Starting phenix.real_space_refine on Mon Dec 30 10:22:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osi_13052/12_2024/7osi_13052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osi_13052/12_2024/7osi_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_13052/12_2024/7osi_13052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osi_13052/12_2024/7osi_13052.map" model { file = "/net/cci-nas-00/data/ceres_data/7osi_13052/12_2024/7osi_13052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osi_13052/12_2024/7osi_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-5532/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: 7.73, per 1000 atoms: 0.60 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: 3.29 Conformation dependent library (CDL) restraints added in 1.8 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: 1.46 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: 3.82 Time building geometry restraints manager: 3.78 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: 0.450 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.490 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- 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 13067 Z= 0.622 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 *********************** 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 : 1.593 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: 0.3534 time to fit residues: 70.7548 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 : 1.563 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 13067 Z= 0.176 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 *********************** 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 : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8930 (mtm) cc_final: 0.8428 (mpp) REVERT: A 125 MET cc_start: 0.8493 (mpp) cc_final: 0.7773 (mpp) REVERT: A 235 LYS cc_start: 0.9156 (tptt) cc_final: 0.8899 (mmmm) REVERT: A 253 MET cc_start: 0.8557 (ptp) cc_final: 0.8349 (ptp) REVERT: A 334 LYS cc_start: 0.9107 (tttt) cc_final: 0.8793 (tttp) REVERT: B 248 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7582 (ttm-80) REVERT: B 261 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6478 (p0) REVERT: C 13 TYR cc_start: 0.8065 (p90) cc_final: 0.7632 (p90) REVERT: C 133 MET cc_start: 0.8566 (mtm) cc_final: 0.8356 (mtm) REVERT: C 268 LEU cc_start: 0.9361 (mt) cc_final: 0.9058 (tt) REVERT: D 219 ASP cc_start: 0.8914 (m-30) cc_final: 0.8412 (m-30) REVERT: E 187 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9076 (pp) REVERT: H 87 ARG cc_start: 0.8999 (mmm160) cc_final: 0.8293 (mmm160) REVERT: H 141 ASP cc_start: 0.8746 (p0) cc_final: 0.8128 (p0) REVERT: H 148 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8671 (ttm) outliers start: 21 outliers final: 8 residues processed: 107 average time/residue: 0.2917 time to fit residues: 45.1027 Evaluate side-chains 80 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 261 ASN E 225 ASN H 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 13067 Z= 0.627 Angle : 0.903 9.426 17726 Z= 0.447 Chirality : 0.049 0.215 2030 Planarity : 0.005 0.050 2276 Dihedral : 5.604 42.379 1805 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.16 % Allowed : 15.19 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.14 (0.20), residues: 1645 helix: -0.23 (0.19), residues: 723 sheet: -2.68 (0.31), residues: 223 loop : -2.21 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 211 HIS 0.006 0.002 HIS H 110 PHE 0.030 0.002 PHE D 157 TYR 0.017 0.002 TYR C 13 ARG 0.007 0.001 ARG C 224 *********************** 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 92 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8967 (mtm) cc_final: 0.8368 (mpp) REVERT: A 125 MET cc_start: 0.8842 (mpp) cc_final: 0.7714 (mpp) REVERT: A 235 LYS cc_start: 0.9216 (tptt) cc_final: 0.8933 (mmmm) REVERT: B 261 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7062 (p0) REVERT: C 133 MET cc_start: 0.8756 (mtm) cc_final: 0.8457 (mtm) REVERT: C 268 LEU cc_start: 0.9367 (mt) cc_final: 0.9048 (tt) REVERT: D 10 LYS cc_start: 0.8883 (tmtt) cc_final: 0.8426 (tmtt) REVERT: D 88 MET cc_start: 0.8234 (tpp) cc_final: 0.7947 (tpp) REVERT: D 147 MET cc_start: 0.8654 (mmm) cc_final: 0.8247 (mmt) REVERT: D 219 ASP cc_start: 0.9035 (m-30) cc_final: 0.8387 (m-30) REVERT: E 93 TYR cc_start: 0.8762 (m-80) cc_final: 0.8440 (m-80) REVERT: E 138 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6293 (ppp) REVERT: H 50 MET cc_start: 0.7813 (ptt) cc_final: 0.7545 (ptt) REVERT: H 70 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8822 (mtpt) REVERT: H 98 MET cc_start: 0.9275 (mmm) cc_final: 0.9023 (mmm) REVERT: H 141 ASP cc_start: 0.8799 (p0) cc_final: 0.8234 (p0) REVERT: H 148 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8195 (tmm) outliers start: 29 outliers final: 20 residues processed: 88 average time/residue: 0.2779 time to fit residues: 36.2954 Evaluate side-chains 82 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 134 VAL 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 226 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 43 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 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 188 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 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13067 Z= 0.186 Angle : 0.586 9.240 17726 Z= 0.295 Chirality : 0.042 0.161 2030 Planarity : 0.004 0.050 2276 Dihedral : 4.947 32.492 1805 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.01 % Allowed : 16.16 % 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: -1.44 (0.21), residues: 1645 helix: 0.56 (0.20), residues: 724 sheet: -2.58 (0.30), residues: 242 loop : -1.99 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.006 0.001 HIS H 40 PHE 0.013 0.001 PHE E 157 TYR 0.012 0.001 TYR B 293 ARG 0.005 0.000 ARG D 272 *********************** 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 100 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8877 (mtm) cc_final: 0.8295 (mpp) REVERT: A 125 MET cc_start: 0.8870 (mpp) cc_final: 0.7612 (mpp) REVERT: A 235 LYS cc_start: 0.9140 (tptt) cc_final: 0.8899 (mmmm) REVERT: A 334 LYS cc_start: 0.9123 (tttt) cc_final: 0.8853 (tttp) REVERT: C 13 TYR cc_start: 0.8163 (p90) cc_final: 0.7801 (p90) REVERT: C 42 LYS cc_start: 0.9301 (tttm) cc_final: 0.8984 (pttt) REVERT: C 133 MET cc_start: 0.8672 (mtm) cc_final: 0.8349 (mtm) REVERT: D 219 ASP cc_start: 0.9003 (m-30) cc_final: 0.8512 (m-30) REVERT: H 70 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8780 (mtpt) REVERT: H 98 MET cc_start: 0.9195 (mmm) cc_final: 0.8982 (mmm) REVERT: H 129 MET cc_start: 0.8956 (tpp) cc_final: 0.8573 (tpp) REVERT: H 141 ASP cc_start: 0.8545 (p0) cc_final: 0.8010 (p0) outliers start: 27 outliers final: 14 residues processed: 98 average time/residue: 0.2845 time to fit residues: 41.1251 Evaluate side-chains 79 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL 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 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 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 192 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN H 40 HIS H 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13067 Z= 0.421 Angle : 0.729 8.629 17726 Z= 0.360 Chirality : 0.045 0.172 2030 Planarity : 0.004 0.047 2276 Dihedral : 5.117 39.120 1805 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.65 % Allowed : 16.01 % 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: -1.21 (0.21), residues: 1645 helix: 0.85 (0.20), residues: 718 sheet: -2.70 (0.30), residues: 242 loop : -1.86 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 211 HIS 0.004 0.001 HIS H 110 PHE 0.022 0.002 PHE D 157 TYR 0.012 0.002 TYR A 258 ARG 0.006 0.001 ARG H 87 *********************** 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 114 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 65 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8842 (mtm) cc_final: 0.8398 (mpp) REVERT: A 125 MET cc_start: 0.8911 (mpp) cc_final: 0.7695 (mpp) REVERT: A 235 LYS cc_start: 0.9164 (tptt) cc_final: 0.8883 (mmmm) REVERT: B 175 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8771 (ptm-80) REVERT: C 13 TYR cc_start: 0.8292 (p90) cc_final: 0.7846 (p90) REVERT: C 42 LYS cc_start: 0.9321 (tttm) cc_final: 0.9013 (pttm) REVERT: C 46 MET cc_start: 0.9014 (tpp) cc_final: 0.8810 (tpp) REVERT: C 133 MET cc_start: 0.8714 (mtm) cc_final: 0.8437 (mtm) REVERT: D 10 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8367 (tmtt) REVERT: D 88 MET cc_start: 0.8405 (tpp) cc_final: 0.8186 (tpp) REVERT: D 147 MET cc_start: 0.8615 (mmm) cc_final: 0.8182 (mmt) REVERT: D 219 ASP cc_start: 0.8988 (m-30) cc_final: 0.8493 (m-30) REVERT: H 70 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8692 (mtpt) REVERT: H 72 CYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7775 (p) REVERT: H 129 MET cc_start: 0.8781 (tpp) cc_final: 0.8349 (tpp) REVERT: H 141 ASP cc_start: 0.8580 (p0) cc_final: 0.8012 (p0) REVERT: H 148 MET cc_start: 0.9022 (ttm) cc_final: 0.8370 (tmm) outliers start: 49 outliers final: 29 residues processed: 110 average time/residue: 0.2682 time to fit residues: 43.3265 Evaluate side-chains 93 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 236 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 175 ARG 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 C residue 167 LEU Chi-restraints excluded: chain C residue 206 LEU 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 117 LEU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 213 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 72 CYS 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 53 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** C 59 GLN E 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13067 Z= 0.222 Angle : 0.602 8.642 17726 Z= 0.301 Chirality : 0.042 0.162 2030 Planarity : 0.003 0.048 2276 Dihedral : 4.726 32.935 1805 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.61 % Allowed : 17.13 % 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: -0.85 (0.22), residues: 1645 helix: 1.22 (0.21), residues: 719 sheet: -2.49 (0.30), residues: 258 loop : -1.74 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 236 HIS 0.013 0.001 HIS H 40 PHE 0.013 0.001 PHE D 157 TYR 0.012 0.001 TYR C 293 ARG 0.004 0.000 ARG D 272 *********************** 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 103 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8904 (mtm) cc_final: 0.8392 (mpp) REVERT: A 125 MET cc_start: 0.8906 (mpp) cc_final: 0.7690 (mpp) REVERT: A 231 MET cc_start: 0.8920 (mtp) cc_final: 0.8675 (mtp) REVERT: A 235 LYS cc_start: 0.9149 (tptt) cc_final: 0.8892 (mmmm) REVERT: C 13 TYR cc_start: 0.8355 (p90) cc_final: 0.8020 (p90) REVERT: C 46 MET cc_start: 0.8986 (tpp) cc_final: 0.8772 (tpp) REVERT: C 133 MET cc_start: 0.8656 (mtm) cc_final: 0.8369 (mtm) REVERT: D 88 MET cc_start: 0.8379 (tpp) cc_final: 0.8003 (tpp) REVERT: D 147 MET cc_start: 0.8574 (mmm) cc_final: 0.8251 (mmm) REVERT: D 219 ASP cc_start: 0.9040 (m-30) cc_final: 0.8543 (m-30) REVERT: E 81 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7929 (mm-30) REVERT: E 219 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8543 (m-30) REVERT: H 70 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8810 (mtpt) REVERT: H 129 MET cc_start: 0.8214 (tpp) cc_final: 0.7584 (tpp) REVERT: H 135 SER cc_start: 0.9578 (OUTLIER) cc_final: 0.9156 (p) REVERT: H 141 ASP cc_start: 0.8582 (p0) cc_final: 0.7972 (p0) outliers start: 35 outliers final: 24 residues processed: 100 average time/residue: 0.2852 time to fit residues: 41.3716 Evaluate side-chains 89 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 134 VAL 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 236 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 B residue 272 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 50 SER 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 192 VAL Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13067 Z= 0.263 Angle : 0.620 9.129 17726 Z= 0.308 Chirality : 0.043 0.160 2030 Planarity : 0.004 0.047 2276 Dihedral : 4.687 34.232 1805 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.13 % Allowed : 16.98 % Favored : 79.90 % 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: -0.67 (0.22), residues: 1645 helix: 1.39 (0.21), residues: 720 sheet: -2.48 (0.31), residues: 248 loop : -1.64 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 240 HIS 0.007 0.001 HIS B 20 PHE 0.015 0.001 PHE D 157 TYR 0.015 0.001 TYR C 291 ARG 0.004 0.000 ARG H 87 *********************** 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 111 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8916 (mtm) cc_final: 0.8399 (mpp) REVERT: A 125 MET cc_start: 0.8929 (mpp) cc_final: 0.7627 (mpp) REVERT: A 231 MET cc_start: 0.8650 (mtp) cc_final: 0.8380 (mtp) REVERT: A 235 LYS cc_start: 0.9193 (tptt) cc_final: 0.8930 (mmmm) REVERT: B 175 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8780 (ptm-80) REVERT: B 183 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 13 TYR cc_start: 0.8282 (p90) cc_final: 0.7962 (p90) REVERT: C 133 MET cc_start: 0.8656 (mtm) cc_final: 0.8357 (mtm) REVERT: D 219 ASP cc_start: 0.8989 (m-30) cc_final: 0.8462 (m-30) REVERT: E 81 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7881 (mm-30) REVERT: E 219 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: H 65 LYS cc_start: 0.9260 (ptmm) cc_final: 0.8663 (ptmm) REVERT: H 72 CYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8220 (p) REVERT: H 88 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9232 (pp) REVERT: H 129 MET cc_start: 0.8226 (tpp) cc_final: 0.7419 (tpp) REVERT: H 135 SER cc_start: 0.9587 (OUTLIER) cc_final: 0.9180 (p) REVERT: H 141 ASP cc_start: 0.8601 (p0) cc_final: 0.7969 (p0) outliers start: 42 outliers final: 28 residues processed: 107 average time/residue: 0.2918 time to fit residues: 45.2698 Evaluate side-chains 95 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 134 VAL 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 236 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 397 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 175 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 20 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13067 Z= 0.210 Angle : 0.616 14.353 17726 Z= 0.300 Chirality : 0.043 0.186 2030 Planarity : 0.004 0.047 2276 Dihedral : 4.581 32.309 1805 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.76 % Allowed : 17.94 % Favored : 79.30 % 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: -0.50 (0.22), residues: 1645 helix: 1.52 (0.21), residues: 720 sheet: -2.39 (0.31), residues: 247 loop : -1.56 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 37 HIS 0.007 0.001 HIS B 20 PHE 0.013 0.001 PHE D 157 TYR 0.015 0.001 TYR B 86 ARG 0.008 0.000 ARG H 87 *********************** 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 103 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 1.717 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: 0.8912 (mtm) cc_final: 0.8399 (mpp) REVERT: A 125 MET cc_start: 0.8911 (mpp) cc_final: 0.7577 (mpp) REVERT: A 231 MET cc_start: 0.8733 (mtp) cc_final: 0.8475 (mtp) REVERT: A 235 LYS cc_start: 0.9151 (tptt) cc_final: 0.8905 (mmmm) REVERT: A 390 MET cc_start: 0.8450 (tpp) cc_final: 0.7941 (mmt) REVERT: B 175 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8752 (ptm-80) REVERT: B 183 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8700 (mt) REVERT: C 13 TYR cc_start: 0.8293 (p90) cc_final: 0.8019 (p90) REVERT: C 133 MET cc_start: 0.8633 (mtm) cc_final: 0.8335 (mtm) REVERT: D 147 MET cc_start: 0.8525 (mmm) cc_final: 0.8140 (mmt) REVERT: D 219 ASP cc_start: 0.9025 (m-30) cc_final: 0.8523 (m-30) REVERT: E 219 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8563 (m-30) REVERT: H 70 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8695 (mtpt) REVERT: H 88 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9210 (pp) REVERT: H 98 MET cc_start: 0.9225 (mmm) cc_final: 0.8968 (mmm) REVERT: H 129 MET cc_start: 0.8238 (tpp) cc_final: 0.7483 (tpp) REVERT: H 141 ASP cc_start: 0.8527 (p0) cc_final: 0.7838 (p0) outliers start: 37 outliers final: 24 residues processed: 99 average time/residue: 0.2801 time to fit residues: 40.6729 Evaluate side-chains 88 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 134 VAL 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 236 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 397 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 175 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0670 chunk 146 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13067 Z= 0.148 Angle : 0.597 12.342 17726 Z= 0.288 Chirality : 0.042 0.150 2030 Planarity : 0.003 0.047 2276 Dihedral : 4.291 28.789 1805 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.86 % Allowed : 18.99 % Favored : 79.15 % 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: 1.63 (0.21), residues: 730 sheet: -2.28 (0.31), residues: 251 loop : -1.57 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.008 0.001 HIS B 20 PHE 0.011 0.001 PHE D 157 TYR 0.019 0.001 TYR C 291 ARG 0.007 0.000 ARG H 87 *********************** 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 103 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 1.542 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: 0.9308 (OUTLIER) cc_final: 0.8931 (mm) REVERT: A 105 MET cc_start: 0.8892 (mtm) cc_final: 0.8339 (mpp) REVERT: A 125 MET cc_start: 0.8840 (mpp) cc_final: 0.7484 (mpp) REVERT: A 235 LYS cc_start: 0.9102 (tptt) cc_final: 0.8875 (mmmm) REVERT: A 390 MET cc_start: 0.8353 (tpp) cc_final: 0.7969 (mmt) REVERT: B 183 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8432 (mm) REVERT: C 13 TYR cc_start: 0.8283 (p90) cc_final: 0.8070 (p90) REVERT: C 49 ILE cc_start: 0.9486 (mt) cc_final: 0.9284 (tt) REVERT: C 133 MET cc_start: 0.8630 (mtm) cc_final: 0.8321 (mtm) REVERT: D 147 MET cc_start: 0.8614 (mmm) cc_final: 0.8182 (mmt) REVERT: D 219 ASP cc_start: 0.9020 (m-30) cc_final: 0.8515 (m-30) REVERT: E 64 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8582 (t80) REVERT: E 219 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8306 (m-30) REVERT: E 254 LEU cc_start: 0.8111 (mt) cc_final: 0.7794 (tt) REVERT: H 70 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8781 (mtpt) REVERT: H 87 ARG cc_start: 0.8883 (mmm160) cc_final: 0.8291 (mmp80) REVERT: H 88 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9218 (pp) REVERT: H 98 MET cc_start: 0.9118 (mmm) cc_final: 0.8884 (mmm) REVERT: H 129 MET cc_start: 0.8240 (tpp) cc_final: 0.7730 (tpp) REVERT: H 135 SER cc_start: 0.9544 (OUTLIER) cc_final: 0.9075 (p) REVERT: H 141 ASP cc_start: 0.8348 (p0) cc_final: 0.7564 (p0) outliers start: 25 outliers final: 14 residues processed: 101 average time/residue: 0.2943 time to fit residues: 42.7780 Evaluate side-chains 88 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain A residue 376 VAL 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 257 VAL 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 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 99 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13067 Z= 0.245 Angle : 0.638 10.098 17726 Z= 0.311 Chirality : 0.043 0.162 2030 Planarity : 0.004 0.049 2276 Dihedral : 4.408 32.773 1805 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.86 % Allowed : 19.29 % Favored : 78.85 % 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: 1.71 (0.21), residues: 723 sheet: -2.28 (0.31), residues: 269 loop : -1.43 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 240 HIS 0.006 0.001 HIS B 20 PHE 0.013 0.001 PHE D 157 TYR 0.017 0.001 TYR E 221 ARG 0.007 0.000 ARG H 87 ********************** 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: 25 poor density : 71 time to evaluate : 1.578 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: 0.9334 (OUTLIER) cc_final: 0.8943 (mm) REVERT: A 105 MET cc_start: 0.8960 (mtm) cc_final: 0.8409 (mpp) REVERT: A 125 MET cc_start: 0.8852 (mpp) cc_final: 0.7637 (mpp) REVERT: A 231 MET cc_start: 0.8927 (mtp) cc_final: 0.8536 (mtp) REVERT: A 235 LYS cc_start: 0.9125 (tptt) cc_final: 0.8917 (mmmm) REVERT: A 253 MET cc_start: 0.8608 (ptp) cc_final: 0.8165 (ptp) REVERT: B 175 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8745 (ptm-80) REVERT: C 13 TYR cc_start: 0.8307 (p90) cc_final: 0.8073 (p90) REVERT: C 49 ILE cc_start: 0.9483 (mt) cc_final: 0.9276 (tt) REVERT: C 133 MET cc_start: 0.8625 (mtm) cc_final: 0.8324 (mtm) REVERT: D 147 MET cc_start: 0.8592 (mmm) cc_final: 0.8133 (mmt) REVERT: D 219 ASP cc_start: 0.8972 (m-30) cc_final: 0.8427 (m-30) REVERT: E 64 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8340 (t80) REVERT: E 219 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: E 254 LEU cc_start: 0.8158 (mt) cc_final: 0.7832 (tp) REVERT: H 70 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8784 (mtpt) REVERT: H 87 ARG cc_start: 0.8928 (mmm160) cc_final: 0.8310 (mmp80) REVERT: H 88 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9213 (pp) REVERT: H 98 MET cc_start: 0.9170 (mmm) cc_final: 0.8896 (mmm) REVERT: H 129 MET cc_start: 0.8300 (tpp) cc_final: 0.7495 (tpp) REVERT: H 135 SER cc_start: 0.9562 (OUTLIER) cc_final: 0.9083 (p) REVERT: H 141 ASP cc_start: 0.8481 (p0) cc_final: 0.7769 (p0) outliers start: 25 outliers final: 15 residues processed: 94 average time/residue: 0.2878 time to fit residues: 39.2496 Evaluate side-chains 88 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 257 VAL 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 213 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.048691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.037479 restraints weight = 62053.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038780 restraints weight = 32618.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.039678 restraints weight = 21350.420| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13067 Z= 0.251 Angle : 0.642 10.012 17726 Z= 0.313 Chirality : 0.043 0.203 2030 Planarity : 0.003 0.046 2276 Dihedral : 4.465 33.040 1805 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.61 % Allowed : 18.91 % Favored : 78.48 % 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: -0.29 (0.22), residues: 1645 helix: 1.71 (0.21), residues: 721 sheet: -2.30 (0.31), residues: 262 loop : -1.42 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 240 HIS 0.007 0.001 HIS C 194 PHE 0.014 0.001 PHE D 157 TYR 0.018 0.001 TYR C 291 ARG 0.006 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.85 seconds wall clock time: 39 minutes 55.26 seconds (2395.26 seconds total)