Starting phenix.real_space_refine on Tue Mar 3 20:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2h_25613/03_2026/7t2h_25613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2h_25613/03_2026/7t2h_25613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t2h_25613/03_2026/7t2h_25613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2h_25613/03_2026/7t2h_25613.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2h_25613/03_2026/7t2h_25613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2h_25613/03_2026/7t2h_25613.cif" } resolution = 3.2 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= -0.001 sd= 0.054 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 66 5.16 5 C 5537 2.51 5 N 1470 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 8677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1720 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2564 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2197 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'EID': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8677 At special positions: 0 Unit cell: (96.46, 118.72, 112.36, 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 66 16.00 O 1604 8.00 N 1470 7.00 C 5537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " 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: 0.54 Conformation dependent library (CDL) restraints added in 256.8 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 36.9% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.634A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.740A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.145A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.031A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.676A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.919A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.706A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'D' and resid 66 through 96 removed outlier: 4.266A pdb=" N THR D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'D' and resid 137 through 171 Processing helix chain 'D' and resid 171 through 179 removed outlier: 4.625A pdb=" N ASP D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 205 removed outlier: 4.101A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 224 through 227 removed outlier: 3.650A pdb=" N TYR D 227 " --> pdb=" O PRO D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.870A pdb=" N LEU D 232 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 260 Processing helix chain 'D' and resid 261 through 266 removed outlier: 6.715A pdb=" N MET D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 266 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 306 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 3.586A pdb=" N THR D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 340 through 344 removed outlier: 3.517A pdb=" N LYS D 344 " --> pdb=" O GLU D 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.840A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.664A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.986A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.599A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.433A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.510A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.606A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.156A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.700A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 147 removed outlier: 3.546A pdb=" N THR E 201 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 206 through 210 399 hydrogen bonds defined for protein. 1143 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: 1.45 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1396 1.31 - 1.44: 2442 1.44 - 1.57: 4920 1.57 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 8857 Sorted by residual: bond pdb=" C03 EID D 401 " pdb=" N05 EID D 401 " ideal model delta sigma weight residual 1.363 1.451 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C27 EID D 401 " pdb=" O29 EID D 401 " ideal model delta sigma weight residual 1.318 1.402 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C24 EID D 401 " pdb=" N15 EID D 401 " ideal model delta sigma weight residual 1.451 1.512 -0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" C12 EID D 401 " pdb=" C13 EID D 401 " ideal model delta sigma weight residual 1.539 1.483 0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" C24 EID D 401 " pdb=" C25 EID D 401 " ideal model delta sigma weight residual 1.534 1.573 -0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 8852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11831 1.72 - 3.45: 145 3.45 - 5.17: 24 5.17 - 6.89: 5 6.89 - 8.62: 2 Bond angle restraints: 12007 Sorted by residual: angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 121.76 -7.36 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N LEU D 121 " pdb=" CA LEU D 121 " pdb=" C LEU D 121 " ideal model delta sigma weight residual 109.81 114.24 -4.43 2.21e+00 2.05e-01 4.01e+00 angle pdb=" N ASN D 332 " pdb=" CA ASN D 332 " pdb=" C ASN D 332 " ideal model delta sigma weight residual 109.81 114.20 -4.39 2.21e+00 2.05e-01 3.95e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 123.14 -6.84 3.50e+00 8.16e-02 3.82e+00 ... (remaining 12002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4718 17.12 - 34.24: 447 34.24 - 51.36: 86 51.36 - 68.48: 18 68.48 - 85.60: 9 Dihedral angle restraints: 5278 sinusoidal: 2028 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " pdb=" OD1 ASP B 298 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA TYR B 111 " pdb=" C TYR B 111 " pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 828 0.030 - 0.059: 345 0.059 - 0.089: 125 0.089 - 0.118: 65 0.118 - 0.148: 12 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" C25 EID D 401 " pdb=" C12 EID D 401 " pdb=" C24 EID D 401 " pdb=" C26 EID D 401 " both_signs ideal model delta sigma weight residual False -2.60 -2.74 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1372 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 332 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 333 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 121 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 122 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 122 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 122 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 78 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C VAL D 78 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL D 78 " -0.008 2.00e-02 2.50e+03 pdb=" N CYS D 79 " -0.007 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 303 2.71 - 3.25: 8618 3.25 - 3.80: 13776 3.80 - 4.35: 17722 4.35 - 4.90: 31181 Nonbonded interactions: 71600 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.158 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.270 3.040 ... (remaining 71595 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: 1.050 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.220 Find NCS groups from input model: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 0.088 8861 Z= 0.174 Angle : 0.532 8.617 12015 Z= 0.290 Chirality : 0.041 0.148 1375 Planarity : 0.003 0.040 1512 Dihedral : 14.188 85.603 3168 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.65 % Allowed : 15.89 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.17 (0.23), residues: 1103 helix: -0.72 (0.25), residues: 377 sheet: -3.31 (0.24), residues: 270 loop : -2.38 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.013 0.001 TYR E 178 PHE 0.009 0.001 PHE B 199 TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8857) covalent geometry : angle 0.53230 (12007) SS BOND : bond 0.01008 ( 4) SS BOND : angle 0.48367 ( 8) hydrogen bonds : bond 0.18098 ( 399) hydrogen bonds : angle 7.81509 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8346 (mttt) cc_final: 0.8133 (mtmm) REVERT: A 18 MET cc_start: 0.7695 (ttm) cc_final: 0.7438 (ttt) REVERT: A 21 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6998 (ttm170) REVERT: A 247 MET cc_start: 0.7541 (mtp) cc_final: 0.7222 (mtp) REVERT: B 217 MET cc_start: 0.7787 (ptt) cc_final: 0.7240 (ptt) REVERT: B 234 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: C 42 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 87 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7218 (mtt180) REVERT: D 84 PHE cc_start: 0.6345 (t80) cc_final: 0.5865 (t80) REVERT: D 174 LYS cc_start: 0.7689 (mttt) cc_final: 0.7192 (mmtt) outliers start: 6 outliers final: 1 residues processed: 166 average time/residue: 0.1079 time to fit residues: 23.6540 Evaluate side-chains 133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 HIS A 306 GLN B 13 GLN B 17 GLN B 44 GLN B 110 ASN B 119 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN E 39 GLN E 82 GLN E 167 GLN E 171 GLN D 124 GLN D 328 ASN D 332 ASN D 342 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.157763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113759 restraints weight = 9846.997| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.38 r_work: 0.2935 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8861 Z= 0.134 Angle : 0.541 8.886 12015 Z= 0.285 Chirality : 0.042 0.152 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.559 65.176 1247 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 18.70 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.11 (0.24), residues: 1103 helix: 0.54 (0.27), residues: 373 sheet: -2.93 (0.24), residues: 294 loop : -1.87 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.021 0.001 TYR E 178 PHE 0.014 0.001 PHE E 68 TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8857) covalent geometry : angle 0.54125 (12007) SS BOND : bond 0.00747 ( 4) SS BOND : angle 0.77071 ( 8) hydrogen bonds : bond 0.03991 ( 399) hydrogen bonds : angle 5.47179 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8077 (mttt) cc_final: 0.7707 (mtmm) REVERT: A 18 MET cc_start: 0.8212 (ttm) cc_final: 0.7956 (ttt) REVERT: A 21 ARG cc_start: 0.7464 (ttp80) cc_final: 0.6570 (ttm170) REVERT: A 247 MET cc_start: 0.7949 (mtp) cc_final: 0.7577 (mtp) REVERT: B 37 ILE cc_start: 0.8220 (tt) cc_final: 0.7696 (pt) REVERT: B 214 ARG cc_start: 0.7549 (mmt180) cc_final: 0.7316 (mmt180) REVERT: B 215 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 234 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: B 303 ASP cc_start: 0.7529 (p0) cc_final: 0.7233 (m-30) REVERT: C 42 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7880 (tm-30) REVERT: E 82 GLN cc_start: 0.7738 (tp40) cc_final: 0.7453 (mm-40) REVERT: E 87 ARG cc_start: 0.6978 (mtt180) cc_final: 0.6775 (mtt-85) REVERT: E 211 ASP cc_start: 0.8497 (m-30) cc_final: 0.8273 (m-30) REVERT: D 84 PHE cc_start: 0.6717 (t80) cc_final: 0.6090 (t80) outliers start: 16 outliers final: 6 residues processed: 154 average time/residue: 0.0962 time to fit residues: 20.5000 Evaluate side-chains 131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN E 182 ASN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116371 restraints weight = 9679.240| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.41 r_work: 0.2949 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8861 Z= 0.124 Angle : 0.525 8.517 12015 Z= 0.274 Chirality : 0.042 0.146 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.279 58.312 1246 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.03 % Allowed : 19.35 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.55 (0.25), residues: 1103 helix: 1.04 (0.27), residues: 375 sheet: -2.60 (0.24), residues: 293 loop : -1.59 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.020 0.001 TYR E 178 PHE 0.010 0.001 PHE D 237 TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8857) covalent geometry : angle 0.52451 (12007) SS BOND : bond 0.00865 ( 4) SS BOND : angle 0.55210 ( 8) hydrogen bonds : bond 0.03701 ( 399) hydrogen bonds : angle 5.10298 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.288 Fit side-chains REVERT: A 10 LYS cc_start: 0.8061 (mttt) cc_final: 0.7692 (mtmm) REVERT: A 18 MET cc_start: 0.8219 (ttm) cc_final: 0.7962 (ttt) REVERT: A 21 ARG cc_start: 0.7455 (ttp80) cc_final: 0.6561 (ttm170) REVERT: A 247 MET cc_start: 0.7920 (mtp) cc_final: 0.7684 (mtp) REVERT: A 279 LYS cc_start: 0.8520 (mttt) cc_final: 0.8270 (mttp) REVERT: B 37 ILE cc_start: 0.8227 (tt) cc_final: 0.7703 (pt) REVERT: B 153 ASP cc_start: 0.8391 (p0) cc_final: 0.8160 (p0) REVERT: B 186 ASP cc_start: 0.8410 (p0) cc_final: 0.7997 (p0) REVERT: B 215 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: B 303 ASP cc_start: 0.7460 (p0) cc_final: 0.7240 (m-30) REVERT: C 42 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7846 (tm-30) REVERT: D 84 PHE cc_start: 0.6630 (t80) cc_final: 0.6113 (t80) outliers start: 28 outliers final: 15 residues processed: 155 average time/residue: 0.0953 time to fit residues: 20.3115 Evaluate side-chains 140 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 171 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.155685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112530 restraints weight = 9997.101| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.43 r_work: 0.2912 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8861 Z= 0.196 Angle : 0.582 10.302 12015 Z= 0.301 Chirality : 0.044 0.156 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.388 59.108 1246 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.35 % Allowed : 20.11 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.44 (0.25), residues: 1103 helix: 1.13 (0.27), residues: 375 sheet: -2.53 (0.25), residues: 295 loop : -1.53 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.022 0.002 TYR E 178 PHE 0.022 0.002 PHE A 274 TRP 0.007 0.001 TRP E 47 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8857) covalent geometry : angle 0.58152 (12007) SS BOND : bond 0.01224 ( 4) SS BOND : angle 0.97072 ( 8) hydrogen bonds : bond 0.03840 ( 399) hydrogen bonds : angle 5.09964 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8161 (mttt) cc_final: 0.7785 (mtmm) REVERT: A 18 MET cc_start: 0.8302 (ttm) cc_final: 0.8016 (ttt) REVERT: A 21 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6607 (ttm170) REVERT: A 247 MET cc_start: 0.7834 (mtp) cc_final: 0.7601 (mtp) REVERT: A 279 LYS cc_start: 0.8561 (mttt) cc_final: 0.8281 (mttt) REVERT: B 37 ILE cc_start: 0.8238 (tt) cc_final: 0.7765 (pt) REVERT: B 186 ASP cc_start: 0.8487 (p0) cc_final: 0.8035 (p0) REVERT: B 217 MET cc_start: 0.8607 (ptt) cc_final: 0.8240 (ppp) REVERT: B 219 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7711 (ttm170) REVERT: B 234 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: B 303 ASP cc_start: 0.7534 (p0) cc_final: 0.7275 (m-30) REVERT: C 42 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 84 PHE cc_start: 0.6659 (t80) cc_final: 0.6153 (t80) REVERT: D 194 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (tp) outliers start: 31 outliers final: 22 residues processed: 147 average time/residue: 0.1057 time to fit residues: 20.9521 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN E 171 GLN D 109 ASN D 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115087 restraints weight = 9760.547| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.44 r_work: 0.2952 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8861 Z= 0.111 Angle : 0.521 8.475 12015 Z= 0.271 Chirality : 0.041 0.144 1375 Planarity : 0.003 0.029 1512 Dihedral : 5.065 59.155 1246 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.35 % Allowed : 20.11 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.11 (0.25), residues: 1103 helix: 1.34 (0.27), residues: 376 sheet: -2.30 (0.26), residues: 294 loop : -1.33 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.021 0.001 TYR E 178 PHE 0.018 0.001 PHE A 274 TRP 0.008 0.001 TRP B 169 HIS 0.002 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8857) covalent geometry : angle 0.52121 (12007) SS BOND : bond 0.00776 ( 4) SS BOND : angle 0.72345 ( 8) hydrogen bonds : bond 0.03554 ( 399) hydrogen bonds : angle 4.89621 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.269 Fit side-chains REVERT: A 10 LYS cc_start: 0.8087 (mttt) cc_final: 0.7726 (mtmm) REVERT: A 18 MET cc_start: 0.8255 (ttm) cc_final: 0.8006 (ttt) REVERT: A 21 ARG cc_start: 0.7481 (ttp80) cc_final: 0.6584 (ttm170) REVERT: A 247 MET cc_start: 0.7872 (mtp) cc_final: 0.7610 (mtp) REVERT: A 279 LYS cc_start: 0.8550 (mttt) cc_final: 0.8309 (mttt) REVERT: B 37 ILE cc_start: 0.8168 (tt) cc_final: 0.7570 (pt) REVERT: B 186 ASP cc_start: 0.8423 (p0) cc_final: 0.7977 (p0) REVERT: B 217 MET cc_start: 0.8479 (ptt) cc_final: 0.8198 (ppp) REVERT: B 219 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7730 (ttm170) REVERT: B 234 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: C 42 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 19 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7450 (tttp) REVERT: D 84 PHE cc_start: 0.6675 (t80) cc_final: 0.6190 (t80) REVERT: D 194 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8259 (tp) REVERT: D 243 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7227 (tmm) outliers start: 31 outliers final: 21 residues processed: 158 average time/residue: 0.0950 time to fit residues: 20.4271 Evaluate side-chains 152 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN D 86 ASN D 124 GLN D 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123658 restraints weight = 9524.098| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.36 r_work: 0.2936 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8861 Z= 0.147 Angle : 0.546 10.098 12015 Z= 0.282 Chirality : 0.042 0.152 1375 Planarity : 0.003 0.028 1512 Dihedral : 5.045 59.613 1246 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.14 % Allowed : 21.51 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.02 (0.25), residues: 1103 helix: 1.40 (0.27), residues: 377 sheet: -2.22 (0.26), residues: 294 loop : -1.28 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.020 0.001 TYR E 178 PHE 0.016 0.001 PHE A 274 TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8857) covalent geometry : angle 0.54603 (12007) SS BOND : bond 0.01023 ( 4) SS BOND : angle 0.84319 ( 8) hydrogen bonds : bond 0.03618 ( 399) hydrogen bonds : angle 4.89244 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.319 Fit side-chains REVERT: A 10 LYS cc_start: 0.8074 (mttt) cc_final: 0.7698 (mtmm) REVERT: A 18 MET cc_start: 0.8218 (ttm) cc_final: 0.7949 (ttt) REVERT: A 21 ARG cc_start: 0.7457 (ttp80) cc_final: 0.6534 (ttm170) REVERT: A 25 GLU cc_start: 0.7925 (tt0) cc_final: 0.7333 (mt-10) REVERT: A 247 MET cc_start: 0.7748 (mtp) cc_final: 0.7499 (mtp) REVERT: A 275 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 279 LYS cc_start: 0.8522 (mttt) cc_final: 0.8269 (mttt) REVERT: B 37 ILE cc_start: 0.8140 (tt) cc_final: 0.7499 (pt) REVERT: B 186 ASP cc_start: 0.8434 (p0) cc_final: 0.7968 (p0) REVERT: B 215 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 217 MET cc_start: 0.8517 (ptt) cc_final: 0.8171 (ppp) REVERT: B 219 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7749 (ttm170) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: C 42 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 19 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7369 (tttp) REVERT: D 84 PHE cc_start: 0.6629 (t80) cc_final: 0.6184 (t80) REVERT: D 194 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8076 (tp) REVERT: D 243 MET cc_start: 0.7527 (ttm) cc_final: 0.7211 (tmm) outliers start: 29 outliers final: 20 residues processed: 154 average time/residue: 0.1012 time to fit residues: 21.2084 Evaluate side-chains 152 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN E 171 GLN D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125724 restraints weight = 9548.632| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.35 r_work: 0.2939 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8861 Z= 0.136 Angle : 0.532 9.259 12015 Z= 0.276 Chirality : 0.042 0.150 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.981 59.824 1246 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.57 % Allowed : 20.97 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.90 (0.25), residues: 1103 helix: 1.46 (0.27), residues: 377 sheet: -2.11 (0.26), residues: 292 loop : -1.23 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.020 0.001 TYR E 178 PHE 0.017 0.001 PHE E 68 TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8857) covalent geometry : angle 0.53140 (12007) SS BOND : bond 0.00839 ( 4) SS BOND : angle 0.85293 ( 8) hydrogen bonds : bond 0.03525 ( 399) hydrogen bonds : angle 4.86407 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.262 Fit side-chains REVERT: A 10 LYS cc_start: 0.8137 (mttt) cc_final: 0.7771 (mtmm) REVERT: A 18 MET cc_start: 0.8236 (ttm) cc_final: 0.7971 (ttt) REVERT: A 21 ARG cc_start: 0.7521 (ttp80) cc_final: 0.6604 (ttm170) REVERT: A 247 MET cc_start: 0.7773 (mtp) cc_final: 0.7522 (mtp) REVERT: A 275 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 279 LYS cc_start: 0.8413 (mttt) cc_final: 0.8164 (mttt) REVERT: B 37 ILE cc_start: 0.8167 (tt) cc_final: 0.7791 (pt) REVERT: B 186 ASP cc_start: 0.8449 (p0) cc_final: 0.8005 (p0) REVERT: B 197 ARG cc_start: 0.8030 (mmp80) cc_final: 0.7791 (mmp80) REVERT: B 212 ASP cc_start: 0.8232 (m-30) cc_final: 0.8029 (m-30) REVERT: B 215 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 217 MET cc_start: 0.8554 (ptt) cc_final: 0.8251 (ppp) REVERT: B 219 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7790 (ttm170) REVERT: B 234 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: C 21 MET cc_start: 0.7916 (ttp) cc_final: 0.7562 (ttt) REVERT: C 42 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7824 (tm-30) REVERT: D 84 PHE cc_start: 0.6627 (t80) cc_final: 0.6202 (t80) REVERT: D 194 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8137 (tp) REVERT: D 243 MET cc_start: 0.7556 (ttm) cc_final: 0.7262 (tmm) outliers start: 33 outliers final: 20 residues processed: 155 average time/residue: 0.0991 time to fit residues: 20.8530 Evaluate side-chains 154 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126394 restraints weight = 9464.271| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.31 r_work: 0.2960 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8861 Z= 0.120 Angle : 0.525 8.851 12015 Z= 0.272 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.030 1512 Dihedral : 4.871 59.999 1246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.03 % Allowed : 21.51 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.77 (0.25), residues: 1103 helix: 1.53 (0.27), residues: 377 sheet: -1.98 (0.26), residues: 292 loop : -1.16 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.020 0.001 TYR E 178 PHE 0.014 0.001 PHE A 274 TRP 0.007 0.001 TRP B 63 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8857) covalent geometry : angle 0.52439 (12007) SS BOND : bond 0.00864 ( 4) SS BOND : angle 0.74024 ( 8) hydrogen bonds : bond 0.03441 ( 399) hydrogen bonds : angle 4.82268 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.348 Fit side-chains REVERT: A 10 LYS cc_start: 0.8132 (mttt) cc_final: 0.7782 (mtmm) REVERT: A 18 MET cc_start: 0.8284 (ttm) cc_final: 0.8030 (ttt) REVERT: A 21 ARG cc_start: 0.7493 (ttp80) cc_final: 0.6591 (ttm170) REVERT: A 25 GLU cc_start: 0.7885 (tt0) cc_final: 0.7303 (mt-10) REVERT: A 247 MET cc_start: 0.7783 (mtp) cc_final: 0.7532 (mtp) REVERT: A 275 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 279 LYS cc_start: 0.8449 (mttt) cc_final: 0.8191 (mttt) REVERT: B 37 ILE cc_start: 0.8139 (tt) cc_final: 0.7757 (pt) REVERT: B 186 ASP cc_start: 0.8409 (p0) cc_final: 0.7949 (p0) REVERT: B 212 ASP cc_start: 0.8247 (m-30) cc_final: 0.8034 (m-30) REVERT: B 215 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 217 MET cc_start: 0.8551 (ptt) cc_final: 0.8272 (ppp) REVERT: B 219 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7840 (ttm170) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: C 21 MET cc_start: 0.7778 (ttp) cc_final: 0.7568 (ttt) REVERT: C 42 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 84 PHE cc_start: 0.6629 (t80) cc_final: 0.6212 (t80) REVERT: D 194 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 243 MET cc_start: 0.7524 (ttm) cc_final: 0.7296 (tmm) REVERT: D 281 MET cc_start: 0.7700 (tpt) cc_final: 0.7497 (tpt) outliers start: 28 outliers final: 20 residues processed: 157 average time/residue: 0.0958 time to fit residues: 20.6639 Evaluate side-chains 155 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.170970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127238 restraints weight = 9393.856| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.32 r_work: 0.2967 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8861 Z= 0.122 Angle : 0.542 10.415 12015 Z= 0.277 Chirality : 0.042 0.149 1375 Planarity : 0.003 0.030 1512 Dihedral : 4.819 59.895 1246 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.81 % Allowed : 21.95 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.74 (0.25), residues: 1103 helix: 1.50 (0.27), residues: 378 sheet: -1.89 (0.26), residues: 292 loop : -1.15 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.020 0.001 TYR E 178 PHE 0.013 0.001 PHE A 274 TRP 0.007 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8857) covalent geometry : angle 0.54163 (12007) SS BOND : bond 0.00870 ( 4) SS BOND : angle 0.72470 ( 8) hydrogen bonds : bond 0.03512 ( 399) hydrogen bonds : angle 4.84546 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.346 Fit side-chains REVERT: A 10 LYS cc_start: 0.8111 (mttt) cc_final: 0.7767 (mtmm) REVERT: A 18 MET cc_start: 0.8275 (ttm) cc_final: 0.8010 (ttt) REVERT: A 21 ARG cc_start: 0.7519 (ttp80) cc_final: 0.6611 (ttm170) REVERT: A 25 GLU cc_start: 0.7861 (tt0) cc_final: 0.7296 (mt-10) REVERT: A 247 MET cc_start: 0.7792 (mtp) cc_final: 0.7545 (mtp) REVERT: B 37 ILE cc_start: 0.8123 (tt) cc_final: 0.7737 (pt) REVERT: B 186 ASP cc_start: 0.8408 (p0) cc_final: 0.7940 (p0) REVERT: B 197 ARG cc_start: 0.7991 (mmp80) cc_final: 0.7760 (mmp80) REVERT: B 212 ASP cc_start: 0.8250 (m-30) cc_final: 0.8030 (m-30) REVERT: B 215 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 217 MET cc_start: 0.8572 (ptt) cc_final: 0.8282 (ppp) REVERT: B 219 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7845 (ttm170) REVERT: B 234 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: C 21 MET cc_start: 0.7779 (ttp) cc_final: 0.7577 (ttt) REVERT: C 42 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 84 PHE cc_start: 0.6624 (t80) cc_final: 0.6209 (t80) REVERT: D 194 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8115 (tp) REVERT: D 243 MET cc_start: 0.7591 (ttm) cc_final: 0.7331 (tmm) REVERT: D 281 MET cc_start: 0.7639 (tpt) cc_final: 0.7432 (tpt) REVERT: D 343 PHE cc_start: 0.7082 (t80) cc_final: 0.6720 (t80) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.0965 time to fit residues: 20.6388 Evaluate side-chains 155 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.170057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126325 restraints weight = 9533.918| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.31 r_work: 0.2966 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8861 Z= 0.127 Angle : 0.555 10.658 12015 Z= 0.283 Chirality : 0.042 0.150 1375 Planarity : 0.003 0.030 1512 Dihedral : 4.795 59.584 1246 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.70 % Allowed : 22.49 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.71 (0.25), residues: 1103 helix: 1.46 (0.28), residues: 378 sheet: -1.82 (0.27), residues: 292 loop : -1.12 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.020 0.001 TYR E 178 PHE 0.013 0.001 PHE A 274 TRP 0.007 0.001 TRP B 63 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8857) covalent geometry : angle 0.55438 (12007) SS BOND : bond 0.00900 ( 4) SS BOND : angle 0.70991 ( 8) hydrogen bonds : bond 0.03492 ( 399) hydrogen bonds : angle 4.81575 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.313 Fit side-chains REVERT: A 10 LYS cc_start: 0.8107 (mttt) cc_final: 0.7778 (mtmm) REVERT: A 18 MET cc_start: 0.8270 (ttm) cc_final: 0.8006 (ttt) REVERT: A 21 ARG cc_start: 0.7519 (ttp80) cc_final: 0.6608 (ttm170) REVERT: A 25 GLU cc_start: 0.7859 (tt0) cc_final: 0.7297 (mt-10) REVERT: A 188 HIS cc_start: 0.6942 (t70) cc_final: 0.6658 (t-90) REVERT: A 247 MET cc_start: 0.7795 (mtp) cc_final: 0.7546 (mtp) REVERT: B 37 ILE cc_start: 0.8116 (tt) cc_final: 0.7730 (pt) REVERT: B 186 ASP cc_start: 0.8414 (p0) cc_final: 0.7956 (p0) REVERT: B 197 ARG cc_start: 0.7995 (mmp80) cc_final: 0.7780 (mmp80) REVERT: B 212 ASP cc_start: 0.8248 (m-30) cc_final: 0.8018 (m-30) REVERT: B 215 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 217 MET cc_start: 0.8580 (ptt) cc_final: 0.8275 (ppp) REVERT: B 219 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7846 (ttm170) REVERT: B 234 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: C 21 MET cc_start: 0.7777 (ttp) cc_final: 0.7564 (ttt) REVERT: C 42 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 180 MET cc_start: 0.8493 (ptt) cc_final: 0.8017 (ptt) REVERT: D 84 PHE cc_start: 0.6563 (t80) cc_final: 0.6150 (t80) REVERT: D 194 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8122 (tp) REVERT: D 243 MET cc_start: 0.7585 (ttm) cc_final: 0.7331 (tmm) REVERT: D 343 PHE cc_start: 0.7125 (t80) cc_final: 0.6853 (t80) outliers start: 25 outliers final: 21 residues processed: 154 average time/residue: 0.0938 time to fit residues: 19.9427 Evaluate side-chains 156 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.156763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114743 restraints weight = 9814.422| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.20 r_work: 0.3167 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8861 Z= 0.164 Angle : 0.582 11.687 12015 Z= 0.298 Chirality : 0.043 0.155 1375 Planarity : 0.003 0.030 1512 Dihedral : 4.949 59.954 1246 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.70 % Allowed : 22.92 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.80 (0.25), residues: 1103 helix: 1.36 (0.28), residues: 377 sheet: -1.87 (0.27), residues: 293 loop : -1.14 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 345 TYR 0.026 0.001 TYR A 296 PHE 0.014 0.001 PHE A 274 TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8857) covalent geometry : angle 0.58155 (12007) SS BOND : bond 0.01092 ( 4) SS BOND : angle 0.83207 ( 8) hydrogen bonds : bond 0.03608 ( 399) hydrogen bonds : angle 4.87505 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.13 seconds wall clock time: 44 minutes 35.11 seconds (2675.11 seconds total)