Starting phenix.real_space_refine on Wed Mar 4 02:20:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3z_32297/03_2026/7w3z_32297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3z_32297/03_2026/7w3z_32297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w3z_32297/03_2026/7w3z_32297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3z_32297/03_2026/7w3z_32297.map" model { file = "/net/cci-nas-00/data/ceres_data/7w3z_32297/03_2026/7w3z_32297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3z_32297/03_2026/7w3z_32297.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6506 2.51 5 N 1744 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10221 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 14, 'TRANS': 286} Chain: "L" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 96 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2887 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 340} Chain: "C" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "H" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Time building chain proxies: 1.99, per 1000 atoms: 0.19 Number of scatterers: 10221 At special positions: 0 Unit cell: (111.54, 117.624, 135.876, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1908 8.00 N 1744 7.00 C 6506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 482.3 milliseconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 14 sheets defined 42.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 37 through 69 Proline residue: A 44 - end of helix removed outlier: 3.519A pdb=" N CYS A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 103 removed outlier: 3.608A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 108 through 144 removed outlier: 4.127A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.523A pdb=" N THR A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 179 removed outlier: 3.583A pdb=" N ILE A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.574A pdb=" N TYR A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 290 removed outlier: 3.718A pdb=" N LYS A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 297 through 326 removed outlier: 3.668A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix removed outlier: 3.823A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.823A pdb=" N ARG B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.687A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.857A pdb=" N LYS B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.580A pdb=" N ASP B 130 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.882A pdb=" N VAL B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.653A pdb=" N ILE B 217 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B 218 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 219 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.435A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.099A pdb=" N TYR B 291 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.872A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.509A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 9.004A pdb=" N VAL A 294 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS A 185 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.348A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.740A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.696A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.661A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.895A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.287A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.595A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.730A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.328A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.617A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1852 1.32 - 1.45: 2708 1.45 - 1.57: 5788 1.57 - 1.69: 0 1.69 - 1.82: 95 Bond restraints: 10443 Sorted by residual: bond pdb=" C ILE A 164 " pdb=" O ILE A 164 " ideal model delta sigma weight residual 1.237 1.307 -0.070 1.17e-02 7.31e+03 3.60e+01 bond pdb=" C VAL A 266 " pdb=" O VAL A 266 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.18e+01 bond pdb=" C ILE A 167 " pdb=" O ILE A 167 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.05e+01 bond pdb=" C ALA A 263 " pdb=" O ALA A 263 " ideal model delta sigma weight residual 1.236 1.288 -0.052 1.15e-02 7.56e+03 2.01e+01 bond pdb=" C LEU A 170 " pdb=" O LEU A 170 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.90e+01 ... (remaining 10438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 11813 1.65 - 3.30: 2008 3.30 - 4.95: 278 4.95 - 6.60: 38 6.60 - 8.25: 13 Bond angle restraints: 14150 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 110.35 102.10 8.25 1.36e+00 5.41e-01 3.68e+01 angle pdb=" N ARG C 48 " pdb=" CA ARG C 48 " pdb=" C ARG C 48 " ideal model delta sigma weight residual 113.23 106.88 6.35 1.24e+00 6.50e-01 2.62e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.88 117.93 3.95 7.80e-01 1.64e+00 2.56e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.43 107.05 6.38 1.26e+00 6.30e-01 2.56e+01 angle pdb=" C LEU A 170 " pdb=" N LEU A 171 " pdb=" CA LEU A 171 " ideal model delta sigma weight residual 120.44 114.00 6.44 1.30e+00 5.92e-01 2.45e+01 ... (remaining 14145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5675 16.73 - 33.46: 452 33.46 - 50.19: 93 50.19 - 66.93: 16 66.93 - 83.66: 2 Dihedral angle restraints: 6238 sinusoidal: 2460 harmonic: 3778 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA TYR H 235 " pdb=" C TYR H 235 " pdb=" N PRO H 236 " pdb=" CA PRO H 236 " ideal model delta harmonic sigma weight residual 0.00 29.05 -29.05 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N TYR C 111 " pdb=" CA TYR C 111 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 6235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 999 0.065 - 0.130: 415 0.130 - 0.195: 127 0.195 - 0.260: 37 0.260 - 0.325: 11 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU H 4 " pdb=" N LEU H 4 " pdb=" C LEU H 4 " pdb=" CB LEU H 4 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA CYS A 158 " pdb=" N CYS A 158 " pdb=" C CYS A 158 " pdb=" CB CYS A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1586 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 175 " 0.016 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR H 175 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR H 175 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 175 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR H 175 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS C 127 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 128 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 315 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C VAL C 315 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 316 " -0.017 2.00e-02 2.50e+03 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2139 2.79 - 3.32: 9678 3.32 - 3.85: 16570 3.85 - 4.37: 20760 4.37 - 4.90: 34262 Nonbonded interactions: 83409 Sorted by model distance: nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.291 3.040 nonbonded pdb=" NE ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.309 3.120 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.323 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.338 3.040 ... (remaining 83404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.010 0.105 10447 Z= 0.703 Angle : 1.251 8.252 14156 Z= 0.903 Chirality : 0.083 0.325 1589 Planarity : 0.006 0.053 1801 Dihedral : 12.512 83.657 3795 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 3.93 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1281 helix: 0.81 (0.23), residues: 486 sheet: 0.00 (0.31), residues: 294 loop : -1.14 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 19 TYR 0.056 0.003 TYR H 175 PHE 0.030 0.003 PHE C 199 TRP 0.035 0.003 TRP C 82 HIS 0.009 0.002 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.01007 (10443) covalent geometry : angle 1.24918 (14150) SS BOND : bond 0.02117 ( 3) SS BOND : angle 3.05859 ( 6) hydrogen bonds : bond 0.17432 ( 513) hydrogen bonds : angle 6.69857 ( 1464) Misc. bond : bond 0.10547 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 GLU cc_start: 0.6980 (tp30) cc_final: 0.6667 (tp30) REVERT: B 332 THR cc_start: 0.8243 (t) cc_final: 0.7598 (m) REVERT: B 337 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7538 (mp) REVERT: C 228 ASP cc_start: 0.7555 (m-30) cc_final: 0.6637 (m-30) REVERT: H 109 ASP cc_start: 0.7308 (p0) cc_final: 0.6975 (p0) REVERT: H 234 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7229 (mt-10) outliers start: 18 outliers final: 6 residues processed: 211 average time/residue: 0.6440 time to fit residues: 144.3154 Evaluate side-chains 137 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain H residue 63 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 239 GLN A 280 ASN A 334 ASN B 274 ASN C 36 ASN C 88 ASN C 110 ASN C 175 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.180762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138234 restraints weight = 11136.020| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.03 r_work: 0.3463 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10447 Z= 0.135 Angle : 0.577 8.394 14156 Z= 0.303 Chirality : 0.041 0.138 1589 Planarity : 0.004 0.053 1801 Dihedral : 5.061 55.254 1426 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.30 % Allowed : 12.05 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1281 helix: 1.95 (0.22), residues: 498 sheet: 0.16 (0.30), residues: 280 loop : -0.85 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.031 0.001 TYR B 80 PHE 0.013 0.001 PHE C 199 TRP 0.020 0.001 TRP C 82 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00271 (10443) covalent geometry : angle 0.57617 (14150) SS BOND : bond 0.01349 ( 3) SS BOND : angle 1.14536 ( 6) hydrogen bonds : bond 0.05062 ( 513) hydrogen bonds : angle 4.61901 ( 1464) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.2344 (OUTLIER) cc_final: 0.2039 (pt) REVERT: A 331 LYS cc_start: 0.7616 (tttt) cc_final: 0.7162 (mmtt) REVERT: B 87 MET cc_start: 0.7746 (tpt) cc_final: 0.7350 (tpt) REVERT: B 94 MET cc_start: 0.4848 (mmt) cc_final: 0.4419 (mmt) REVERT: B 277 ASP cc_start: 0.7713 (m-30) cc_final: 0.6453 (m-30) REVERT: B 281 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: B 337 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 129 ARG cc_start: 0.7701 (tmm160) cc_final: 0.7324 (ttm-80) REVERT: D 47 GLU cc_start: 0.8355 (mp0) cc_final: 0.8093 (mt-10) REVERT: H 18 ARG cc_start: 0.7059 (tpp80) cc_final: 0.6762 (tpt-90) REVERT: H 109 ASP cc_start: 0.7834 (p0) cc_final: 0.7624 (p0) outliers start: 37 outliers final: 15 residues processed: 175 average time/residue: 0.6725 time to fit residues: 124.9808 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 39 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 122 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN L 19 ASN C 36 ASN C 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.179026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136034 restraints weight = 11126.191| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.14 r_work: 0.3423 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10447 Z= 0.126 Angle : 0.539 6.536 14156 Z= 0.284 Chirality : 0.041 0.139 1589 Planarity : 0.004 0.052 1801 Dihedral : 4.770 59.247 1423 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.86 % Allowed : 14.91 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1281 helix: 2.29 (0.22), residues: 498 sheet: 0.38 (0.30), residues: 271 loop : -0.83 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.031 0.001 TYR B 80 PHE 0.015 0.002 PHE C 199 TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00274 (10443) covalent geometry : angle 0.53885 (14150) SS BOND : bond 0.00710 ( 3) SS BOND : angle 1.36026 ( 6) hydrogen bonds : bond 0.04617 ( 513) hydrogen bonds : angle 4.32825 ( 1464) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.7585 (tttt) cc_final: 0.7092 (mmpt) REVERT: L 19 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5996 (p0) REVERT: B 87 MET cc_start: 0.7811 (tpt) cc_final: 0.7463 (tpt) REVERT: B 94 MET cc_start: 0.4592 (mmt) cc_final: 0.4296 (mmt) REVERT: B 124 PHE cc_start: 0.3243 (OUTLIER) cc_final: 0.2661 (t80) REVERT: B 277 ASP cc_start: 0.7517 (m-30) cc_final: 0.6095 (m-30) REVERT: B 281 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: B 337 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7324 (pp) REVERT: D 47 GLU cc_start: 0.8263 (mp0) cc_final: 0.8043 (mt-10) REVERT: H 109 ASP cc_start: 0.7483 (p0) cc_final: 0.7283 (p0) outliers start: 32 outliers final: 19 residues processed: 161 average time/residue: 0.6877 time to fit residues: 117.6543 Evaluate side-chains 151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 110 optimal weight: 0.0970 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 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 334 ASN L 19 ASN C 36 ASN C 237 ASN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136070 restraints weight = 11159.630| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.02 r_work: 0.3354 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10447 Z= 0.118 Angle : 0.530 8.019 14156 Z= 0.276 Chirality : 0.041 0.173 1589 Planarity : 0.004 0.052 1801 Dihedral : 4.657 59.011 1422 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.21 % Allowed : 16.07 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1281 helix: 2.38 (0.23), residues: 500 sheet: 0.53 (0.30), residues: 267 loop : -0.83 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.028 0.001 TYR B 80 PHE 0.015 0.001 PHE C 199 TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00257 (10443) covalent geometry : angle 0.52995 (14150) SS BOND : bond 0.00638 ( 3) SS BOND : angle 1.25825 ( 6) hydrogen bonds : bond 0.04259 ( 513) hydrogen bonds : angle 4.18956 ( 1464) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.7452 (tttt) cc_final: 0.6928 (mmpt) REVERT: B 87 MET cc_start: 0.7758 (tpt) cc_final: 0.7409 (tpt) REVERT: B 90 MET cc_start: 0.6671 (ttp) cc_final: 0.6330 (ttp) REVERT: B 94 MET cc_start: 0.4797 (mmt) cc_final: 0.4566 (mmt) REVERT: B 124 PHE cc_start: 0.3169 (OUTLIER) cc_final: 0.2593 (t80) REVERT: B 277 ASP cc_start: 0.7721 (m-30) cc_final: 0.6354 (m-30) REVERT: B 281 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: B 285 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6516 (p90) REVERT: B 321 ASP cc_start: 0.7998 (t0) cc_final: 0.7749 (t0) REVERT: H 109 ASP cc_start: 0.7784 (p0) cc_final: 0.7556 (p0) outliers start: 36 outliers final: 22 residues processed: 159 average time/residue: 0.6505 time to fit residues: 109.8549 Evaluate side-chains 152 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN L 19 ASN C 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135656 restraints weight = 11135.263| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.96 r_work: 0.3347 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10447 Z= 0.124 Angle : 0.539 8.458 14156 Z= 0.280 Chirality : 0.041 0.133 1589 Planarity : 0.004 0.050 1801 Dihedral : 4.383 34.409 1420 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.12 % Allowed : 17.68 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1281 helix: 2.47 (0.23), residues: 499 sheet: 0.46 (0.30), residues: 270 loop : -0.75 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 197 TYR 0.031 0.001 TYR B 80 PHE 0.016 0.001 PHE C 199 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00277 (10443) covalent geometry : angle 0.53891 (14150) SS BOND : bond 0.00637 ( 3) SS BOND : angle 1.26249 ( 6) hydrogen bonds : bond 0.04214 ( 513) hydrogen bonds : angle 4.13436 ( 1464) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8027 (tt) cc_final: 0.7728 (pt) REVERT: A 242 TYR cc_start: 0.6889 (p90) cc_final: 0.6678 (p90) REVERT: A 331 LYS cc_start: 0.7505 (tttt) cc_final: 0.6956 (mmpt) REVERT: B 87 MET cc_start: 0.7681 (tpt) cc_final: 0.7268 (tpt) REVERT: B 90 MET cc_start: 0.6656 (ttp) cc_final: 0.6310 (ttp) REVERT: B 124 PHE cc_start: 0.3195 (OUTLIER) cc_final: 0.2610 (t80) REVERT: B 277 ASP cc_start: 0.7689 (m-30) cc_final: 0.6308 (m-30) REVERT: B 281 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: D 21 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6876 (tmm) REVERT: H 109 ASP cc_start: 0.7788 (p0) cc_final: 0.7569 (p0) outliers start: 35 outliers final: 23 residues processed: 154 average time/residue: 0.6971 time to fit residues: 114.1123 Evaluate side-chains 152 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 68 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 334 ASN L 19 ASN B 357 ASN C 36 ASN C 237 ASN H 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.178854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136185 restraints weight = 11139.586| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.96 r_work: 0.3326 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10447 Z= 0.112 Angle : 0.522 9.052 14156 Z= 0.271 Chirality : 0.040 0.134 1589 Planarity : 0.004 0.051 1801 Dihedral : 4.244 33.533 1418 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.04 % Allowed : 18.93 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1281 helix: 2.56 (0.23), residues: 500 sheet: 0.59 (0.30), residues: 275 loop : -0.77 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 38 TYR 0.033 0.001 TYR B 80 PHE 0.014 0.001 PHE C 199 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00246 (10443) covalent geometry : angle 0.52191 (14150) SS BOND : bond 0.00589 ( 3) SS BOND : angle 0.95642 ( 6) hydrogen bonds : bond 0.03940 ( 513) hydrogen bonds : angle 4.05021 ( 1464) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6899 (mt) REVERT: A 331 LYS cc_start: 0.7482 (tttt) cc_final: 0.7027 (tptt) REVERT: L 19 ASN cc_start: 0.6381 (OUTLIER) cc_final: 0.6160 (p0) REVERT: B 87 MET cc_start: 0.7670 (tpt) cc_final: 0.7329 (tpt) REVERT: B 90 MET cc_start: 0.6608 (ttp) cc_final: 0.6255 (ttp) REVERT: B 124 PHE cc_start: 0.3213 (OUTLIER) cc_final: 0.2666 (t80) REVERT: B 277 ASP cc_start: 0.7752 (m-30) cc_final: 0.6375 (m-30) REVERT: B 281 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: D 21 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6804 (tmm) REVERT: H 109 ASP cc_start: 0.7787 (p0) cc_final: 0.7560 (p0) outliers start: 34 outliers final: 16 residues processed: 153 average time/residue: 0.6767 time to fit residues: 110.3266 Evaluate side-chains 141 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 334 ASN L 19 ASN C 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134232 restraints weight = 11142.721| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.00 r_work: 0.3323 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10447 Z= 0.135 Angle : 0.544 9.516 14156 Z= 0.282 Chirality : 0.041 0.137 1589 Planarity : 0.004 0.053 1801 Dihedral : 4.290 35.487 1417 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.04 % Allowed : 19.73 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1281 helix: 2.47 (0.23), residues: 500 sheet: 0.51 (0.30), residues: 277 loop : -0.82 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 38 TYR 0.034 0.002 TYR B 80 PHE 0.019 0.002 PHE A 329 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00310 (10443) covalent geometry : angle 0.54301 (14150) SS BOND : bond 0.00689 ( 3) SS BOND : angle 1.26454 ( 6) hydrogen bonds : bond 0.04222 ( 513) hydrogen bonds : angle 4.07792 ( 1464) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6922 (mt) REVERT: B 87 MET cc_start: 0.7715 (tpt) cc_final: 0.7334 (tpt) REVERT: B 90 MET cc_start: 0.6696 (ttp) cc_final: 0.6355 (ttp) REVERT: B 124 PHE cc_start: 0.3203 (OUTLIER) cc_final: 0.2633 (t80) REVERT: B 249 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 277 ASP cc_start: 0.7748 (m-30) cc_final: 0.6366 (m-30) REVERT: B 281 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: B 285 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6915 (p90) REVERT: D 21 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6810 (tmm) REVERT: H 109 ASP cc_start: 0.7814 (p0) cc_final: 0.7585 (p0) outliers start: 34 outliers final: 21 residues processed: 145 average time/residue: 0.6521 time to fit residues: 100.4882 Evaluate side-chains 145 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS L 19 ASN B 88 GLN C 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135966 restraints weight = 11099.706| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.90 r_work: 0.3356 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10447 Z= 0.114 Angle : 0.526 10.004 14156 Z= 0.273 Chirality : 0.040 0.134 1589 Planarity : 0.004 0.053 1801 Dihedral : 4.205 33.432 1417 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.86 % Allowed : 20.00 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.23), residues: 1281 helix: 2.59 (0.23), residues: 498 sheet: 0.64 (0.30), residues: 275 loop : -0.84 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 38 TYR 0.035 0.001 TYR B 80 PHE 0.019 0.001 PHE A 329 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00253 (10443) covalent geometry : angle 0.52574 (14150) SS BOND : bond 0.00617 ( 3) SS BOND : angle 1.12095 ( 6) hydrogen bonds : bond 0.03915 ( 513) hydrogen bonds : angle 3.97867 ( 1464) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6925 (mt) REVERT: B 90 MET cc_start: 0.6708 (ttp) cc_final: 0.6362 (ttp) REVERT: B 124 PHE cc_start: 0.3071 (OUTLIER) cc_final: 0.2448 (t80) REVERT: B 234 GLU cc_start: 0.8126 (tt0) cc_final: 0.7789 (tm-30) REVERT: B 277 ASP cc_start: 0.7803 (m-30) cc_final: 0.6357 (m-30) REVERT: B 281 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: D 21 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6822 (tmm) REVERT: H 109 ASP cc_start: 0.7786 (p0) cc_final: 0.7544 (p0) outliers start: 32 outliers final: 25 residues processed: 141 average time/residue: 0.6639 time to fit residues: 99.6358 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 85 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 0.0040 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS C 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137049 restraints weight = 11064.059| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.90 r_work: 0.3368 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10447 Z= 0.102 Angle : 0.526 10.058 14156 Z= 0.270 Chirality : 0.040 0.132 1589 Planarity : 0.004 0.061 1801 Dihedral : 4.109 31.635 1417 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.68 % Allowed : 20.27 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1281 helix: 2.68 (0.23), residues: 498 sheet: 0.74 (0.30), residues: 275 loop : -0.81 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 38 TYR 0.036 0.001 TYR B 80 PHE 0.015 0.001 PHE A 329 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS L 20 Details of bonding type rmsd covalent geometry : bond 0.00218 (10443) covalent geometry : angle 0.52575 (14150) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.05085 ( 6) hydrogen bonds : bond 0.03654 ( 513) hydrogen bonds : angle 3.92064 ( 1464) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6893 (mt) REVERT: B 124 PHE cc_start: 0.3074 (OUTLIER) cc_final: 0.2458 (t80) REVERT: B 234 GLU cc_start: 0.8105 (tt0) cc_final: 0.7747 (tm-30) REVERT: B 277 ASP cc_start: 0.7725 (m-30) cc_final: 0.6207 (m-30) REVERT: B 281 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: C 325 MET cc_start: 0.7989 (mmt) cc_final: 0.7762 (mmm) REVERT: D 21 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6842 (tmm) REVERT: H 109 ASP cc_start: 0.7759 (p0) cc_final: 0.7516 (p0) REVERT: H 192 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8316 (ttp) outliers start: 30 outliers final: 20 residues processed: 146 average time/residue: 0.6641 time to fit residues: 103.2182 Evaluate side-chains 145 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS L 19 ASN B 274 ASN C 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133601 restraints weight = 11042.835| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.98 r_work: 0.3420 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10447 Z= 0.123 Angle : 0.553 11.791 14156 Z= 0.283 Chirality : 0.041 0.135 1589 Planarity : 0.004 0.066 1801 Dihedral : 4.199 33.255 1417 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.50 % Allowed : 20.80 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1281 helix: 2.60 (0.23), residues: 498 sheet: 0.68 (0.30), residues: 277 loop : -0.78 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 38 TYR 0.035 0.001 TYR B 80 PHE 0.018 0.001 PHE A 329 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00279 (10443) covalent geometry : angle 0.55237 (14150) SS BOND : bond 0.00654 ( 3) SS BOND : angle 1.32131 ( 6) hydrogen bonds : bond 0.03923 ( 513) hydrogen bonds : angle 3.97281 ( 1464) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7066 (mt) REVERT: B 124 PHE cc_start: 0.3146 (OUTLIER) cc_final: 0.2508 (t80) REVERT: B 277 ASP cc_start: 0.7917 (m-30) cc_final: 0.6481 (m-30) REVERT: B 281 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: C 325 MET cc_start: 0.7987 (mmt) cc_final: 0.7756 (mmm) REVERT: D 21 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6919 (tmm) REVERT: H 109 ASP cc_start: 0.7838 (p0) cc_final: 0.7602 (p0) outliers start: 28 outliers final: 21 residues processed: 136 average time/residue: 0.6332 time to fit residues: 91.6849 Evaluate side-chains 141 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 48 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 114 optimal weight: 0.0970 chunk 118 optimal weight: 0.1980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS C 36 ASN D 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134790 restraints weight = 11144.956| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.95 r_work: 0.3329 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 10447 Z= 0.213 Angle : 0.869 59.199 14156 Z= 0.504 Chirality : 0.044 0.697 1589 Planarity : 0.004 0.062 1801 Dihedral : 4.273 33.237 1417 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.50 % Allowed : 21.25 % Favored : 76.25 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1281 helix: 2.61 (0.23), residues: 498 sheet: 0.68 (0.30), residues: 277 loop : -0.79 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 38 TYR 0.034 0.001 TYR B 80 PHE 0.018 0.001 PHE A 329 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00430 (10443) covalent geometry : angle 0.86909 (14150) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.32152 ( 6) hydrogen bonds : bond 0.03907 ( 513) hydrogen bonds : angle 3.97562 ( 1464) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4005.69 seconds wall clock time: 68 minutes 53.11 seconds (4133.11 seconds total)