Starting phenix.real_space_refine on Wed Jul 30 23:43:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osi_13052/07_2025/7osi_13052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osi_13052/07_2025/7osi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7osi_13052/07_2025/7osi_13052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osi_13052/07_2025/7osi_13052.map" model { file = "/net/cci-nas-00/data/ceres_data/7osi_13052/07_2025/7osi_13052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osi_13052/07_2025/7osi_13052.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.97, per 1000 atoms: 0.62 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.56 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: 3.84 Time building geometry restraints manager: 3.68 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.000 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.003 TRP C 236 HIS 0.020 0.003 HIS C 37 PHE 0.031 0.003 PHE B 35 TYR 0.028 0.003 TYR A 204 ARG 0.007 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.30127 ( 516) hydrogen bonds : angle 10.70386 ( 1449) metal coordination : bond 0.04124 ( 3) covalent geometry : bond 0.00956 (13067) covalent geometry : angle 1.21117 (17726) *********************** 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 : 1.412 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: 0.8503 (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: 0.6346 (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: 0.8535 (mtm) REVERT: D 10 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8547 (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: 0.3438 time to fit residues: 68.7128 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 : 1.415 ------------------------------------------------------------------------------- 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 137 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 174 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.043908 restraints weight = 60241.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045365 restraints weight = 30358.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046337 restraints weight = 19325.887| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2246 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= 0.125 Angle : 0.635 10.011 17726 Z= 0.325 Chirality : 0.042 0.150 2030 Planarity : 0.005 0.060 2276 Dihedral : 5.644 54.724 1815 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.56 % Allowed : 12.43 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.17), residues: 1645 helix: -1.96 (0.15), residues: 724 sheet: -2.92 (0.29), residues: 239 loop : -2.46 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.005 0.001 HIS H 40 PHE 0.013 0.001 PHE A 303 TYR 0.017 0.001 TYR B 86 ARG 0.006 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 516) hydrogen bonds : angle 5.05426 ( 1449) metal coordination : bond 0.00434 ( 3) covalent geometry : bond 0.00271 (13067) covalent geometry : angle 0.63531 (17726) *********************** 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 : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8765 (mtm) cc_final: 0.8235 (mpp) REVERT: A 125 MET cc_start: 0.8531 (mpp) cc_final: 0.7973 (mpp) REVERT: A 334 LYS cc_start: 0.9228 (tttt) cc_final: 0.8945 (tttp) REVERT: A 420 MET cc_start: 0.8765 (mmm) cc_final: 0.8551 (mmt) REVERT: B 261 ASN cc_start: 0.7068 (OUTLIER) cc_final: 0.6619 (p0) REVERT: C 13 TYR cc_start: 0.7802 (p90) cc_final: 0.7514 (p90) REVERT: C 268 LEU cc_start: 0.9338 (mt) cc_final: 0.9023 (tt) REVERT: D 219 ASP cc_start: 0.8573 (m-30) cc_final: 0.8214 (m-30) REVERT: E 187 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9107 (pp) REVERT: H 87 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8366 (mmm160) REVERT: H 141 ASP cc_start: 0.8575 (p0) cc_final: 0.7883 (p0) outliers start: 21 outliers final: 8 residues processed: 107 average time/residue: 0.2729 time to fit residues: 42.1614 Evaluate side-chains 77 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 19 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 96 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 123 ASN A 145 ASN A 175 ASN E 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.053103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041898 restraints weight = 60663.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.043321 restraints weight = 30769.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044267 restraints weight = 19672.805| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2613 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= 0.113 Angle : 0.577 8.460 17726 Z= 0.293 Chirality : 0.041 0.177 2030 Planarity : 0.004 0.052 2276 Dihedral : 4.882 31.333 1805 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.41 % Allowed : 13.78 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1645 helix: -0.40 (0.19), residues: 729 sheet: -2.70 (0.30), residues: 236 loop : -2.24 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.004 0.001 HIS H 40 PHE 0.012 0.001 PHE E 157 TYR 0.015 0.001 TYR B 86 ARG 0.004 0.000 ARG H 66 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 516) hydrogen bonds : angle 4.42003 ( 1449) metal coordination : bond 0.00157 ( 3) covalent geometry : bond 0.00249 (13067) covalent geometry : angle 0.57661 (17726) *********************** 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 93 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.9098 (pt) cc_final: 0.8881 (pp) REVERT: A 105 MET cc_start: 0.8880 (mtm) cc_final: 0.8337 (mpp) REVERT: A 125 MET cc_start: 0.8801 (mpp) cc_final: 0.7713 (mpp) REVERT: A 193 HIS cc_start: 0.7921 (m90) cc_final: 0.7678 (m170) REVERT: A 334 LYS cc_start: 0.9235 (tttt) cc_final: 0.8936 (tttp) REVERT: C 13 TYR cc_start: 0.7912 (p90) cc_final: 0.7623 (p90) REVERT: D 147 MET cc_start: 0.8564 (mmm) cc_final: 0.8096 (mmt) REVERT: D 219 ASP cc_start: 0.8750 (m-30) cc_final: 0.8320 (m-30) REVERT: E 187 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9086 (pp) REVERT: H 70 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8821 (mtpt) REVERT: H 87 ARG cc_start: 0.8925 (mmm160) cc_final: 0.8343 (mmm160) REVERT: H 141 ASP cc_start: 0.8555 (p0) cc_final: 0.7891 (p0) outliers start: 19 outliers final: 10 residues processed: 91 average time/residue: 0.2568 time to fit residues: 34.4712 Evaluate side-chains 77 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 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 138 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 71 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040475 restraints weight = 61587.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.041795 restraints weight = 32117.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.042681 restraints weight = 21044.928| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13070 Z= 0.312 Angle : 0.744 8.696 17726 Z= 0.371 Chirality : 0.045 0.172 2030 Planarity : 0.004 0.046 2276 Dihedral : 5.152 39.479 1805 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.94 % Allowed : 14.89 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1645 helix: 0.38 (0.20), residues: 724 sheet: -2.62 (0.30), residues: 228 loop : -2.02 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 211 HIS 0.004 0.001 HIS C 194 PHE 0.022 0.002 PHE D 157 TYR 0.014 0.002 TYR A 258 ARG 0.005 0.001 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 516) hydrogen bonds : angle 4.60615 ( 1449) metal coordination : bond 0.00432 ( 3) covalent geometry : bond 0.00675 (13067) covalent geometry : angle 0.74412 (17726) *********************** 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 91 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8772 (mtm) cc_final: 0.8201 (mpp) REVERT: A 125 MET cc_start: 0.8913 (mpp) cc_final: 0.7932 (mpp) REVERT: C 268 LEU cc_start: 0.9309 (mt) cc_final: 0.9032 (tt) REVERT: D 219 ASP cc_start: 0.8686 (m-30) cc_final: 0.8317 (m-30) REVERT: E 93 TYR cc_start: 0.8823 (m-80) cc_final: 0.8612 (m-80) REVERT: E 219 ASP cc_start: 0.8442 (m-30) cc_final: 0.8182 (m-30) REVERT: H 50 MET cc_start: 0.7429 (ptp) cc_final: 0.7159 (ptp) REVERT: H 70 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8656 (mtpt) REVERT: H 87 ARG cc_start: 0.8941 (mmm160) cc_final: 0.8686 (mmm160) REVERT: H 141 ASP cc_start: 0.8515 (p0) cc_final: 0.7851 (p0) REVERT: H 148 MET cc_start: 0.8787 (ttm) cc_final: 0.8173 (tmm) outliers start: 26 outliers final: 15 residues processed: 88 average time/residue: 0.2518 time to fit residues: 33.0376 Evaluate side-chains 75 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 261 ASN 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 Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 9 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.051793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040973 restraints weight = 60954.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.042304 restraints weight = 31671.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.043165 restraints weight = 20659.937| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13070 Z= 0.228 Angle : 0.649 9.655 17726 Z= 0.324 Chirality : 0.043 0.160 2030 Planarity : 0.004 0.046 2276 Dihedral : 4.888 35.429 1805 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.46 % Allowed : 15.71 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.21), residues: 1645 helix: 0.86 (0.20), residues: 724 sheet: -2.58 (0.31), residues: 229 loop : -1.89 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 236 HIS 0.003 0.001 HIS H 110 PHE 0.017 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.003 0.000 ARG H 66 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 516) hydrogen bonds : angle 4.35417 ( 1449) metal coordination : bond 0.00330 ( 3) covalent geometry : bond 0.00501 (13067) covalent geometry : angle 0.64893 (17726) *********************** 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 98 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8714 (mtm) cc_final: 0.8189 (mpp) REVERT: A 125 MET cc_start: 0.8893 (mpp) cc_final: 0.7893 (mpp) REVERT: C 13 TYR cc_start: 0.7999 (p90) cc_final: 0.7650 (p90) REVERT: D 147 MET cc_start: 0.8580 (mmm) cc_final: 0.8069 (mmt) REVERT: D 219 ASP cc_start: 0.8638 (m-30) cc_final: 0.8287 (m-30) REVERT: E 81 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7811 (mm-30) REVERT: H 66 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.8174 (mmm-85) REVERT: H 70 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8639 (mtpt) REVERT: H 141 ASP cc_start: 0.8362 (p0) cc_final: 0.7758 (p0) REVERT: H 148 MET cc_start: 0.8835 (ttm) cc_final: 0.8129 (tmm) outliers start: 33 outliers final: 20 residues processed: 95 average time/residue: 0.2718 time to fit residues: 38.0809 Evaluate side-chains 82 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 417 HIS Chi-restraints excluded: chain B residue 84 THR 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 188 VAL Chi-restraints excluded: chain E residue 192 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 87 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.048661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.037439 restraints weight = 62106.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.038769 restraints weight = 32260.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.039666 restraints weight = 20833.617| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3309 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 : 0.622 8.975 17726 Z= 0.309 Chirality : 0.043 0.160 2030 Planarity : 0.004 0.046 2276 Dihedral : 4.742 34.256 1805 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.08 % Allowed : 16.23 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1645 helix: 1.20 (0.21), residues: 720 sheet: -2.62 (0.30), residues: 244 loop : -1.70 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 236 HIS 0.003 0.001 HIS B 37 PHE 0.015 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.008 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 516) hydrogen bonds : angle 4.18321 ( 1449) metal coordination : bond 0.00305 ( 3) covalent geometry : bond 0.00416 (13067) covalent geometry : angle 0.62151 (17726) *********************** 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 97 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8842 (mtm) cc_final: 0.8362 (mpp) REVERT: A 125 MET cc_start: 0.8850 (mpp) cc_final: 0.7713 (mpp) REVERT: B 37 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.7100 (t70) REVERT: C 13 TYR cc_start: 0.8261 (p90) cc_final: 0.7952 (p90) REVERT: C 37 HIS cc_start: 0.7066 (t70) cc_final: 0.6611 (t70) REVERT: C 49 ILE cc_start: 0.9521 (mt) cc_final: 0.9320 (tt) REVERT: D 147 MET cc_start: 0.8485 (mmm) cc_final: 0.8205 (mmt) REVERT: D 219 ASP cc_start: 0.8929 (m-30) cc_final: 0.8437 (m-30) REVERT: E 81 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7953 (mm-30) REVERT: E 219 ASP cc_start: 0.8542 (m-30) cc_final: 0.7957 (m-30) REVERT: H 65 LYS cc_start: 0.9320 (ptmm) cc_final: 0.8559 (ptmm) REVERT: H 70 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8654 (mtpt) REVERT: H 72 CYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8131 (p) REVERT: H 141 ASP cc_start: 0.8543 (p0) cc_final: 0.7918 (p0) REVERT: H 148 MET cc_start: 0.9042 (ttm) cc_final: 0.8209 (tmm) outliers start: 28 outliers final: 19 residues processed: 92 average time/residue: 0.2709 time to fit residues: 36.5141 Evaluate side-chains 85 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 294 LEU 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 37 HIS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 266 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 138 MET 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 72 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 104 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 40.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.038093 restraints weight = 61381.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.039420 restraints weight = 31696.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.040321 restraints weight = 20448.210| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13070 Z= 0.139 Angle : 0.596 10.074 17726 Z= 0.294 Chirality : 0.042 0.156 2030 Planarity : 0.003 0.046 2276 Dihedral : 4.576 32.338 1805 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.01 % Allowed : 16.83 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1645 helix: 1.48 (0.21), residues: 720 sheet: -2.50 (0.31), residues: 244 loop : -1.63 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 236 HIS 0.003 0.001 HIS B 20 PHE 0.013 0.001 PHE D 157 TYR 0.015 0.001 TYR C 291 ARG 0.007 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 516) hydrogen bonds : angle 4.02538 ( 1449) metal coordination : bond 0.00324 ( 3) covalent geometry : bond 0.00313 (13067) covalent geometry : angle 0.59615 (17726) *********************** 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 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8903 (mtm) cc_final: 0.8354 (mpp) REVERT: A 125 MET cc_start: 0.8884 (mpp) cc_final: 0.7608 (mpp) REVERT: A 390 MET cc_start: 0.8531 (tpp) cc_final: 0.7966 (mmt) REVERT: B 183 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8764 (mt) REVERT: C 13 TYR cc_start: 0.8326 (p90) cc_final: 0.8070 (p90) REVERT: D 219 ASP cc_start: 0.8972 (m-30) cc_final: 0.8504 (m-30) REVERT: H 129 MET cc_start: 0.8320 (tpp) cc_final: 0.7883 (tpp) REVERT: H 141 ASP cc_start: 0.8474 (p0) cc_final: 0.7800 (p0) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.2643 time to fit residues: 36.8982 Evaluate side-chains 80 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 294 LEU 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 183 LEU Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU 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 117 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.049235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.038036 restraints weight = 62372.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.039366 restraints weight = 32389.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.040279 restraints weight = 21008.201| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13070 Z= 0.129 Angle : 0.591 10.453 17726 Z= 0.292 Chirality : 0.042 0.210 2030 Planarity : 0.003 0.047 2276 Dihedral : 4.473 31.932 1805 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.23 % Allowed : 17.57 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1645 helix: 1.60 (0.21), residues: 720 sheet: -2.37 (0.31), residues: 248 loop : -1.55 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 236 HIS 0.003 0.001 HIS B 20 PHE 0.012 0.001 PHE D 157 TYR 0.012 0.001 TYR C 293 ARG 0.007 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 516) hydrogen bonds : angle 3.93583 ( 1449) metal coordination : bond 0.00148 ( 3) covalent geometry : bond 0.00292 (13067) covalent geometry : angle 0.59142 (17726) *********************** 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 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8903 (mtm) cc_final: 0.8361 (mpp) REVERT: A 125 MET cc_start: 0.8872 (mpp) cc_final: 0.7582 (mpp) REVERT: A 390 MET cc_start: 0.8511 (tpp) cc_final: 0.8033 (mmt) REVERT: B 183 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8793 (mt) REVERT: C 13 TYR cc_start: 0.8366 (p90) cc_final: 0.8098 (p90) REVERT: C 37 HIS cc_start: 0.6872 (t-90) cc_final: 0.6568 (t70) REVERT: D 147 MET cc_start: 0.8733 (mmm) cc_final: 0.8295 (mmt) REVERT: D 219 ASP cc_start: 0.8977 (m-30) cc_final: 0.8484 (m-30) REVERT: E 64 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8433 (t80) REVERT: H 65 LYS cc_start: 0.9025 (ptmm) cc_final: 0.8357 (ptmm) REVERT: H 70 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8680 (mtpt) REVERT: H 129 MET cc_start: 0.8277 (tpp) cc_final: 0.7757 (tpp) REVERT: H 141 ASP cc_start: 0.8447 (p0) cc_final: 0.7751 (p0) outliers start: 30 outliers final: 22 residues processed: 93 average time/residue: 0.2642 time to fit residues: 36.3968 Evaluate side-chains 86 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 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 294 LEU 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 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.037486 restraints weight = 62018.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038797 restraints weight = 32529.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.039684 restraints weight = 21257.275| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13070 Z= 0.167 Angle : 0.614 10.057 17726 Z= 0.303 Chirality : 0.042 0.186 2030 Planarity : 0.004 0.048 2276 Dihedral : 4.527 33.398 1805 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.38 % Allowed : 17.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1645 helix: 1.62 (0.21), residues: 721 sheet: -2.33 (0.31), residues: 248 loop : -1.49 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 240 HIS 0.004 0.001 HIS C 37 PHE 0.014 0.001 PHE D 157 TYR 0.017 0.001 TYR C 291 ARG 0.007 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 516) hydrogen bonds : angle 3.97574 ( 1449) metal coordination : bond 0.00245 ( 3) covalent geometry : bond 0.00374 (13067) covalent geometry : angle 0.61422 (17726) *********************** 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 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8935 (mm) REVERT: A 105 MET cc_start: 0.8925 (mtm) cc_final: 0.8387 (mpp) REVERT: A 125 MET cc_start: 0.8852 (mpp) cc_final: 0.7595 (mpp) REVERT: A 390 MET cc_start: 0.8623 (tpp) cc_final: 0.8084 (mmt) REVERT: B 86 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8644 (m-80) REVERT: B 183 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8816 (mt) REVERT: C 13 TYR cc_start: 0.8391 (p90) cc_final: 0.8148 (p90) REVERT: D 147 MET cc_start: 0.8757 (mmm) cc_final: 0.8345 (mmt) REVERT: D 219 ASP cc_start: 0.8923 (m-30) cc_final: 0.8417 (m-30) REVERT: E 64 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8376 (t80) REVERT: E 81 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7950 (mm-30) REVERT: H 70 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8681 (mtpt) REVERT: H 129 MET cc_start: 0.8239 (tpp) cc_final: 0.7698 (tpp) REVERT: H 141 ASP cc_start: 0.8504 (p0) cc_final: 0.7829 (p0) outliers start: 32 outliers final: 25 residues processed: 93 average time/residue: 0.2535 time to fit residues: 35.2510 Evaluate side-chains 91 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 231 MET Chi-restraints excluded: chain A residue 294 LEU 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 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR 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 192 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 103 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.038018 restraints weight = 62230.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.039351 restraints weight = 32334.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.040255 restraints weight = 20942.994| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13070 Z= 0.131 Angle : 0.591 11.189 17726 Z= 0.291 Chirality : 0.042 0.201 2030 Planarity : 0.004 0.047 2276 Dihedral : 4.405 31.442 1805 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.46 % Allowed : 17.27 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1645 helix: 1.73 (0.21), residues: 721 sheet: -2.20 (0.31), residues: 257 loop : -1.46 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 240 HIS 0.003 0.001 HIS B 20 PHE 0.012 0.001 PHE D 157 TYR 0.017 0.001 TYR C 291 ARG 0.008 0.000 ARG H 66 Details of bonding type rmsd hydrogen bonds : bond 0.02797 ( 516) hydrogen bonds : angle 3.86374 ( 1449) metal coordination : bond 0.00183 ( 3) covalent geometry : bond 0.00297 (13067) covalent geometry : angle 0.59123 (17726) ********************** 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 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8921 (mm) REVERT: A 105 MET cc_start: 0.8911 (mtm) cc_final: 0.8380 (mpp) REVERT: A 125 MET cc_start: 0.8811 (mpp) cc_final: 0.7527 (mpp) REVERT: A 390 MET cc_start: 0.8552 (tpp) cc_final: 0.8081 (mmt) REVERT: B 86 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: B 183 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8772 (mt) REVERT: D 147 MET cc_start: 0.8773 (mmm) cc_final: 0.8321 (mmt) REVERT: D 219 ASP cc_start: 0.8980 (m-30) cc_final: 0.8485 (m-30) REVERT: E 64 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8346 (t80) REVERT: E 81 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7910 (mm-30) REVERT: E 219 ASP cc_start: 0.8827 (m-30) cc_final: 0.8488 (m-30) REVERT: H 70 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8696 (mtpt) REVERT: H 129 MET cc_start: 0.8100 (tpp) cc_final: 0.7407 (tpp) REVERT: H 140 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: H 141 ASP cc_start: 0.8432 (p0) cc_final: 0.7757 (p0) outliers start: 33 outliers final: 24 residues processed: 93 average time/residue: 0.2582 time to fit residues: 35.4581 Evaluate side-chains 91 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 294 LEU 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 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR 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 192 VAL 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 91 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 0.0000 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 chunk 144 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 3.1190 ------------------------------------------------------------------------------- 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** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.037174 restraints weight = 62256.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.038465 restraints weight = 32696.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.039341 restraints weight = 21387.236| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13070 Z= 0.192 Angle : 0.640 12.692 17726 Z= 0.316 Chirality : 0.043 0.230 2030 Planarity : 0.004 0.046 2276 Dihedral : 4.524 34.327 1805 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.46 % Allowed : 17.20 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1645 helix: 1.66 (0.21), residues: 721 sheet: -2.28 (0.31), residues: 250 loop : -1.42 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 240 HIS 0.002 0.001 HIS B 194 PHE 0.014 0.001 PHE D 157 TYR 0.019 0.001 TYR C 291 ARG 0.007 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 516) hydrogen bonds : angle 3.99918 ( 1449) metal coordination : bond 0.00320 ( 3) covalent geometry : bond 0.00427 (13067) covalent geometry : angle 0.64014 (17726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.36 seconds wall clock time: 58 minutes 26.90 seconds (3506.90 seconds total)