1194 Planarity : 0.004 0.038 1357 Dihedral : 5.851 39.899 1064 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 4.64 % Allowed : 18.07 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 959 helix: 1.00 (0.27), residues: 342 sheet: -1.85 (0.33), residues: 212 loop : -1.31 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.003 0.001 HIS A 362 PHE 0.014 0.001 PHE R 104 TYR 0.018 0.002 TYR R 171 ARG 0.006 0.000 ARG R 128 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 360) hydrogen bonds : angle 5.30513 ( 1035) SS BOND : bond 0.00284 ( 4) SS BOND : angle 1.08005 ( 8) covalent geometry : bond 0.00308 ( 7886) covalent geometry : angle 0.58798 (10688) *********************** 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 128 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5838 (mt-10) REVERT: A 29 GLN cc_start: 0.6045 (tm-30) cc_final: 0.5819 (mp10) REVERT: A 31 GLN cc_start: 0.6623 (mt0) cc_final: 0.6103 (tp-100) REVERT: A 60 MET cc_start: 0.3165 (OUTLIER) cc_final: 0.1329 (ppp) REVERT: A 271 ASN cc_start: 0.5346 (OUTLIER) cc_final: 0.5125 (m110) REVERT: B 46 ARG cc_start: 0.6107 (mtp-110) cc_final: 0.5877 (ptt90) REVERT: B 96 ARG cc_start: 0.6990 (ttm-80) cc_final: 0.6697 (ttm-80) REVERT: B 142 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.7852 (m-70) REVERT: B 214 ARG cc_start: 0.7147 (mmt180) cc_final: 0.6906 (mmt-90) REVERT: B 229 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6587 (mm) REVERT: B 262 MET cc_start: 0.5704 (ppp) cc_final: 0.5243 (ppp) REVERT: R 65 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5413 (mm) REVERT: R 72 ASP cc_start: 0.6831 (t0) cc_final: 0.6527 (t70) REVERT: R 124 PHE cc_start: 0.5431 (t80) cc_final: 0.4553 (p90) REVERT: R 128 ARG cc_start: 0.6565 (ttm110) cc_final: 0.6362 (mtt90) REVERT: R 133 MET cc_start: 0.6187 (mtp) cc_final: 0.5799 (mtp) REVERT: R 149 MET cc_start: 0.5847 (ptm) cc_final: 0.5614 (ptp) REVERT: R 271 MET cc_start: 0.3411 (mtm) cc_final: 0.3009 (mmt) REVERT: R 301 MET cc_start: 0.5792 (tmt) cc_final: 0.4065 (tpt) outliers start: 39 outliers final: 23 residues processed: 119 average time/residue: 1.8796 time to fit residues: 243.0103 Evaluate side-chains 114 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 175 GLN 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 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 27 PHE Chi-restraints excluded: chain N residue 48 VAL 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 Chi-restraints excluded: chain R residue 225 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 2 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** A 29 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 = 0.4695 r_free = 0.4695 target = 0.249251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.218543 restraints weight = 26034.249| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 1.91 r_work: 0.4383 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7890 Z= 0.212 Angle : 0.678 8.443 10696 Z= 0.369 Chirality : 0.043 0.152 1194 Planarity : 0.005 0.041 1357 Dihedral : 6.358 48.607 1064 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 4.40 % Allowed : 18.91 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 959 helix: 0.71 (0.27), residues: 337 sheet: -1.94 (0.33), residues: 205 loop : -1.51 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.002 PHE B 241 TYR 0.016 0.002 TYR A 391 ARG 0.009 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05994 ( 360) hydrogen bonds : angle 5.54609 ( 1035) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.33269 ( 8) covalent geometry : bond 0.00473 ( 7886) covalent geometry : angle 0.67767 (10688) *********************** 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 123 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6211 (tm-30) cc_final: 0.5857 (mm110) REVERT: A 31 GLN cc_start: 0.6620 (mt0) cc_final: 0.6067 (tp-100) REVERT: A 271 ASN cc_start: 0.5568 (OUTLIER) cc_final: 0.5342 (m110) REVERT: A 338 LYS cc_start: 0.3720 (OUTLIER) cc_final: 0.3242 (ttpt) REVERT: B 46 ARG cc_start: 0.6120 (mtp-110) cc_final: 0.5854 (ptt90) REVERT: B 96 ARG cc_start: 0.7003 (ttm-80) cc_final: 0.6710 (ttm-80) REVERT: B 142 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8041 (m-70) REVERT: B 214 ARG cc_start: 0.7180 (mmt180) cc_final: 0.6774 (mpt90) REVERT: B 229 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6728 (mm) REVERT: R 65 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5431 (mm) REVERT: R 72 ASP cc_start: 0.6799 (t0) cc_final: 0.6523 (t70) REVERT: R 124 PHE cc_start: 0.5537 (t80) cc_final: 0.4578 (p90) REVERT: R 133 MET cc_start: 0.6282 (mtp) cc_final: 0.5915 (mtp) REVERT: R 149 MET cc_start: 0.6007 (ptm) cc_final: 0.5755 (ptp) REVERT: R 271 MET cc_start: 0.3279 (mtm) cc_final: 0.2953 (mmm) REVERT: R 301 MET cc_start: 0.5903 (tmt) cc_final: 0.4424 (tpt) outliers start: 37 outliers final: 23 residues processed: 113 average time/residue: 2.0816 time to fit residues: 253.3334 Evaluate side-chains 110 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 271 ASN Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 GLN 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 275 SER Chi-restraints excluded: chain B residue 276 VAL 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 97 ASN Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 225 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 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.258358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.232736 restraints weight = 26176.269| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 1.73 r_work: 0.4507 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4414 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7890 Z= 0.131 Angle : 0.593 8.530 10696 Z= 0.320 Chirality : 0.041 0.143 1194 Planarity : 0.004 0.040 1357 Dihedral : 5.885 49.899 1064 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 2.73 % Allowed : 21.05 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 959 helix: 0.93 (0.27), residues: 339 sheet: -1.89 (0.33), residues: 212 loop : -1.33 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 281 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE R 104 TYR 0.017 0.001 TYR R 171 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 360) hydrogen bonds : angle 5.25726 ( 1035) SS BOND : bond 0.00266 ( 4) SS BOND : angle 1.07824 ( 8) covalent geometry : bond 0.00284 ( 7886) covalent geometry : angle 0.59265 (10688) ********************** 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 108 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6117 (tm-30) cc_final: 0.5910 (mp10) REVERT: A 31 GLN cc_start: 0.6481 (mt0) cc_final: 0.6186 (tp-100) REVERT: A 60 MET cc_start: 0.3197 (mpm) cc_final: 0.1511 (ppp) REVERT: A 360 TYR cc_start: 0.6949 (m-80) cc_final: 0.6132 (m-80) REVERT: B 96 ARG cc_start: 0.6977 (ttm-80) cc_final: 0.6707 (ttm-80) REVERT: B 142 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.7952 (m-70) REVERT: B 214 ARG cc_start: 0.7178 (mmt180) cc_final: 0.6776 (mpt90) REVERT: B 290 ASP cc_start: 0.6783 (m-30) cc_final: 0.6568 (m-30) REVERT: R 65 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5396 (mm) REVERT: R 72 ASP cc_start: 0.6746 (t0) cc_final: 0.6474 (t70) REVERT: R 124 PHE cc_start: 0.5426 (t80) cc_final: 0.4591 (p90) REVERT: R 128 ARG cc_start: 0.6736 (mtm180) cc_final: 0.6532 (mtt90) REVERT: R 149 MET cc_start: 0.5905 (ptm) cc_final: 0.5658 (ptp) REVERT: R 271 MET cc_start: 0.3356 (mtm) cc_final: 0.2883 (mmm) REVERT: R 301 MET cc_start: 0.5800 (tmt) cc_final: 0.4369 (tpt) outliers start: 23 outliers final: 18 residues processed: 104 average time/residue: 2.4132 time to fit residues: 271.0573 Evaluate side-chains 99 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 225 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 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 97 ASN Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 225 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 72 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.258136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.229902 restraints weight = 26032.950| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 1.78 r_work: 0.4505 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4413 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7890 Z= 0.138 Angle : 0.590 8.414 10696 Z= 0.319 Chirality : 0.041 0.139 1194 Planarity : 0.004 0.038 1357 Dihedral : 5.938 64.859 1064 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 3.21 % Allowed : 20.21 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 959 helix: 1.01 (0.27), residues: 341 sheet: -1.93 (0.33), residues: 210 loop : -1.23 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 281 HIS 0.003 0.001 HIS R 14 PHE 0.016 0.001 PHE R 104 TYR 0.018 0.002 TYR R 171 ARG 0.005 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 360) hydrogen bonds : angle 5.20384 ( 1035) SS BOND : bond 0.00289 ( 4) SS BOND : angle 1.07935 ( 8) covalent geometry : bond 0.00305 ( 7886) covalent geometry : angle 0.58982 (10688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12151.34 seconds wall clock time: 212 minutes 23.22 seconds (12743.22 seconds total)