Starting phenix.real_space_refine on Thu Jul 2 14:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew2_31345/07_2026/7ew2_31345.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew2_31345/07_2026/7ew2_31345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ew2_31345/07_2026/7ew2_31345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew2_31345/07_2026/7ew2_31345.map" model { file = "/net/cci-nas-00/data/ceres_data/7ew2_31345/07_2026/7ew2_31345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew2_31345/07_2026/7ew2_31345.cif" } resolution = 3.1 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= 0.003 sd= 0.052 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 48 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 P 1 5.49 5 S 68 5.16 5 C 5731 2.51 5 N 1531 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9001 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2294 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 9001 At special positions: 0 Unit cell: (93.5, 121.55, 130.9, 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 68 16.00 P 1 15.00 O 1670 8.00 N 1531 7.00 C 5731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.04 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " 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: 0.51 Conformation dependent library (CDL) restraints added in 360.3 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 37.2% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.786A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.127A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.721A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.419A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.647A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.503A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.508A pdb=" N GLU C 58 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 59' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.616A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.591A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'R' and resid 17 through 26 Processing helix chain 'R' and resid 40 through 67 removed outlier: 3.594A pdb=" N ASN R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 100 removed outlier: 3.993A pdb=" N PHE R 77 " --> pdb=" O ARG R 73 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.796A pdb=" N TRP R 111 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 130 " --> pdb=" O THR R 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA R 131 " --> pdb=" O CYS R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 removed outlier: 3.802A pdb=" N PHE R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 175 Processing helix chain 'R' and resid 193 through 229 removed outlier: 3.616A pdb=" N ILE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG R 217 " --> pdb=" O ILE R 213 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 269 removed outlier: 3.711A pdb=" N CYS R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 274 through 279 Processing helix chain 'R' and resid 280 through 291 removed outlier: 4.243A pdb=" N LEU R 286 " --> pdb=" O TRP R 282 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 299 Processing helix chain 'R' and resid 302 through 312 removed outlier: 4.065A pdb=" N LEU R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.874A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.544A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.757A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.679A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.520A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.586A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.544A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 296 through 297 removed outlier: 6.865A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.868A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.790A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU S 174 " --> pdb=" O ILE S 189 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE S 189 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TRP S 176 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU S 187 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU S 178 " --> pdb=" O PRO S 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 155 through 160 419 hydrogen bonds defined for protein. 1170 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: 1.25 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1453 1.29 - 1.42: 2419 1.42 - 1.56: 5210 1.56 - 1.69: 1 1.69 - 1.82: 99 Bond restraints: 9182 Sorted by residual: bond pdb=" CA CYS R 127 " pdb=" C CYS R 127 " ideal model delta sigma weight residual 1.522 1.421 0.101 1.31e-02 5.83e+03 5.92e+01 bond pdb=" C SER R 125 " pdb=" O SER R 125 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.17e-02 7.31e+03 4.24e+01 bond pdb=" C LEU R 122 " pdb=" O LEU R 122 " ideal model delta sigma weight residual 1.237 1.165 0.071 1.17e-02 7.31e+03 3.71e+01 bond pdb=" C CYS R 127 " pdb=" O CYS R 127 " ideal model delta sigma weight residual 1.236 1.160 0.075 1.39e-02 5.18e+03 2.95e+01 bond pdb=" CA LEU R 122 " pdb=" C LEU R 122 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.30e-02 5.92e+03 2.16e+01 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 12396 5.41 - 10.82: 19 10.82 - 16.23: 3 16.23 - 21.64: 2 21.64 - 27.05: 2 Bond angle restraints: 12422 Sorted by residual: angle pdb=" N SER R 99 " pdb=" CA SER R 99 " pdb=" C SER R 99 " ideal model delta sigma weight residual 111.28 126.61 -15.33 1.09e+00 8.42e-01 1.98e+02 angle pdb=" N GLY R 100 " pdb=" CA GLY R 100 " pdb=" C GLY R 100 " ideal model delta sigma weight residual 112.50 124.66 -12.16 1.16e+00 7.43e-01 1.10e+02 angle pdb=" C16 J89 R 401 " pdb=" C17 J89 R 401 " pdb=" N26 J89 R 401 " ideal model delta sigma weight residual 112.73 85.68 27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" C16 J89 R 401 " pdb=" C17 J89 R 401 " pdb=" C18 J89 R 401 " ideal model delta sigma weight residual 111.94 87.00 24.94 3.00e+00 1.11e-01 6.91e+01 angle pdb=" C18 J89 R 401 " pdb=" C17 J89 R 401 " pdb=" N26 J89 R 401 " ideal model delta sigma weight residual 105.89 123.23 -17.34 3.00e+00 1.11e-01 3.34e+01 ... (remaining 12417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4893 17.52 - 35.04: 465 35.04 - 52.56: 94 52.56 - 70.08: 15 70.08 - 87.60: 10 Dihedral angle restraints: 5477 sinusoidal: 2145 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 178 " pdb=" SG CYS R 178 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual 93.00 39.19 53.81 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA CYS R 185 " pdb=" C CYS R 185 " pdb=" N SER R 186 " pdb=" CA SER R 186 " ideal model delta harmonic sigma weight residual 180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1375 0.112 - 0.223: 32 0.223 - 0.335: 1 0.335 - 0.446: 3 0.446 - 0.558: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA SER R 99 " pdb=" N SER R 99 " pdb=" C SER R 99 " pdb=" CB SER R 99 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CA LEU R 122 " pdb=" N LEU R 122 " pdb=" C LEU R 122 " pdb=" CB LEU R 122 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA CYS R 127 " pdb=" N CYS R 127 " pdb=" C CYS R 127 " pdb=" CB CYS R 127 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 1409 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 122 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C LEU R 122 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU R 122 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY R 123 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 97 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C LEU R 97 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU R 97 " 0.021 2.00e-02 2.50e+03 pdb=" N MET R 98 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 127 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C CYS R 127 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS R 127 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 128 " -0.014 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 641 2.74 - 3.28: 8714 3.28 - 3.82: 14379 3.82 - 4.36: 16804 4.36 - 4.90: 29985 Nonbonded interactions: 70523 Sorted by model distance: nonbonded pdb=" O LEU R 168 " pdb=" OH TYR R 196 " model vdw 2.201 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.216 3.040 nonbonded pdb=" NE2 GLN S 142 " pdb=" O ALA S 241 " model vdw 2.240 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.246 3.040 nonbonded pdb=" OG SER B 279 " pdb=" OD1 ASP C 48 " model vdw 2.270 3.040 ... (remaining 70518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9185 Z= 0.233 Angle : 0.798 27.053 12428 Z= 0.429 Chirality : 0.049 0.558 1412 Planarity : 0.004 0.039 1562 Dihedral : 14.278 87.601 3316 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.61 % Allowed : 0.20 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.25 (0.25), residues: 1133 helix: 1.94 (0.28), residues: 368 sheet: -0.90 (0.29), residues: 303 loop : -1.37 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 73 TYR 0.007 0.001 TYR S 228 PHE 0.017 0.001 PHE B 234 TRP 0.016 0.001 TRP S 47 HIS 0.003 0.001 HIS R 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.23 ( 9182) covalent geometry : angle 0.79800 / 0.43 (12422) SS BOND : bond 0.00506 / 0.30 ( 3) SS BOND : angle 1.10692 / 0.55 ( 6) hydrogen bonds : bond 0.14981 / 9.58 ( 410) hydrogen bonds : angle 6.02998 / 4.13 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: B 332 TRP cc_start: 0.6646 (m-10) cc_final: 0.6437 (m-10) REVERT: S 176 TRP cc_start: 0.6749 (m100) cc_final: 0.6457 (m100) REVERT: R 126 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7476 (m) REVERT: R 143 MET cc_start: 0.6990 (mmt) cc_final: 0.6729 (mmt) REVERT: R 202 SER cc_start: 0.7355 (t) cc_final: 0.7137 (m) REVERT: R 264 LEU cc_start: 0.6897 (pp) cc_final: 0.6441 (tt) REVERT: R 265 ILE cc_start: 0.6098 (tp) cc_final: 0.5755 (pt) outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.0692 time to fit residues: 14.4702 Evaluate side-chains 114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN S 231 GLN ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.200868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152943 restraints weight = 10482.935| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 4.11 r_work: 0.3599 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9185 Z= 0.146 Angle : 0.586 6.784 12428 Z= 0.306 Chirality : 0.043 0.167 1412 Planarity : 0.004 0.042 1562 Dihedral : 6.416 81.545 1271 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.23 % Allowed : 9.01 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.16 (0.25), residues: 1133 helix: 2.18 (0.28), residues: 368 sheet: -1.00 (0.27), residues: 309 loop : -1.34 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 72 TYR 0.012 0.001 TYR S 227 PHE 0.016 0.002 PHE B 234 TRP 0.015 0.002 TRP S 47 HIS 0.007 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9182) covalent geometry : angle 0.58535 / 0.31 (12422) SS BOND : bond 0.00295 / 0.18 ( 3) SS BOND : angle 1.33787 / 0.66 ( 6) hydrogen bonds : bond 0.04416 / 2.91 ( 410) hydrogen bonds : angle 4.56303 / 3.16 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.346 Fit side-chains REVERT: A 305 CYS cc_start: 0.7019 (t) cc_final: 0.5655 (p) REVERT: S 220 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6258 (mp0) REVERT: R 202 SER cc_start: 0.7148 (t) cc_final: 0.6902 (m) REVERT: R 264 LEU cc_start: 0.7453 (pp) cc_final: 0.6950 (tt) REVERT: R 265 ILE cc_start: 0.6306 (tp) cc_final: 0.5752 (pt) outliers start: 12 outliers final: 9 residues processed: 124 average time/residue: 0.0891 time to fit residues: 16.2863 Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 231 GLN R 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.200395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156750 restraints weight = 10523.703| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.75 r_work: 0.3593 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9185 Z= 0.107 Angle : 0.516 6.843 12428 Z= 0.270 Chirality : 0.041 0.136 1412 Planarity : 0.003 0.032 1562 Dihedral : 5.989 82.733 1265 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.02 % Allowed : 12.08 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.09 (0.25), residues: 1133 helix: 2.45 (0.28), residues: 369 sheet: -0.78 (0.28), residues: 307 loop : -1.34 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 114 TYR 0.020 0.001 TYR R 92 PHE 0.014 0.001 PHE S 177 TRP 0.017 0.001 TRP S 47 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9182) covalent geometry : angle 0.51502 / 0.27 (12422) SS BOND : bond 0.00303 / 0.18 ( 3) SS BOND : angle 1.22905 / 0.62 ( 6) hydrogen bonds : bond 0.03658 / 2.41 ( 410) hydrogen bonds : angle 4.24094 / 2.94 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.342 Fit side-chains REVERT: A 204 GLN cc_start: 0.6640 (tp-100) cc_final: 0.6075 (tp-100) REVERT: A 305 CYS cc_start: 0.7032 (t) cc_final: 0.5681 (p) REVERT: S 220 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6391 (mp0) REVERT: R 47 LEU cc_start: 0.6795 (mm) cc_final: 0.6466 (tp) REVERT: R 160 MET cc_start: 0.5317 (tpp) cc_final: 0.5104 (tpp) REVERT: R 202 SER cc_start: 0.7114 (t) cc_final: 0.6907 (m) REVERT: R 264 LEU cc_start: 0.7443 (pp) cc_final: 0.6939 (tt) REVERT: R 265 ILE cc_start: 0.6258 (tp) cc_final: 0.5705 (pt) REVERT: R 289 LEU cc_start: 0.6595 (mt) cc_final: 0.6379 (mt) outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 0.0867 time to fit residues: 15.6774 Evaluate side-chains 116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 163 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 11 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 39 GLN S 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.200174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.155917 restraints weight = 10696.188| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 4.19 r_work: 0.3570 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9185 Z= 0.107 Angle : 0.511 7.002 12428 Z= 0.267 Chirality : 0.041 0.136 1412 Planarity : 0.003 0.029 1562 Dihedral : 5.417 69.984 1265 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.84 % Allowed : 13.51 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.20 (0.25), residues: 1133 helix: 2.56 (0.27), residues: 369 sheet: -0.68 (0.28), residues: 307 loop : -1.32 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 114 TYR 0.016 0.001 TYR S 227 PHE 0.015 0.001 PHE S 177 TRP 0.023 0.001 TRP S 47 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9182) covalent geometry : angle 0.51102 / 0.27 (12422) SS BOND : bond 0.00229 / 0.14 ( 3) SS BOND : angle 1.08021 / 0.53 ( 6) hydrogen bonds : bond 0.03573 / 2.35 ( 410) hydrogen bonds : angle 4.12216 / 2.87 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.334 Fit side-chains REVERT: A 305 CYS cc_start: 0.7049 (t) cc_final: 0.5688 (p) REVERT: S 18 ARG cc_start: 0.6066 (mmm160) cc_final: 0.5778 (mmm160) REVERT: S 160 ARG cc_start: 0.5913 (tpp-160) cc_final: 0.5536 (tpt170) REVERT: R 47 LEU cc_start: 0.6827 (mm) cc_final: 0.6508 (tp) REVERT: R 74 MET cc_start: 0.7384 (mmm) cc_final: 0.7092 (mmm) REVERT: R 160 MET cc_start: 0.5322 (tpp) cc_final: 0.5096 (tpp) REVERT: R 202 SER cc_start: 0.7126 (t) cc_final: 0.6916 (m) REVERT: R 264 LEU cc_start: 0.7441 (pp) cc_final: 0.6939 (tt) REVERT: R 265 ILE cc_start: 0.6260 (tp) cc_final: 0.5709 (pt) outliers start: 18 outliers final: 16 residues processed: 123 average time/residue: 0.0886 time to fit residues: 15.7876 Evaluate side-chains 126 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.200808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158076 restraints weight = 10596.757| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.52 r_work: 0.3588 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9185 Z= 0.127 Angle : 0.535 8.501 12428 Z= 0.278 Chirality : 0.041 0.137 1412 Planarity : 0.003 0.030 1562 Dihedral : 5.389 69.582 1265 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.05 % Allowed : 14.23 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.21 (0.25), residues: 1133 helix: 2.54 (0.27), residues: 369 sheet: -0.67 (0.28), residues: 307 loop : -1.29 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 114 TYR 0.015 0.001 TYR S 227 PHE 0.014 0.001 PHE S 177 TRP 0.031 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9182) covalent geometry : angle 0.53464 / 0.28 (12422) SS BOND : bond 0.00171 / 0.09 ( 3) SS BOND : angle 1.16590 / 0.58 ( 6) hydrogen bonds : bond 0.03830 / 2.52 ( 410) hydrogen bonds : angle 4.14682 / 2.89 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.325 Fit side-chains REVERT: A 204 GLN cc_start: 0.6738 (tp-100) cc_final: 0.6269 (tp-100) REVERT: A 305 CYS cc_start: 0.7106 (t) cc_final: 0.5745 (p) REVERT: B 332 TRP cc_start: 0.7253 (m-10) cc_final: 0.6833 (m-10) REVERT: S 18 ARG cc_start: 0.6106 (mmm160) cc_final: 0.5779 (mmm160) REVERT: S 220 GLU cc_start: 0.6214 (mp0) cc_final: 0.5919 (mp0) REVERT: R 47 LEU cc_start: 0.6777 (mm) cc_final: 0.6433 (tp) REVERT: R 74 MET cc_start: 0.7564 (mmm) cc_final: 0.7198 (mmm) REVERT: R 160 MET cc_start: 0.5457 (tpp) cc_final: 0.5233 (tpp) REVERT: R 202 SER cc_start: 0.7139 (t) cc_final: 0.6901 (m) REVERT: R 264 LEU cc_start: 0.7413 (pp) cc_final: 0.6869 (tt) REVERT: R 265 ILE cc_start: 0.6309 (tp) cc_final: 0.5742 (pt) outliers start: 20 outliers final: 18 residues processed: 120 average time/residue: 0.0869 time to fit residues: 15.2323 Evaluate side-chains 128 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 66 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.202218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161195 restraints weight = 10634.890| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.64 r_work: 0.3617 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9185 Z= 0.101 Angle : 0.508 8.940 12428 Z= 0.264 Chirality : 0.040 0.132 1412 Planarity : 0.003 0.029 1562 Dihedral : 5.052 63.112 1265 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.84 % Allowed : 15.76 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.33 (0.25), residues: 1133 helix: 2.67 (0.27), residues: 369 sheet: -0.61 (0.28), residues: 307 loop : -1.25 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 114 TYR 0.019 0.001 TYR S 227 PHE 0.018 0.001 PHE S 177 TRP 0.027 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9182) covalent geometry : angle 0.50807 / 0.26 (12422) SS BOND : bond 0.00214 / 0.12 ( 3) SS BOND : angle 0.99992 / 0.50 ( 6) hydrogen bonds : bond 0.03428 / 2.27 ( 410) hydrogen bonds : angle 4.05615 / 2.82 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.342 Fit side-chains REVERT: A 204 GLN cc_start: 0.6608 (tp-100) cc_final: 0.6263 (tp40) REVERT: A 305 CYS cc_start: 0.7083 (t) cc_final: 0.5733 (p) REVERT: B 332 TRP cc_start: 0.7238 (m-10) cc_final: 0.6816 (m-10) REVERT: B 338 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7798 (mp) REVERT: S 18 ARG cc_start: 0.6071 (mmm160) cc_final: 0.5709 (mmm160) REVERT: R 47 LEU cc_start: 0.6743 (mm) cc_final: 0.6387 (tp) REVERT: R 160 MET cc_start: 0.5427 (tpp) cc_final: 0.5218 (tpp) REVERT: R 202 SER cc_start: 0.7093 (t) cc_final: 0.6880 (m) REVERT: R 264 LEU cc_start: 0.7426 (pp) cc_final: 0.6882 (tt) REVERT: R 265 ILE cc_start: 0.6351 (tp) cc_final: 0.5819 (pt) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.0837 time to fit residues: 14.8185 Evaluate side-chains 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 163 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.201635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160458 restraints weight = 10695.845| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.62 r_work: 0.3575 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9185 Z= 0.112 Angle : 0.525 9.014 12428 Z= 0.273 Chirality : 0.041 0.129 1412 Planarity : 0.003 0.029 1562 Dihedral : 4.936 60.324 1265 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.15 % Allowed : 15.66 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.33 (0.25), residues: 1133 helix: 2.69 (0.27), residues: 369 sheet: -0.60 (0.28), residues: 307 loop : -1.29 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 114 TYR 0.017 0.001 TYR S 227 PHE 0.017 0.001 PHE S 177 TRP 0.030 0.001 TRP S 47 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9182) covalent geometry : angle 0.52489 / 0.27 (12422) SS BOND : bond 0.00267 / 0.14 ( 3) SS BOND : angle 1.01213 / 0.50 ( 6) hydrogen bonds : bond 0.03577 / 2.37 ( 410) hydrogen bonds : angle 4.04958 / 2.82 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.282 Fit side-chains REVERT: A 204 GLN cc_start: 0.6619 (tp-100) cc_final: 0.6251 (tp40) REVERT: A 305 CYS cc_start: 0.7073 (t) cc_final: 0.5719 (p) REVERT: B 332 TRP cc_start: 0.7230 (m-10) cc_final: 0.6809 (m-10) REVERT: B 338 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7822 (mp) REVERT: R 47 LEU cc_start: 0.6801 (mm) cc_final: 0.6433 (tp) REVERT: R 74 MET cc_start: 0.7409 (mmm) cc_final: 0.7101 (mmm) REVERT: R 202 SER cc_start: 0.7098 (t) cc_final: 0.6880 (m) REVERT: R 264 LEU cc_start: 0.7416 (pp) cc_final: 0.6872 (tt) REVERT: R 265 ILE cc_start: 0.6345 (tp) cc_final: 0.5822 (pt) outliers start: 21 outliers final: 16 residues processed: 123 average time/residue: 0.0803 time to fit residues: 14.3151 Evaluate side-chains 125 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 246 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.202560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155742 restraints weight = 10533.547| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 4.12 r_work: 0.3616 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9185 Z= 0.099 Angle : 0.518 8.961 12428 Z= 0.265 Chirality : 0.040 0.134 1412 Planarity : 0.003 0.027 1562 Dihedral : 4.707 55.649 1265 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.43 % Allowed : 16.38 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.42 (0.26), residues: 1133 helix: 2.79 (0.27), residues: 369 sheet: -0.54 (0.28), residues: 309 loop : -1.27 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 67 TYR 0.015 0.001 TYR S 227 PHE 0.017 0.001 PHE S 177 TRP 0.026 0.001 TRP S 47 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 9182) covalent geometry : angle 0.51750 / 0.26 (12422) SS BOND : bond 0.00259 / 0.14 ( 3) SS BOND : angle 0.95622 / 0.49 ( 6) hydrogen bonds : bond 0.03340 / 2.21 ( 410) hydrogen bonds : angle 3.97630 / 2.78 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.345 Fit side-chains REVERT: A 305 CYS cc_start: 0.6919 (t) cc_final: 0.5553 (p) REVERT: B 332 TRP cc_start: 0.7237 (m-10) cc_final: 0.6782 (m-10) REVERT: B 338 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7780 (mp) REVERT: S 18 ARG cc_start: 0.6022 (mmm160) cc_final: 0.5717 (mmm160) REVERT: S 64 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7463 (t) REVERT: R 47 LEU cc_start: 0.6831 (mm) cc_final: 0.6481 (tp) REVERT: R 160 MET cc_start: 0.5951 (tpp) cc_final: 0.5645 (tpt) REVERT: R 202 SER cc_start: 0.6951 (t) cc_final: 0.6746 (m) REVERT: R 264 LEU cc_start: 0.7420 (pp) cc_final: 0.6901 (tt) REVERT: R 265 ILE cc_start: 0.6247 (tp) cc_final: 0.5729 (pt) REVERT: R 306 ARG cc_start: 0.4385 (ttp-170) cc_final: 0.4046 (mtm180) outliers start: 14 outliers final: 12 residues processed: 119 average time/residue: 0.0886 time to fit residues: 15.1452 Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 56 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.201499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157881 restraints weight = 10593.253| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.55 r_work: 0.3609 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9185 Z= 0.108 Angle : 0.525 8.018 12428 Z= 0.270 Chirality : 0.041 0.184 1412 Planarity : 0.003 0.028 1562 Dihedral : 4.640 53.878 1265 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.74 % Allowed : 16.79 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.44 (0.26), residues: 1133 helix: 2.81 (0.27), residues: 370 sheet: -0.50 (0.28), residues: 309 loop : -1.28 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 67 TYR 0.017 0.001 TYR S 227 PHE 0.015 0.001 PHE S 177 TRP 0.025 0.001 TRP S 47 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9182) covalent geometry : angle 0.52419 / 0.27 (12422) SS BOND : bond 0.00260 / 0.16 ( 3) SS BOND : angle 1.07393 / 0.52 ( 6) hydrogen bonds : bond 0.03499 / 2.32 ( 410) hydrogen bonds : angle 3.97508 / 2.77 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.328 Fit side-chains REVERT: A 204 GLN cc_start: 0.6647 (tp-100) cc_final: 0.6271 (tp-100) REVERT: A 305 CYS cc_start: 0.7013 (t) cc_final: 0.5666 (p) REVERT: B 332 TRP cc_start: 0.7217 (m-10) cc_final: 0.6768 (m-10) REVERT: B 338 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7817 (mp) REVERT: S 18 ARG cc_start: 0.6051 (mmm160) cc_final: 0.5738 (mmm160) REVERT: S 64 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7482 (t) REVERT: S 220 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6516 (mp0) REVERT: R 47 LEU cc_start: 0.6830 (mm) cc_final: 0.6454 (tp) REVERT: R 160 MET cc_start: 0.6085 (tpp) cc_final: 0.5782 (tpt) REVERT: R 202 SER cc_start: 0.7068 (t) cc_final: 0.6855 (m) REVERT: R 264 LEU cc_start: 0.7484 (pp) cc_final: 0.6964 (tt) REVERT: R 265 ILE cc_start: 0.6277 (tp) cc_final: 0.5784 (pt) REVERT: R 306 ARG cc_start: 0.4438 (ttp-170) cc_final: 0.4098 (mtm180) outliers start: 17 outliers final: 14 residues processed: 114 average time/residue: 0.0911 time to fit residues: 14.9760 Evaluate side-chains 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 56 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.201618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158405 restraints weight = 10565.138| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.40 r_work: 0.3610 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9185 Z= 0.106 Angle : 0.522 7.669 12428 Z= 0.269 Chirality : 0.041 0.132 1412 Planarity : 0.003 0.028 1562 Dihedral : 4.612 52.832 1265 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.74 % Allowed : 17.09 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.47 (0.26), residues: 1133 helix: 2.83 (0.27), residues: 370 sheet: -0.49 (0.28), residues: 309 loop : -1.26 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 67 TYR 0.024 0.001 TYR S 227 PHE 0.015 0.001 PHE S 177 TRP 0.025 0.001 TRP S 47 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9182) covalent geometry : angle 0.52166 / 0.27 (12422) SS BOND : bond 0.00229 / 0.14 ( 3) SS BOND : angle 1.02352 / 0.50 ( 6) hydrogen bonds : bond 0.03470 / 2.30 ( 410) hydrogen bonds : angle 3.95763 / 2.76 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.354 Fit side-chains REVERT: A 204 GLN cc_start: 0.6650 (tp-100) cc_final: 0.6269 (tp-100) REVERT: A 305 CYS cc_start: 0.7012 (t) cc_final: 0.5669 (p) REVERT: B 332 TRP cc_start: 0.7232 (m-10) cc_final: 0.6789 (m-10) REVERT: B 338 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7809 (mp) REVERT: S 18 ARG cc_start: 0.6059 (mmm160) cc_final: 0.5748 (mmm160) REVERT: S 64 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7506 (t) REVERT: S 220 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6453 (mp0) REVERT: R 47 LEU cc_start: 0.6827 (mm) cc_final: 0.6456 (tp) REVERT: R 160 MET cc_start: 0.6109 (tpp) cc_final: 0.5795 (tpt) REVERT: R 202 SER cc_start: 0.7079 (t) cc_final: 0.6865 (m) REVERT: R 264 LEU cc_start: 0.7480 (pp) cc_final: 0.6956 (tt) REVERT: R 265 ILE cc_start: 0.6282 (tp) cc_final: 0.5790 (pt) REVERT: R 306 ARG cc_start: 0.4445 (ttp-170) cc_final: 0.4100 (mtm180) outliers start: 17 outliers final: 15 residues processed: 115 average time/residue: 0.0915 time to fit residues: 15.1188 Evaluate side-chains 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 56 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.199183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152794 restraints weight = 10400.269| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.59 r_work: 0.3598 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9185 Z= 0.151 Angle : 0.576 9.251 12428 Z= 0.295 Chirality : 0.043 0.172 1412 Planarity : 0.004 0.030 1562 Dihedral : 4.906 56.912 1265 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.84 % Allowed : 17.09 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.33 (0.26), residues: 1133 helix: 2.69 (0.27), residues: 369 sheet: -0.58 (0.28), residues: 309 loop : -1.30 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 67 TYR 0.027 0.002 TYR S 227 PHE 0.014 0.001 PHE S 177 TRP 0.028 0.002 TRP S 47 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9182) covalent geometry : angle 0.57515 / 0.29 (12422) SS BOND : bond 0.00255 / 0.16 ( 3) SS BOND : angle 1.36608 / 0.65 ( 6) hydrogen bonds : bond 0.04076 / 2.69 ( 410) hydrogen bonds : angle 4.09365 / 2.85 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3494.04 seconds wall clock time: 60 minutes 24.57 seconds (3624.57 seconds total)