Starting phenix.real_space_refine on Wed Mar 4 10:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osi_13052/03_2026/7osi_13052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osi_13052/03_2026/7osi_13052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7osi_13052/03_2026/7osi_13052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osi_13052/03_2026/7osi_13052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7osi_13052/03_2026/7osi_13052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osi_13052/03_2026/7osi_13052.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8200 2.51 5 N 2249 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 12826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1092 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11839 SG CYS H 45 45.497 43.363 48.339 1.00124.97 S ATOM 11862 SG CYS H 48 43.467 44.396 45.986 1.00123.33 S ATOM 12043 SG CYS H 72 46.344 45.442 44.473 1.00127.30 S Time building chain proxies: 2.82, per 1000 atoms: 0.22 Number of scatterers: 12826 At special positions: 0 Unit cell: (81.648, 92.016, 191.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2329 8.00 N 2249 7.00 C 8200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.66 Conformation dependent library (CDL) restraints added in 436.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.283A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.702A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.608A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.607A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.608A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.774A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.560A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.234A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 236 through 244 removed outlier: 4.250A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.954A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.552A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.642A pdb=" N ARG C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 106 through 111 removed outlier: 4.489A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 111' Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.719A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.896A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.864A pdb=" N TRP C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.775A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.680A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.016A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.544A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.594A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.678A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.112A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 168 removed outlier: 4.496A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.813A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.549A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.505A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.679A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.546A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.678A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.547A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 4.034A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.575A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.684A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.781A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.619A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.541A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.652A pdb=" N LEU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 removed outlier: 4.072A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.095A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.772A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.647A pdb=" N GLY H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.679A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.072A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.746A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.948A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 333 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS A 311 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.574A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.332A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 25 removed outlier: 5.831A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 25 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.475A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.654A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.530A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.591A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.939A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 225 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.553A pdb=" N VAL H 121 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG H 152 " --> pdb=" O VAL H 121 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1449 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: 1.95 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4104 1.34 - 1.45: 2233 1.45 - 1.57: 6650 1.57 - 1.69: 3 1.69 - 1.81: 77 Bond restraints: 13067 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.590 -0.065 2.10e-02 2.27e+03 9.44e+00 bond pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.12e+00 bond pdb=" CG LEU A 173 " pdb=" CD1 LEU A 173 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.76e+00 bond pdb=" CB VAL A 336 " pdb=" CG1 VAL A 336 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.58e+00 bond pdb=" CB TYR A 291 " pdb=" CG TYR A 291 " ideal model delta sigma weight residual 1.512 1.464 0.048 2.20e-02 2.07e+03 4.70e+00 ... (remaining 13062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 17267 3.27 - 6.54: 394 6.54 - 9.81: 54 9.81 - 13.08: 10 13.08 - 16.35: 1 Bond angle restraints: 17726 Sorted by residual: angle pdb=" C SER C 231 " pdb=" N GLU C 232 " pdb=" CA GLU C 232 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C LYS C 47 " pdb=" N LEU C 48 " pdb=" CA LEU C 48 " ideal model delta sigma weight residual 120.38 128.38 -8.00 1.37e+00 5.33e-01 3.41e+01 angle pdb=" CA THR A 226 " pdb=" CB THR A 226 " pdb=" CG2 THR A 226 " ideal model delta sigma weight residual 110.50 119.20 -8.70 1.70e+00 3.46e-01 2.62e+01 angle pdb=" N THR A 226 " pdb=" CA THR A 226 " pdb=" CB THR A 226 " ideal model delta sigma weight residual 110.57 118.99 -8.42 1.69e+00 3.50e-01 2.48e+01 angle pdb=" N GLY C 229 " pdb=" CA GLY C 229 " pdb=" C GLY C 229 " ideal model delta sigma weight residual 113.18 101.63 11.55 2.37e+00 1.78e-01 2.38e+01 ... (remaining 17721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.82: 7131 20.82 - 41.64: 526 41.64 - 62.47: 64 62.47 - 83.29: 12 83.29 - 104.11: 3 Dihedral angle restraints: 7736 sinusoidal: 3041 harmonic: 4695 Sorted by residual: dihedral pdb=" CA GLY C 229 " pdb=" C GLY C 229 " pdb=" N ILE C 230 " pdb=" CA ILE C 230 " ideal model delta harmonic sigma weight residual -180.00 -75.89 -104.11 0 5.00e+00 4.00e-02 4.34e+02 dihedral pdb=" CA GLU C 232 " pdb=" C GLU C 232 " pdb=" N ARG C 233 " pdb=" CA ARG C 233 " ideal model delta harmonic sigma weight residual -180.00 -109.11 -70.89 0 5.00e+00 4.00e-02 2.01e+02 dihedral pdb=" CA GLU B 305 " pdb=" C GLU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 149.59 30.41 0 5.00e+00 4.00e-02 3.70e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1744 0.090 - 0.179: 245 0.179 - 0.269: 35 0.269 - 0.359: 5 0.359 - 0.449: 1 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CB VAL B 260 " pdb=" CA VAL B 260 " pdb=" CG1 VAL B 260 " pdb=" CG2 VAL B 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP A 182 " pdb=" N ASP A 182 " pdb=" C ASP A 182 " pdb=" CB ASP A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2027 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.065 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO E 210 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 282 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ILE B 282 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE B 282 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS B 283 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 298 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA B 298 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA B 298 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY B 299 " -0.020 2.00e-02 2.50e+03 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 115 2.54 - 3.13: 8963 3.13 - 3.72: 20094 3.72 - 4.31: 28466 4.31 - 4.90: 46811 Nonbonded interactions: 104449 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.948 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 1.978 2.320 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.135 2.170 nonbonded pdb=" O LEU A 365 " pdb="MG MG A 501 " model vdw 2.152 2.170 nonbonded pdb=" SD MET A 231 " pdb="CU CU A 502 " model vdw 2.186 2.600 ... (remaining 104444 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 13070 Z= 0.427 Angle : 1.211 16.346 17726 Z= 0.647 Chirality : 0.068 0.449 2030 Planarity : 0.008 0.097 2276 Dihedral : 14.632 104.111 4740 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 1.12 % Allowed : 9.38 % Favored : 89.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.48 (0.15), residues: 1645 helix: -4.33 (0.09), residues: 695 sheet: -3.13 (0.30), residues: 200 loop : -2.93 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 177 TYR 0.028 0.003 TYR A 204 PHE 0.031 0.003 PHE B 35 TRP 0.050 0.003 TRP C 236 HIS 0.020 0.003 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00956 (13067) covalent geometry : angle 1.21117 (17726) hydrogen bonds : bond 0.30127 ( 516) hydrogen bonds : angle 10.70386 ( 1449) metal coordination : bond 0.04124 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 235 LYS cc_start: 0.9215 (tptt) cc_final: 0.8898 (mmmm) REVERT: A 420 MET cc_start: 0.9114 (mmm) cc_final: 0.8504 (mmt) REVERT: B 200 ILE cc_start: 0.9626 (mt) cc_final: 0.9360 (tt) REVERT: B 242 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6347 (p0) REVERT: B 248 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7876 (ttm-80) REVERT: C 133 MET cc_start: 0.8753 (mtm) cc_final: 0.8534 (mtm) REVERT: D 10 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8548 (ttpp) REVERT: D 219 ASP cc_start: 0.8742 (m-30) cc_final: 0.8158 (m-30) REVERT: E 88 MET cc_start: 0.8400 (mmt) cc_final: 0.8156 (tpp) REVERT: H 52 ILE cc_start: 0.9522 (mt) cc_final: 0.9306 (mm) REVERT: H 64 GLU cc_start: 0.7641 (tt0) cc_final: 0.7275 (tm-30) REVERT: H 87 ARG cc_start: 0.9088 (mmm160) cc_final: 0.8401 (mmm160) outliers start: 15 outliers final: 6 residues processed: 150 average time/residue: 0.1594 time to fit residues: 31.8355 Evaluate side-chains 85 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 123 ASN A 141 GLN A 145 ASN A 160 ASN A 174 HIS A 175 ASN A 179 ASN A 212 ASN A 241 ASN A 301 ASN A 324 ASN A 417 HIS B 11 GLN B 20 HIS B 37 HIS B 176 GLN B 261 ASN C 176 GLN C 194 HIS D 225 ASN E 225 ASN H 40 HIS H 96 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043891 restraints weight = 60782.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045341 restraints weight = 30506.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046296 restraints weight = 19405.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.046944 restraints weight = 14275.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047320 restraints weight = 11499.803| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13070 Z= 0.124 Angle : 0.632 9.675 17726 Z= 0.325 Chirality : 0.042 0.149 2030 Planarity : 0.005 0.060 2276 Dihedral : 5.634 54.815 1815 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.56 % Allowed : 12.14 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.56 (0.17), residues: 1645 helix: -1.93 (0.15), residues: 724 sheet: -2.94 (0.29), residues: 232 loop : -2.46 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 233 TYR 0.017 0.001 TYR B 86 PHE 0.013 0.001 PHE A 303 TRP 0.011 0.001 TRP B 236 HIS 0.005 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00268 (13067) covalent geometry : angle 0.63202 (17726) hydrogen bonds : bond 0.03819 ( 516) hydrogen bonds : angle 5.04728 ( 1449) metal coordination : bond 0.00388 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8727 (mtm) cc_final: 0.8203 (mpp) REVERT: A 125 MET cc_start: 0.8503 (mpp) cc_final: 0.7945 (mpp) REVERT: A 226 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (p) REVERT: A 334 LYS cc_start: 0.9204 (tttt) cc_final: 0.8913 (tttp) REVERT: A 420 MET cc_start: 0.8800 (mmm) cc_final: 0.8563 (mmt) REVERT: B 261 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6602 (p0) REVERT: C 13 TYR cc_start: 0.7742 (p90) cc_final: 0.7464 (p90) REVERT: D 219 ASP cc_start: 0.8583 (m-30) cc_final: 0.8217 (m-30) REVERT: E 187 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9099 (pp) REVERT: H 87 ARG cc_start: 0.8856 (mmm160) cc_final: 0.8349 (mmm160) REVERT: H 141 ASP cc_start: 0.8521 (p0) cc_final: 0.7841 (p0) outliers start: 21 outliers final: 7 residues processed: 107 average time/residue: 0.1235 time to fit residues: 19.1161 Evaluate side-chains 74 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 157 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.055406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044214 restraints weight = 60730.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045707 restraints weight = 29833.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046679 restraints weight = 18772.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.047292 restraints weight = 13687.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047737 restraints weight = 11110.107| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13070 Z= 0.111 Angle : 0.580 8.416 17726 Z= 0.294 Chirality : 0.041 0.173 2030 Planarity : 0.004 0.051 2276 Dihedral : 4.873 31.147 1805 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.56 % Allowed : 13.85 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.30 (0.20), residues: 1645 helix: -0.41 (0.19), residues: 730 sheet: -2.73 (0.29), residues: 246 loop : -2.22 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 66 TYR 0.015 0.001 TYR B 86 PHE 0.011 0.001 PHE E 157 TRP 0.009 0.001 TRP B 236 HIS 0.006 0.001 HIS H 40 Details of bonding type rmsd covalent geometry : bond 0.00245 (13067) covalent geometry : angle 0.57960 (17726) hydrogen bonds : bond 0.03186 ( 516) hydrogen bonds : angle 4.39968 ( 1449) metal coordination : bond 0.00160 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8760 (mtm) cc_final: 0.8224 (mpp) REVERT: A 125 MET cc_start: 0.8843 (mpp) cc_final: 0.7697 (mpp) REVERT: A 193 HIS cc_start: 0.7865 (m90) cc_final: 0.7629 (m170) REVERT: A 334 LYS cc_start: 0.9219 (tttt) cc_final: 0.8925 (tttp) REVERT: C 13 TYR cc_start: 0.7773 (p90) cc_final: 0.7549 (p90) REVERT: C 268 LEU cc_start: 0.9234 (mt) cc_final: 0.8975 (tt) REVERT: D 147 MET cc_start: 0.8307 (mmm) cc_final: 0.8054 (mmt) REVERT: D 219 ASP cc_start: 0.8639 (m-30) cc_final: 0.8257 (m-30) REVERT: E 187 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9071 (pp) REVERT: H 70 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8818 (mtpt) REVERT: H 87 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8344 (mmm160) REVERT: H 140 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: H 141 ASP cc_start: 0.8319 (p0) cc_final: 0.7786 (p0) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 0.1237 time to fit residues: 17.3027 Evaluate side-chains 75 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 80 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041996 restraints weight = 61215.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043376 restraints weight = 31535.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044290 restraints weight = 20426.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044874 restraints weight = 15170.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045221 restraints weight = 12444.866| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13070 Z= 0.188 Angle : 0.621 8.159 17726 Z= 0.312 Chirality : 0.042 0.158 2030 Planarity : 0.004 0.051 2276 Dihedral : 4.766 34.714 1805 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.79 % Allowed : 14.97 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.21), residues: 1645 helix: 0.43 (0.20), residues: 728 sheet: -2.54 (0.31), residues: 228 loop : -1.96 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.012 0.001 TYR B 86 PHE 0.016 0.001 PHE D 157 TRP 0.011 0.001 TRP E 211 HIS 0.003 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00414 (13067) covalent geometry : angle 0.62074 (17726) hydrogen bonds : bond 0.03236 ( 516) hydrogen bonds : angle 4.27044 ( 1449) metal coordination : bond 0.00203 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8784 (mtm) cc_final: 0.8171 (mpp) REVERT: A 125 MET cc_start: 0.8842 (mpp) cc_final: 0.7921 (mpp) REVERT: A 334 LYS cc_start: 0.9216 (tttt) cc_final: 0.8964 (tttp) REVERT: C 268 LEU cc_start: 0.9305 (mt) cc_final: 0.9064 (tt) REVERT: D 219 ASP cc_start: 0.8668 (m-30) cc_final: 0.8262 (m-30) REVERT: H 70 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8801 (mtpt) REVERT: H 87 ARG cc_start: 0.8888 (mmm160) cc_final: 0.8617 (mmm160) REVERT: H 141 ASP cc_start: 0.8482 (p0) cc_final: 0.8035 (p0) REVERT: H 148 MET cc_start: 0.8672 (ttm) cc_final: 0.8139 (tmm) outliers start: 24 outliers final: 14 residues processed: 89 average time/residue: 0.1205 time to fit residues: 15.4686 Evaluate side-chains 75 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 116 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 93 optimal weight: 40.0000 chunk 161 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.038118 restraints weight = 62139.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.039467 restraints weight = 32312.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.040387 restraints weight = 21004.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.040960 restraints weight = 15627.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.041419 restraints weight = 12801.145| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13070 Z= 0.149 Angle : 0.586 10.758 17726 Z= 0.292 Chirality : 0.042 0.157 2030 Planarity : 0.003 0.047 2276 Dihedral : 4.573 32.385 1805 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.86 % Allowed : 15.86 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.21), residues: 1645 helix: 0.86 (0.20), residues: 731 sheet: -2.39 (0.30), residues: 242 loop : -1.86 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 66 TYR 0.011 0.001 TYR B 86 PHE 0.014 0.001 PHE D 157 TRP 0.009 0.001 TRP E 211 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00334 (13067) covalent geometry : angle 0.58554 (17726) hydrogen bonds : bond 0.03007 ( 516) hydrogen bonds : angle 4.08661 ( 1449) metal coordination : bond 0.00207 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8887 (mtm) cc_final: 0.8297 (mpp) REVERT: A 125 MET cc_start: 0.8808 (mpp) cc_final: 0.7728 (mpp) REVERT: A 334 LYS cc_start: 0.9140 (tttt) cc_final: 0.8841 (tttp) REVERT: C 13 TYR cc_start: 0.8182 (p90) cc_final: 0.7795 (p90) REVERT: C 37 HIS cc_start: 0.6830 (t70) cc_final: 0.6422 (t70) REVERT: D 219 ASP cc_start: 0.8975 (m-30) cc_final: 0.8484 (m-30) REVERT: E 187 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9086 (pp) REVERT: H 140 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8597 (mp10) REVERT: H 141 ASP cc_start: 0.8600 (p0) cc_final: 0.8221 (p0) REVERT: H 148 MET cc_start: 0.8976 (ttm) cc_final: 0.8280 (tmm) outliers start: 25 outliers final: 12 residues processed: 93 average time/residue: 0.1316 time to fit residues: 17.8480 Evaluate side-chains 73 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 40.0000 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.037387 restraints weight = 61814.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038691 restraints weight = 32542.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.039590 restraints weight = 21278.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.040204 restraints weight = 15935.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.040535 restraints weight = 12979.807| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13070 Z= 0.199 Angle : 0.634 9.083 17726 Z= 0.315 Chirality : 0.043 0.158 2030 Planarity : 0.004 0.045 2276 Dihedral : 4.627 34.842 1805 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.23 % Allowed : 15.64 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.22), residues: 1645 helix: 1.15 (0.20), residues: 730 sheet: -2.52 (0.30), residues: 247 loop : -1.77 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 272 TYR 0.014 0.001 TYR C 291 PHE 0.016 0.001 PHE D 157 TRP 0.018 0.001 TRP B 236 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00440 (13067) covalent geometry : angle 0.63404 (17726) hydrogen bonds : bond 0.03174 ( 516) hydrogen bonds : angle 4.13780 ( 1449) metal coordination : bond 0.00480 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8924 (mtm) cc_final: 0.8342 (mpp) REVERT: A 125 MET cc_start: 0.8863 (mpp) cc_final: 0.7735 (mpp) REVERT: B 86 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: C 13 TYR cc_start: 0.8291 (p90) cc_final: 0.7939 (p90) REVERT: D 147 MET cc_start: 0.8352 (mmm) cc_final: 0.8036 (mmt) REVERT: D 201 GLU cc_start: 0.8897 (pp20) cc_final: 0.8694 (pm20) REVERT: D 219 ASP cc_start: 0.8912 (m-30) cc_final: 0.8424 (m-30) REVERT: E 219 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: H 70 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8648 (mtpt) REVERT: H 140 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: H 141 ASP cc_start: 0.8549 (p0) cc_final: 0.8186 (p0) outliers start: 30 outliers final: 21 residues processed: 90 average time/residue: 0.1060 time to fit residues: 14.2612 Evaluate side-chains 84 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 135 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN D 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.038966 restraints weight = 61316.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.040284 restraints weight = 31792.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.041152 restraints weight = 20681.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041735 restraints weight = 15450.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042085 restraints weight = 12659.738| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13070 Z= 0.262 Angle : 0.692 9.253 17726 Z= 0.342 Chirality : 0.044 0.162 2030 Planarity : 0.004 0.045 2276 Dihedral : 4.840 37.462 1805 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.46 % Allowed : 16.46 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1645 helix: 1.27 (0.21), residues: 722 sheet: -2.48 (0.31), residues: 238 loop : -1.66 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 272 TYR 0.012 0.002 TYR E 221 PHE 0.019 0.001 PHE D 157 TRP 0.019 0.001 TRP B 236 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00572 (13067) covalent geometry : angle 0.69215 (17726) hydrogen bonds : bond 0.03402 ( 516) hydrogen bonds : angle 4.32688 ( 1449) metal coordination : bond 0.00518 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8859 (mtm) cc_final: 0.8294 (mpp) REVERT: A 125 MET cc_start: 0.8927 (mpp) cc_final: 0.7820 (mpp) REVERT: B 86 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8909 (m-80) REVERT: B 183 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8855 (mt) REVERT: C 13 TYR cc_start: 0.8067 (p90) cc_final: 0.7785 (p90) REVERT: D 147 MET cc_start: 0.8521 (mmm) cc_final: 0.8123 (mmt) REVERT: D 219 ASP cc_start: 0.8836 (m-30) cc_final: 0.8431 (m-30) REVERT: E 219 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: H 65 LYS cc_start: 0.9316 (ptmm) cc_final: 0.8373 (ptmm) REVERT: H 70 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8658 (mtpt) REVERT: H 129 MET cc_start: 0.8361 (tpp) cc_final: 0.7785 (tpp) REVERT: H 140 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8430 (mp10) REVERT: H 141 ASP cc_start: 0.8518 (p0) cc_final: 0.8200 (p0) outliers start: 33 outliers final: 24 residues processed: 88 average time/residue: 0.1091 time to fit residues: 14.1980 Evaluate side-chains 87 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 144 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037842 restraints weight = 61716.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.039153 restraints weight = 32286.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.040055 restraints weight = 21056.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.040618 restraints weight = 15729.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.041081 restraints weight = 12892.416| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13070 Z= 0.129 Angle : 0.586 9.111 17726 Z= 0.291 Chirality : 0.042 0.154 2030 Planarity : 0.003 0.046 2276 Dihedral : 4.544 31.685 1805 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.31 % Allowed : 17.05 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1645 helix: 1.56 (0.21), residues: 723 sheet: -2.39 (0.31), residues: 243 loop : -1.57 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 66 TYR 0.018 0.001 TYR C 291 PHE 0.013 0.001 PHE D 157 TRP 0.013 0.001 TRP B 236 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00292 (13067) covalent geometry : angle 0.58608 (17726) hydrogen bonds : bond 0.02898 ( 516) hydrogen bonds : angle 3.93759 ( 1449) metal coordination : bond 0.00121 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8877 (mtm) cc_final: 0.8350 (mpp) REVERT: A 125 MET cc_start: 0.8797 (mpp) cc_final: 0.7617 (mpp) REVERT: A 231 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: A 390 MET cc_start: 0.8494 (tpp) cc_final: 0.8039 (mmt) REVERT: B 86 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8703 (m-80) REVERT: B 175 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8745 (ptm-80) REVERT: B 183 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 13 TYR cc_start: 0.8260 (p90) cc_final: 0.8054 (p90) REVERT: D 147 MET cc_start: 0.8709 (mmm) cc_final: 0.8226 (mmt) REVERT: D 219 ASP cc_start: 0.8902 (m-30) cc_final: 0.8419 (m-30) REVERT: E 64 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8367 (t80) REVERT: E 81 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7885 (mm-30) REVERT: E 219 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: H 70 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8651 (mtpt) REVERT: H 129 MET cc_start: 0.7958 (tpp) cc_final: 0.7258 (tpp) REVERT: H 140 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: H 141 ASP cc_start: 0.8461 (p0) cc_final: 0.8058 (p0) outliers start: 31 outliers final: 18 residues processed: 94 average time/residue: 0.1205 time to fit residues: 16.3216 Evaluate side-chains 86 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 151 optimal weight: 0.0570 chunk 20 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.037802 restraints weight = 62201.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.039114 restraints weight = 32510.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.040023 restraints weight = 21218.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.040599 restraints weight = 15813.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041053 restraints weight = 12955.840| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13070 Z= 0.142 Angle : 0.595 9.416 17726 Z= 0.295 Chirality : 0.042 0.186 2030 Planarity : 0.003 0.045 2276 Dihedral : 4.449 32.631 1805 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.46 % Allowed : 16.98 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.22), residues: 1645 helix: 1.60 (0.21), residues: 725 sheet: -2.28 (0.32), residues: 243 loop : -1.48 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.015 0.001 TYR C 291 PHE 0.014 0.001 PHE D 157 TRP 0.011 0.001 TRP B 236 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00321 (13067) covalent geometry : angle 0.59548 (17726) hydrogen bonds : bond 0.02904 ( 516) hydrogen bonds : angle 3.88912 ( 1449) metal coordination : bond 0.00223 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8919 (mm) REVERT: A 105 MET cc_start: 0.8905 (mtm) cc_final: 0.8348 (mpp) REVERT: A 125 MET cc_start: 0.8817 (mpp) cc_final: 0.7609 (mpp) REVERT: A 390 MET cc_start: 0.8532 (tpp) cc_final: 0.8053 (mmt) REVERT: B 86 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8815 (m-80) REVERT: B 175 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8747 (ptm-80) REVERT: B 183 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8765 (mt) REVERT: C 13 TYR cc_start: 0.8284 (p90) cc_final: 0.8076 (p90) REVERT: D 147 MET cc_start: 0.8697 (mmm) cc_final: 0.8181 (mmt) REVERT: D 219 ASP cc_start: 0.8898 (m-30) cc_final: 0.8410 (m-30) REVERT: E 64 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8394 (t80) REVERT: E 219 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: H 65 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8494 (ptmm) REVERT: H 70 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8659 (mtpt) REVERT: H 129 MET cc_start: 0.8023 (tpp) cc_final: 0.7369 (tpp) REVERT: H 140 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8547 (mp10) REVERT: H 141 ASP cc_start: 0.8473 (p0) cc_final: 0.8085 (p0) outliers start: 33 outliers final: 20 residues processed: 90 average time/residue: 0.1136 time to fit residues: 14.8424 Evaluate side-chains 86 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 156 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.048986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037762 restraints weight = 62753.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.039068 restraints weight = 32703.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.039974 restraints weight = 21297.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.040546 restraints weight = 15881.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041010 restraints weight = 12992.441| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13070 Z= 0.150 Angle : 0.608 12.130 17726 Z= 0.301 Chirality : 0.042 0.225 2030 Planarity : 0.003 0.045 2276 Dihedral : 4.458 32.745 1805 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.31 % Allowed : 17.20 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.22), residues: 1645 helix: 1.66 (0.21), residues: 725 sheet: -2.22 (0.32), residues: 243 loop : -1.46 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.016 0.001 TYR C 291 PHE 0.014 0.001 PHE D 157 TRP 0.010 0.001 TRP B 236 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00339 (13067) covalent geometry : angle 0.60763 (17726) hydrogen bonds : bond 0.02893 ( 516) hydrogen bonds : angle 3.86926 ( 1449) metal coordination : bond 0.00230 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 105 MET cc_start: 0.8906 (mtm) cc_final: 0.8351 (mpp) REVERT: A 125 MET cc_start: 0.8830 (mpp) cc_final: 0.7569 (mpp) REVERT: A 390 MET cc_start: 0.8527 (tpp) cc_final: 0.8039 (mmt) REVERT: B 86 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (m-80) REVERT: B 175 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8764 (ptm-80) REVERT: B 183 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8765 (mt) REVERT: D 147 MET cc_start: 0.8694 (mmm) cc_final: 0.8184 (mmt) REVERT: D 219 ASP cc_start: 0.8906 (m-30) cc_final: 0.8411 (m-30) REVERT: E 64 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8380 (t80) REVERT: E 219 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: H 70 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8676 (mtpt) REVERT: H 129 MET cc_start: 0.8012 (tpp) cc_final: 0.7390 (tpp) REVERT: H 140 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8563 (mp10) REVERT: H 141 ASP cc_start: 0.8451 (p0) cc_final: 0.8067 (p0) outliers start: 31 outliers final: 20 residues processed: 87 average time/residue: 0.1115 time to fit residues: 14.4548 Evaluate side-chains 86 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 0.0970 chunk 161 optimal weight: 0.0270 chunk 80 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 0.0020 chunk 65 optimal weight: 8.9990 chunk 137 optimal weight: 0.0980 chunk 151 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.039604 restraints weight = 61653.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.040975 restraints weight = 31923.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.041907 restraints weight = 20555.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042488 restraints weight = 15241.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042964 restraints weight = 12403.352| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13070 Z= 0.098 Angle : 0.578 11.979 17726 Z= 0.284 Chirality : 0.041 0.222 2030 Planarity : 0.003 0.050 2276 Dihedral : 4.163 28.300 1805 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.86 % Allowed : 17.72 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.22), residues: 1645 helix: 1.81 (0.21), residues: 726 sheet: -2.12 (0.32), residues: 245 loop : -1.43 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 66 TYR 0.016 0.001 TYR C 291 PHE 0.011 0.001 PHE D 157 TRP 0.008 0.001 TRP A 98 HIS 0.004 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00220 (13067) covalent geometry : angle 0.57770 (17726) hydrogen bonds : bond 0.02552 ( 516) hydrogen bonds : angle 3.62299 ( 1449) metal coordination : bond 0.00135 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1623.64 seconds wall clock time: 29 minutes 0.06 seconds (1740.06 seconds total)