Starting phenix.real_space_refine on Mon Dec 30 10:18:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osh_13051/12_2024/7osh_13051.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osh_13051/12_2024/7osh_13051.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/7osh_13051/12_2024/7osh_13051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osh_13051/12_2024/7osh_13051.map" model { file = "/net/cci-nas-00/data/ceres_data/7osh_13051/12_2024/7osh_13051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osh_13051/12_2024/7osh_13051.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= 0.004 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 47 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 45.430 43.120 48.151 1.00133.21 S ATOM 11862 SG CYS H 48 43.343 44.213 45.789 1.00130.17 S ATOM 12043 SG CYS H 72 46.172 45.161 44.243 1.00137.89 S Time building chain proxies: 8.10, per 1000 atoms: 0.63 Number of scatterers: 12826 At special positions: 0 Unit cell: (80.352, 92.016, 193.104, 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: 2.87 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 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " 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: 57 helices and 13 sheets defined 44.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.535A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.507A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.645A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.753A 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: 3.851A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.595A pdb=" N GLN B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.743A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 233 through 244 removed outlier: 4.406A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.013A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.624A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.519A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 107 through 114 removed outlier: 3.881A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) 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: 3.616A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.828A pdb=" N GLN C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.644A pdb=" N LEU C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.568A pdb=" N ALA C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.155A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.524A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.658A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (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: 3.784A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.108A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.519A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.869A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.620A 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 Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.993A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.637A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.756A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.644A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.648A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.586A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.549A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.092A 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: 3.787A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.501A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.535A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 207 through 213 removed outlier: 4.044A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.516A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.233A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.803A 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 150 Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.681A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 7.937A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.797A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.591A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.037A 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: 6.522A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.653A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.241A 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) removed outlier: 7.594A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 25 removed outlier: 5.368A pdb=" N HIS B 20 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN B 11 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU B 24 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN B 7 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.006A 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: 7.703A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 251 removed outlier: 6.692A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.791A pdb=" N VAL C 4 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.604A 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: 6.782A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 228 removed outlier: 3.676A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (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: 3.523A pdb=" N VAL H 121 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG H 152 " --> pdb=" O VAL H 121 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1491 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: 3.74 Time building geometry restraints manager: 3.36 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: 4182 1.34 - 1.46: 2340 1.46 - 1.57: 6466 1.57 - 1.69: 2 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 1.586 -0.061 2.10e-02 2.27e+03 8.35e+00 bond pdb=" CG1 ILE B 181 " pdb=" CD1 ILE B 181 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.24e+00 bond pdb=" CB VAL A 202 " pdb=" CG1 VAL A 202 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.34e+00 bond pdb=" CB GLN A 232 " pdb=" CG GLN A 232 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.99e+00 bond pdb=" CB TYR A 291 " pdb=" CG TYR A 291 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.20e-02 2.07e+03 4.61e+00 ... (remaining 13062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 17443 3.47 - 6.94: 241 6.94 - 10.41: 35 10.41 - 13.88: 5 13.88 - 17.34: 2 Bond angle restraints: 17726 Sorted by residual: angle pdb=" CA LEU A 356 " pdb=" CB LEU A 356 " pdb=" CG LEU A 356 " ideal model delta sigma weight residual 116.30 133.64 -17.34 3.50e+00 8.16e-02 2.46e+01 angle pdb=" C GLU H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 125.02 133.63 -8.61 1.76e+00 3.23e-01 2.39e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 122.07 128.93 -6.86 1.43e+00 4.89e-01 2.30e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C GLU H 138 " pdb=" N GLU H 139 " pdb=" CA GLU H 139 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 ... (remaining 17721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 6835 16.98 - 33.97: 714 33.97 - 50.95: 162 50.95 - 67.93: 18 67.93 - 84.92: 7 Dihedral angle restraints: 7736 sinusoidal: 3041 harmonic: 4695 Sorted by residual: dihedral pdb=" CA ASP H 108 " pdb=" C ASP H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual 180.00 148.88 31.12 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA ARG C 233 " pdb=" C ARG C 233 " pdb=" N ASP C 234 " pdb=" CA ASP C 234 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual 180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1704 0.082 - 0.164: 277 0.164 - 0.245: 41 0.245 - 0.327: 5 0.327 - 0.409: 3 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 -2.22 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN C 261 " pdb=" N ASN C 261 " pdb=" C ASN C 261 " pdb=" CB ASN C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2027 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO E 210 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.048 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=" C MET D 66 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO D 67 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO E 67 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.041 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 120 2.56 - 3.14: 9266 3.14 - 3.73: 20139 3.73 - 4.31: 28354 4.31 - 4.90: 46659 Nonbonded interactions: 104538 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.971 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.002 2.320 nonbonded pdb=" SD MET H 50 " pdb="CU CU A 502 " model vdw 2.113 2.600 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.129 2.170 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.157 2.170 ... (remaining 104533 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: 0.500 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 32.460 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.008 0.097 13067 Z= 0.548 Angle : 1.089 17.345 17726 Z= 0.575 Chirality : 0.065 0.409 2030 Planarity : 0.007 0.096 2276 Dihedral : 14.372 84.915 4740 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.60 % Allowed : 10.05 % Favored : 89.35 % Cbeta Deviations : 0.07 % 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: -5.50 (0.14), residues: 1645 helix: -4.39 (0.08), residues: 697 sheet: -2.98 (0.29), residues: 235 loop : -2.90 (0.19), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 211 HIS 0.013 0.002 HIS C 37 PHE 0.018 0.003 PHE D 157 TYR 0.014 0.002 TYR C 13 ARG 0.006 0.001 ARG A 378 *********************** 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 147 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8644 (mtt) cc_final: 0.8101 (mpp) REVERT: A 235 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9167 (mmmm) REVERT: A 420 MET cc_start: 0.8766 (mmm) cc_final: 0.8566 (mmm) REVERT: B 47 LYS cc_start: 0.9295 (mttm) cc_final: 0.8987 (mtpp) REVERT: B 133 MET cc_start: 0.9101 (ttm) cc_final: 0.8872 (mtm) REVERT: C 37 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6290 (t-90) REVERT: C 61 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8658 (mmmm) REVERT: C 86 TYR cc_start: 0.8996 (m-80) cc_final: 0.8694 (m-10) REVERT: C 181 ILE cc_start: 0.9376 (mt) cc_final: 0.9143 (mm) REVERT: C 283 HIS cc_start: 0.7721 (m90) cc_final: 0.7275 (m90) REVERT: C 304 GLN cc_start: 0.8583 (mp10) cc_final: 0.8208 (pt0) REVERT: D 132 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7425 (pm20) REVERT: E 3 GLN cc_start: 0.8501 (mt0) cc_final: 0.7909 (mt0) REVERT: E 10 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8799 (tmtt) REVERT: H 65 LYS cc_start: 0.8715 (pttm) cc_final: 0.7840 (pttt) REVERT: H 77 MET cc_start: 0.9564 (ttp) cc_final: 0.9336 (ttm) REVERT: H 87 ARG cc_start: 0.9178 (mmm160) cc_final: 0.8893 (mmm160) REVERT: H 90 ASP cc_start: 0.8695 (t0) cc_final: 0.8067 (p0) REVERT: H 92 LYS cc_start: 0.9377 (tttp) cc_final: 0.9038 (ttmm) REVERT: H 98 MET cc_start: 0.8958 (mmm) cc_final: 0.8663 (mmm) REVERT: H 155 ARG cc_start: 0.8947 (mmm-85) cc_final: 0.8692 (mmm-85) outliers start: 8 outliers final: 1 residues processed: 147 average time/residue: 0.3613 time to fit residues: 70.8138 Evaluate side-chains 94 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 37 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 190 ASN A 212 ASN A 241 ASN A 301 ASN A 324 ASN B 20 HIS B 37 HIS B 38 ASN B 176 GLN C 25 ASN C 194 HIS C 238 GLN C 270 GLN D 225 ASN E 108 HIS E 225 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2083 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= 0.180 Angle : 0.600 10.438 17726 Z= 0.310 Chirality : 0.042 0.171 2030 Planarity : 0.005 0.059 2276 Dihedral : 5.146 35.808 1806 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.12 % Allowed : 12.88 % Favored : 86.00 % 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: -3.41 (0.18), residues: 1645 helix: -1.87 (0.16), residues: 712 sheet: -2.69 (0.30), residues: 233 loop : -2.38 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 253 HIS 0.003 0.001 HIS H 110 PHE 0.012 0.001 PHE D 157 TYR 0.011 0.001 TYR B 86 ARG 0.008 0.000 ARG C 307 *********************** 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 135 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7323 (mtt) cc_final: 0.6883 (mpp) REVERT: A 125 MET cc_start: 0.8602 (mtt) cc_final: 0.8154 (mpp) REVERT: A 420 MET cc_start: 0.8689 (mmm) cc_final: 0.8487 (mmm) REVERT: B 46 MET cc_start: 0.9448 (mmp) cc_final: 0.9248 (mmt) REVERT: C 37 HIS cc_start: 0.6909 (OUTLIER) cc_final: 0.6648 (t-90) REVERT: C 61 LYS cc_start: 0.9189 (mtpt) cc_final: 0.8771 (mmmm) REVERT: C 181 ILE cc_start: 0.9271 (mt) cc_final: 0.9011 (mm) REVERT: C 283 HIS cc_start: 0.7576 (m90) cc_final: 0.7098 (m90) REVERT: D 132 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7402 (pm20) REVERT: E 3 GLN cc_start: 0.8536 (mt0) cc_final: 0.7998 (mt0) REVERT: H 65 LYS cc_start: 0.8494 (pttm) cc_final: 0.7638 (pttt) REVERT: H 87 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8851 (mmm160) REVERT: H 90 ASP cc_start: 0.8599 (t0) cc_final: 0.7859 (p0) REVERT: H 155 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8609 (mmm-85) outliers start: 15 outliers final: 4 residues processed: 130 average time/residue: 0.2625 time to fit residues: 49.9312 Evaluate side-chains 97 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** B 11 GLN B 38 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2385 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= 0.214 Angle : 0.579 9.326 17726 Z= 0.293 Chirality : 0.042 0.165 2030 Planarity : 0.004 0.046 2276 Dihedral : 4.820 34.817 1806 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.49 % Allowed : 14.74 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1645 helix: -0.21 (0.19), residues: 713 sheet: -2.45 (0.31), residues: 243 loop : -2.11 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.003 0.001 HIS H 110 PHE 0.012 0.001 PHE D 157 TYR 0.015 0.001 TYR H 118 ARG 0.005 0.000 ARG H 66 *********************** 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 118 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9035 (mp) REVERT: A 62 MET cc_start: 0.7391 (mtt) cc_final: 0.6850 (mpp) REVERT: A 125 MET cc_start: 0.8616 (mtt) cc_final: 0.8156 (mpp) REVERT: A 214 ASN cc_start: 0.8036 (t0) cc_final: 0.7724 (t0) REVERT: B 133 MET cc_start: 0.8979 (mtm) cc_final: 0.8761 (mtt) REVERT: C 37 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6647 (t-90) REVERT: C 61 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8813 (mmmm) REVERT: C 181 ILE cc_start: 0.9284 (mt) cc_final: 0.9032 (mm) REVERT: C 283 HIS cc_start: 0.7619 (m90) cc_final: 0.7149 (m90) REVERT: D 132 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7455 (pm20) REVERT: D 201 GLU cc_start: 0.8252 (pm20) cc_final: 0.7997 (pm20) REVERT: E 3 GLN cc_start: 0.8600 (mt0) cc_final: 0.8084 (mt0) REVERT: H 51 ILE cc_start: 0.9514 (mm) cc_final: 0.9192 (mm) REVERT: H 87 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8859 (mmm160) REVERT: H 90 ASP cc_start: 0.8581 (t0) cc_final: 0.7846 (p0) REVERT: H 155 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8627 (mmm-85) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.2659 time to fit residues: 45.4337 Evaluate side-chains 104 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 0.0000 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 chunk 141 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2645 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= 0.185 Angle : 0.559 11.718 17726 Z= 0.280 Chirality : 0.042 0.162 2030 Planarity : 0.003 0.042 2276 Dihedral : 4.581 34.447 1806 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.86 % Allowed : 16.16 % Favored : 81.98 % 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: -1.34 (0.21), residues: 1645 helix: 0.62 (0.20), residues: 715 sheet: -2.30 (0.30), residues: 262 loop : -1.92 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.005 0.001 HIS C 194 PHE 0.011 0.001 PHE D 157 TYR 0.016 0.001 TYR B 86 ARG 0.002 0.000 ARG D 17 *********************** 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 122 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8949 (mp) REVERT: A 62 MET cc_start: 0.7376 (mtt) cc_final: 0.6839 (mpp) REVERT: A 125 MET cc_start: 0.8671 (mtt) cc_final: 0.7965 (mpp) REVERT: A 214 ASN cc_start: 0.7968 (t0) cc_final: 0.7679 (t0) REVERT: C 61 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8808 (mmmm) REVERT: C 181 ILE cc_start: 0.9281 (mt) cc_final: 0.9023 (mm) REVERT: C 283 HIS cc_start: 0.7616 (m90) cc_final: 0.7151 (m90) REVERT: D 132 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7541 (pm20) REVERT: E 3 GLN cc_start: 0.8679 (mt0) cc_final: 0.8144 (mt0) REVERT: H 51 ILE cc_start: 0.9513 (mm) cc_final: 0.9211 (mm) REVERT: H 65 LYS cc_start: 0.8588 (ptmt) cc_final: 0.7824 (ptmt) REVERT: H 87 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8855 (mmm160) REVERT: H 90 ASP cc_start: 0.8572 (t0) cc_final: 0.7781 (p0) REVERT: H 155 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8511 (mmm-85) outliers start: 25 outliers final: 12 residues processed: 117 average time/residue: 0.2617 time to fit residues: 45.1413 Evaluate side-chains 104 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 23 ASN B 38 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2763 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= 0.191 Angle : 0.548 9.151 17726 Z= 0.274 Chirality : 0.042 0.154 2030 Planarity : 0.003 0.039 2276 Dihedral : 4.493 34.191 1806 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.71 % Allowed : 17.13 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1645 helix: 1.06 (0.21), residues: 715 sheet: -2.24 (0.30), residues: 264 loop : -1.81 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.011 0.001 HIS C 194 PHE 0.012 0.001 PHE D 157 TYR 0.017 0.001 TYR B 86 ARG 0.007 0.000 ARG H 66 *********************** 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 119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8937 (mp) REVERT: A 62 MET cc_start: 0.7407 (mtt) cc_final: 0.6866 (mpp) REVERT: A 125 MET cc_start: 0.8671 (mtt) cc_final: 0.7990 (mpp) REVERT: A 214 ASN cc_start: 0.7984 (t0) cc_final: 0.7709 (t0) REVERT: A 390 MET cc_start: 0.8422 (tpt) cc_final: 0.8187 (tpp) REVERT: B 46 MET cc_start: 0.9350 (tpp) cc_final: 0.9147 (mmt) REVERT: C 61 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8826 (mmmm) REVERT: C 181 ILE cc_start: 0.9275 (mt) cc_final: 0.9020 (mm) REVERT: C 283 HIS cc_start: 0.7635 (m90) cc_final: 0.7181 (m90) REVERT: D 132 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7530 (pm20) REVERT: E 3 GLN cc_start: 0.8702 (mt0) cc_final: 0.8133 (mt0) REVERT: E 135 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7846 (tm-30) REVERT: H 51 ILE cc_start: 0.9520 (mm) cc_final: 0.9252 (mm) REVERT: H 87 ARG cc_start: 0.9161 (mmm160) cc_final: 0.8869 (mmm160) REVERT: H 90 ASP cc_start: 0.8529 (t0) cc_final: 0.7636 (p0) REVERT: H 155 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8542 (mmm-85) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.2565 time to fit residues: 44.1109 Evaluate side-chains 106 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 63 VAL 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: 0.0570 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 157 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 97 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13067 Z= 0.139 Angle : 0.540 9.413 17726 Z= 0.267 Chirality : 0.041 0.156 2030 Planarity : 0.003 0.037 2276 Dihedral : 4.288 33.063 1806 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.86 % Allowed : 17.65 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.22), residues: 1645 helix: 1.42 (0.21), residues: 717 sheet: -1.99 (0.30), residues: 278 loop : -1.75 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.006 0.001 HIS C 194 PHE 0.010 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.005 0.000 ARG H 66 *********************** 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 132 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8895 (mp) REVERT: A 62 MET cc_start: 0.7371 (mtt) cc_final: 0.6682 (mpp) REVERT: A 125 MET cc_start: 0.8635 (mtt) cc_final: 0.7959 (mpp) REVERT: A 214 ASN cc_start: 0.7908 (t0) cc_final: 0.7626 (t0) REVERT: B 133 MET cc_start: 0.8958 (mtm) cc_final: 0.8754 (mtt) REVERT: C 37 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6802 (t-90) REVERT: C 38 ASN cc_start: 0.8376 (m-40) cc_final: 0.8057 (m-40) REVERT: C 61 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8849 (mmtm) REVERT: C 181 ILE cc_start: 0.9308 (mt) cc_final: 0.9058 (mm) REVERT: C 283 HIS cc_start: 0.7628 (m90) cc_final: 0.7143 (m90) REVERT: D 81 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8246 (mt-10) REVERT: D 132 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7467 (pm20) REVERT: E 3 GLN cc_start: 0.8641 (mt0) cc_final: 0.8095 (mt0) REVERT: E 135 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7900 (tm-30) REVERT: H 51 ILE cc_start: 0.9499 (mm) cc_final: 0.9251 (mm) REVERT: H 90 ASP cc_start: 0.8533 (t0) cc_final: 0.7560 (p0) REVERT: H 155 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8645 (tpp80) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 0.2389 time to fit residues: 45.5281 Evaluate side-chains 112 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 88 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13067 Z= 0.327 Angle : 0.633 8.491 17726 Z= 0.314 Chirality : 0.044 0.163 2030 Planarity : 0.003 0.034 2276 Dihedral : 4.567 36.442 1806 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.01 % Allowed : 17.80 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1645 helix: 1.44 (0.21), residues: 722 sheet: -2.10 (0.31), residues: 263 loop : -1.72 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 211 HIS 0.007 0.001 HIS C 194 PHE 0.017 0.002 PHE D 157 TYR 0.014 0.002 TYR B 86 ARG 0.005 0.000 ARG H 66 *********************** 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 117 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8191 (mp-120) REVERT: A 58 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 62 MET cc_start: 0.7370 (mtt) cc_final: 0.6554 (mpp) REVERT: A 105 MET cc_start: 0.8437 (mtt) cc_final: 0.8208 (mtm) REVERT: A 125 MET cc_start: 0.8699 (mtt) cc_final: 0.8007 (mpp) REVERT: A 214 ASN cc_start: 0.8231 (t0) cc_final: 0.7988 (t0) REVERT: C 61 LYS cc_start: 0.9266 (mtpt) cc_final: 0.8821 (mmtm) REVERT: C 181 ILE cc_start: 0.9280 (mt) cc_final: 0.8942 (mm) REVERT: C 283 HIS cc_start: 0.7843 (m90) cc_final: 0.7387 (m90) REVERT: D 132 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7515 (pm20) REVERT: E 3 GLN cc_start: 0.8726 (mt0) cc_final: 0.8151 (mt0) REVERT: E 135 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7968 (tm-30) REVERT: H 51 ILE cc_start: 0.9544 (mm) cc_final: 0.9240 (mm) REVERT: H 65 LYS cc_start: 0.8508 (ptmt) cc_final: 0.8065 (ptmt) REVERT: H 87 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8709 (mmm160) REVERT: H 90 ASP cc_start: 0.8554 (t0) cc_final: 0.7517 (p0) outliers start: 27 outliers final: 21 residues processed: 114 average time/residue: 0.2413 time to fit residues: 41.7539 Evaluate side-chains 109 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.0030 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3096 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= 0.226 Angle : 0.587 9.683 17726 Z= 0.291 Chirality : 0.043 0.181 2030 Planarity : 0.003 0.034 2276 Dihedral : 4.489 35.640 1806 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.86 % Allowed : 18.02 % Favored : 80.12 % 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: -0.42 (0.22), residues: 1645 helix: 1.60 (0.21), residues: 718 sheet: -2.05 (0.31), residues: 265 loop : -1.64 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.006 0.001 HIS C 194 PHE 0.013 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.004 0.000 ARG H 66 *********************** 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 119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8254 (mp-120) REVERT: A 58 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 62 MET cc_start: 0.7474 (mtt) cc_final: 0.6702 (mpp) REVERT: A 105 MET cc_start: 0.8373 (mtt) cc_final: 0.8161 (mtm) REVERT: A 125 MET cc_start: 0.8621 (mtt) cc_final: 0.7902 (mpp) REVERT: A 214 ASN cc_start: 0.8129 (t0) cc_final: 0.7880 (t0) REVERT: C 61 LYS cc_start: 0.9251 (mtpt) cc_final: 0.8824 (mmtm) REVERT: C 181 ILE cc_start: 0.9262 (mt) cc_final: 0.8910 (mm) REVERT: C 283 HIS cc_start: 0.7811 (m90) cc_final: 0.7328 (m90) REVERT: D 132 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7308 (pm20) REVERT: E 3 GLN cc_start: 0.8699 (mt0) cc_final: 0.8100 (mt0) REVERT: E 135 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8009 (tm-30) REVERT: H 51 ILE cc_start: 0.9532 (mm) cc_final: 0.9234 (mm) REVERT: H 87 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8840 (mmm160) REVERT: H 90 ASP cc_start: 0.8541 (t0) cc_final: 0.7479 (p0) outliers start: 25 outliers final: 20 residues processed: 115 average time/residue: 0.2426 time to fit residues: 42.3653 Evaluate side-chains 113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 126 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 0.0040 chunk 96 optimal weight: 0.2980 overall best weight: 2.0598 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13067 Z= 0.223 Angle : 0.594 11.864 17726 Z= 0.295 Chirality : 0.043 0.232 2030 Planarity : 0.003 0.037 2276 Dihedral : 4.463 37.413 1806 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.79 % Allowed : 18.09 % Favored : 80.12 % 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: -0.33 (0.22), residues: 1645 helix: 1.68 (0.21), residues: 718 sheet: -2.02 (0.31), residues: 265 loop : -1.58 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.006 0.001 HIS C 194 PHE 0.013 0.001 PHE D 157 TYR 0.031 0.001 TYR B 86 ARG 0.004 0.000 ARG H 66 *********************** 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 117 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 62 MET cc_start: 0.7518 (mtt) cc_final: 0.6678 (mpp) REVERT: A 125 MET cc_start: 0.8643 (mtt) cc_final: 0.7928 (mpp) REVERT: A 214 ASN cc_start: 0.8114 (t0) cc_final: 0.7878 (t0) REVERT: C 61 LYS cc_start: 0.9227 (mtpt) cc_final: 0.8865 (mmtm) REVERT: C 181 ILE cc_start: 0.9263 (mt) cc_final: 0.8913 (mm) REVERT: C 283 HIS cc_start: 0.7802 (m90) cc_final: 0.7325 (m90) REVERT: D 21 LEU cc_start: 0.9191 (tp) cc_final: 0.8962 (tt) REVERT: D 81 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8229 (mt-10) REVERT: D 132 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7320 (pm20) REVERT: D 147 MET cc_start: 0.8846 (mtm) cc_final: 0.8361 (mpp) REVERT: E 3 GLN cc_start: 0.8691 (mt0) cc_final: 0.8096 (mt0) REVERT: E 135 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 51 ILE cc_start: 0.9532 (mm) cc_final: 0.9236 (mm) REVERT: H 87 ARG cc_start: 0.9181 (mmm160) cc_final: 0.8836 (mmm160) REVERT: H 90 ASP cc_start: 0.8720 (t0) cc_final: 0.7583 (p0) outliers start: 24 outliers final: 21 residues processed: 113 average time/residue: 0.2428 time to fit residues: 41.7986 Evaluate side-chains 112 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 107 optimal weight: 0.1980 chunk 162 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13067 Z= 0.235 Angle : 0.604 10.955 17726 Z= 0.298 Chirality : 0.043 0.213 2030 Planarity : 0.003 0.033 2276 Dihedral : 4.328 19.270 1804 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.86 % Allowed : 18.09 % Favored : 80.04 % 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: 1.72 (0.21), residues: 718 sheet: -2.09 (0.30), residues: 267 loop : -1.53 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 211 HIS 0.006 0.001 HIS C 194 PHE 0.014 0.001 PHE D 157 TYR 0.028 0.001 TYR B 86 ARG 0.004 0.000 ARG H 66 ********************** 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 118 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 62 MET cc_start: 0.7539 (mtt) cc_final: 0.6684 (mpp) REVERT: A 125 MET cc_start: 0.8649 (mtt) cc_final: 0.7931 (mpp) REVERT: C 61 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8826 (mmtm) REVERT: C 181 ILE cc_start: 0.9286 (mt) cc_final: 0.9009 (mm) REVERT: C 283 HIS cc_start: 0.7829 (m90) cc_final: 0.7349 (m90) REVERT: D 81 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8183 (mt-10) REVERT: D 132 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7276 (pm20) REVERT: D 147 MET cc_start: 0.8847 (mtm) cc_final: 0.8319 (mpp) REVERT: E 3 GLN cc_start: 0.8653 (mt0) cc_final: 0.8053 (mt0) REVERT: E 135 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8014 (tm-30) REVERT: H 51 ILE cc_start: 0.9535 (mm) cc_final: 0.9236 (mm) REVERT: H 87 ARG cc_start: 0.9161 (mmm160) cc_final: 0.8826 (mmm160) REVERT: H 90 ASP cc_start: 0.8715 (t0) cc_final: 0.7568 (p0) outliers start: 25 outliers final: 22 residues processed: 114 average time/residue: 0.2334 time to fit residues: 40.2345 Evaluate side-chains 115 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 126 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.043695 restraints weight = 53664.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045327 restraints weight = 26559.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046400 restraints weight = 16851.624| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13067 Z= 0.181 Angle : 0.576 9.754 17726 Z= 0.285 Chirality : 0.042 0.205 2030 Planarity : 0.003 0.033 2276 Dihedral : 4.206 17.339 1804 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.49 % Allowed : 18.32 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1645 helix: 1.84 (0.21), residues: 719 sheet: -2.04 (0.30), residues: 265 loop : -1.49 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.005 0.001 HIS C 194 PHE 0.012 0.001 PHE D 157 TYR 0.022 0.001 TYR B 86 ARG 0.003 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.37 seconds wall clock time: 39 minutes 48.68 seconds (2388.68 seconds total)