Starting phenix.real_space_refine on Thu Jul 2 13:13:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6s_35205/07_2026/8i6s_35205.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.032 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5581 2.51 5 N 1432 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8641 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2261 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 20, 'GLN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2316 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1679 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 641 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8641 At special positions: 0 Unit cell: (66.066, 78.936, 179.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 6 15.00 Mg 2 11.99 O 1600 8.00 N 1432 7.00 C 5581 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 483.8 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 56.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.726A pdb=" N SER A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.953A pdb=" N MET A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.573A pdb=" N GLY A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.644A pdb=" N ALA A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 178 removed outlier: 3.715A pdb=" N ARG A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 231 removed outlier: 3.541A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 4.262A pdb=" N ILE A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 293 removed outlier: 3.547A pdb=" N ARG A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix removed outlier: 3.651A pdb=" N TYR A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.508A pdb=" N THR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.925A pdb=" N LEU B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.858A pdb=" N ASN B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.028A pdb=" N LEU B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.694A pdb=" N LEU B 138 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 removed outlier: 4.120A pdb=" N GLN B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 186 removed outlier: 4.690A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.632A pdb=" N ALA B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 202 " --> pdb=" O LEU B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 55 through 69 removed outlier: 3.632A pdb=" N PHE C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.833A pdb=" N MET C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.587A pdb=" N ARG C 92 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.565A pdb=" N ASP C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.912A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 removed outlier: 3.732A pdb=" N ALA C 173 " --> pdb=" O GLY C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 173' Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.610A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.722A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 202 through 233 removed outlier: 3.536A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.510A pdb=" N GLU C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 292 removed outlier: 3.712A pdb=" N VAL C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) Proline residue: C 254 - end of helix removed outlier: 3.684A pdb=" N TYR C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N SER C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 332 removed outlier: 3.869A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 3.661A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.927A pdb=" N LEU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 101 through 108 removed outlier: 3.742A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.574A pdb=" N ARG D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 4.027A pdb=" N ARG D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.957A pdb=" N SER D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 removed outlier: 3.612A pdb=" N GLN E 96 " --> pdb=" O LYS E 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 163 removed outlier: 3.507A pdb=" N ARG E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 25 removed outlier: 6.829A pdb=" N VAL B 21 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 6 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 4 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.118A pdb=" N PHE B 32 " --> pdb=" O LEU B 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.468A pdb=" N LEU B 59 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 126 through 128 removed outlier: 4.181A pdb=" N GLN C 126 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 128 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 4.016A pdb=" N GLU D 5 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 58 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 61 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 64 " --> pdb=" O LEU D 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 190 through 193 removed outlier: 3.882A pdb=" N VAL D 33 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N LEU D 208 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE D 32 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU D 210 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 34 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.611A pdb=" N GLY D 82 " --> pdb=" O LEU D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 361 hydrogen bonds defined for protein. 1071 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: 0.87 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2048 1.33 - 1.46: 1723 1.46 - 1.58: 4967 1.58 - 1.70: 10 1.70 - 1.83: 38 Bond restraints: 8786 Sorted by residual: bond pdb=" C6 ATP D 301 " pdb=" N6 ATP D 301 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C6 ATP B 302 " pdb=" N6 ATP B 302 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" C5 ATP B 302 " pdb=" N7 ATP B 302 " ideal model delta sigma weight residual 1.387 1.469 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C5 ATP D 301 " pdb=" N7 ATP D 301 " ideal model delta sigma weight residual 1.387 1.468 -0.081 1.00e-02 1.00e+04 6.57e+01 bond pdb=" O5' ATP D 301 " pdb=" PA ATP D 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.10e-02 8.26e+03 4.14e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 11671 4.67 - 9.34: 180 9.34 - 14.01: 29 14.01 - 18.68: 5 18.68 - 23.35: 1 Bond angle restraints: 11886 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 116.52 23.35 1.00e+00 1.00e+00 5.45e+02 angle pdb=" PB ATP D 301 " pdb=" O3B ATP D 301 " pdb=" PG ATP D 301 " ideal model delta sigma weight residual 139.87 125.37 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" PA ATP B 302 " pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " ideal model delta sigma weight residual 136.83 122.76 14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O3A ATP B 302 " pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " ideal model delta sigma weight residual 101.57 116.72 -15.15 1.54e+00 4.24e-01 9.73e+01 angle pdb=" PA ATP D 301 " pdb=" O3A ATP D 301 " pdb=" PB ATP D 301 " ideal model delta sigma weight residual 136.83 127.43 9.40 1.00e+00 1.00e+00 8.84e+01 ... (remaining 11881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4623 17.97 - 35.95: 547 35.95 - 53.92: 108 53.92 - 71.89: 20 71.89 - 89.86: 6 Dihedral angle restraints: 5304 sinusoidal: 2116 harmonic: 3188 Sorted by residual: dihedral pdb=" CA VAL A 192 " pdb=" C VAL A 192 " pdb=" N TRP A 193 " pdb=" CA TRP A 193 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA ASP C 190 " pdb=" C ASP C 190 " pdb=" N LEU C 191 " pdb=" CA LEU C 191 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" N HIS A 230 " pdb=" CA HIS A 230 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1133 0.073 - 0.146: 224 0.146 - 0.219: 46 0.219 - 0.292: 5 0.292 - 0.365: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CB ILE B 215 " pdb=" CA ILE B 215 " pdb=" CG1 ILE B 215 " pdb=" CG2 ILE B 215 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE D 2 " pdb=" CA ILE D 2 " pdb=" CG1 ILE D 2 " pdb=" CG2 ILE D 2 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL B 125 " pdb=" CA VAL B 125 " pdb=" CG1 VAL B 125 " pdb=" CG2 VAL B 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1408 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 195 " -0.045 2.00e-02 2.50e+03 6.17e-02 5.71e+01 pdb=" CG HIS B 195 " 0.107 2.00e-02 2.50e+03 pdb=" ND1 HIS B 195 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS B 195 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 195 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS B 195 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 192 " -0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C VAL A 192 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL A 192 " -0.032 2.00e-02 2.50e+03 pdb=" N TRP A 193 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 280 " -0.013 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP C 280 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 280 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 280 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 280 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 280 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 280 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 280 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 280 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 280 " 0.001 2.00e-02 2.50e+03 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 84 2.64 - 3.20: 7059 3.20 - 3.77: 13820 3.77 - 4.33: 17569 4.33 - 4.90: 27254 Nonbonded interactions: 65786 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 301 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3A ATP D 301 " model vdw 2.077 2.170 nonbonded pdb=" O1A ATP B 302 " pdb="MG MG B 303 " model vdw 2.133 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2B ATP D 301 " model vdw 2.135 2.170 nonbonded pdb=" O1B ATP B 302 " pdb="MG MG B 303 " model vdw 2.253 2.170 ... (remaining 65781 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 'A' selection = (chain 'C' and (resid 35 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 or (resid 91 through 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 or (resid 167 through 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 or (resid 171 and (name N or name CA or name C or name O or n \ ame CB )) or resid 172 through 194 or (resid 195 and (name N or name CA or name \ C or name O or name CB )) or resid 196 or (resid 197 through 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 335)) } ncs_group { reference = (chain 'B' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 12 through 222)) selection = (chain 'D' and resid 1 through 222) } 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: 10.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.006 0.112 8787 Z= 0.413 Angle : 1.394 23.352 11886 Z= 0.763 Chirality : 0.063 0.365 1411 Planarity : 0.007 0.062 1476 Dihedral : 15.969 89.863 3254 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 0.97 % Allowed : 2.48 % Favored : 96.54 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.18 (0.17), residues: 1115 helix: -4.23 (0.09), residues: 575 sheet: -0.91 (0.68), residues: 55 loop : -2.52 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 118 TYR 0.040 0.002 TYR A 250 PHE 0.039 0.001 PHE D 180 TRP 0.041 0.002 TRP C 280 HIS 0.080 0.004 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.41 ( 8786) covalent geometry : angle 1.39357 / 0.76 (11886) hydrogen bonds : bond 0.31506 / 20.92 ( 361) hydrogen bonds : angle 10.18497 / 6.87 ( 1071) Misc. bond : bond 0.01761 / 0.93 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.6693 (mmp) cc_final: 0.6455 (mmp) REVERT: A 215 LEU cc_start: 0.6983 (mm) cc_final: 0.5502 (tp) REVERT: B 162 ASP cc_start: 0.7197 (p0) cc_final: 0.6967 (p0) REVERT: C 66 MET cc_start: 0.4364 (tpt) cc_final: 0.3998 (tpt) REVERT: D 154 HIS cc_start: 0.6844 (p-80) cc_final: 0.5443 (t-90) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.0631 time to fit residues: 12.1987 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0060 chunk 106 optimal weight: 4.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 230 HIS C 82 ASN E 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.097980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.080701 restraints weight = 53125.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.082464 restraints weight = 37599.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.083715 restraints weight = 29318.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.084626 restraints weight = 24525.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.085287 restraints weight = 21435.350| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8787 Z= 0.124 Angle : 0.653 7.201 11886 Z= 0.329 Chirality : 0.041 0.187 1411 Planarity : 0.004 0.035 1476 Dihedral : 5.709 50.775 1151 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.41 % Favored : 96.41 % Rotamer: Outliers : 1.08 % Allowed : 5.29 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.22), residues: 1115 helix: -1.54 (0.18), residues: 585 sheet: -0.86 (0.71), residues: 53 loop : -1.99 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.008 0.001 TYR A 250 PHE 0.011 0.001 PHE C 207 TRP 0.013 0.001 TRP A 271 HIS 0.020 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 8786) covalent geometry : angle 0.65262 / 0.33 (11886) hydrogen bonds : bond 0.05592 / 3.81 ( 361) hydrogen bonds : angle 4.90357 / 3.32 ( 1071) Misc. bond : bond 0.00633 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9205 (tt) cc_final: 0.8934 (pp) REVERT: B 162 ASP cc_start: 0.7275 (p0) cc_final: 0.6789 (p0) outliers start: 10 outliers final: 9 residues processed: 113 average time/residue: 0.0596 time to fit residues: 10.4273 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 188 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.093368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.076749 restraints weight = 56252.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.078251 restraints weight = 41314.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.079349 restraints weight = 33171.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.080123 restraints weight = 28242.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.080658 restraints weight = 25135.257| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8787 Z= 0.155 Angle : 0.675 7.131 11886 Z= 0.339 Chirality : 0.043 0.150 1411 Planarity : 0.004 0.033 1476 Dihedral : 5.493 53.715 1151 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.68 % Favored : 96.14 % Rotamer: Outliers : 0.86 % Allowed : 7.78 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1115 helix: -0.23 (0.21), residues: 587 sheet: -1.38 (0.58), residues: 67 loop : -1.80 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 104 TYR 0.010 0.002 TYR E 141 PHE 0.026 0.002 PHE D 180 TRP 0.009 0.001 TRP C 318 HIS 0.014 0.002 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 8786) covalent geometry : angle 0.67512 / 0.34 (11886) hydrogen bonds : bond 0.04738 / 3.25 ( 361) hydrogen bonds : angle 4.45671 / 2.99 ( 1071) Misc. bond : bond 0.00200 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9318 (tt) cc_final: 0.9064 (pp) REVERT: B 162 ASP cc_start: 0.7399 (p0) cc_final: 0.6761 (p0) REVERT: D 180 PHE cc_start: 0.8807 (m-80) cc_final: 0.8533 (m-80) outliers start: 8 outliers final: 8 residues processed: 102 average time/residue: 0.0680 time to fit residues: 10.7709 Evaluate side-chains 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.094298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.077378 restraints weight = 56409.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.078937 restraints weight = 41257.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.079864 restraints weight = 33031.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.080791 restraints weight = 28398.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.081402 restraints weight = 25061.417| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8787 Z= 0.122 Angle : 0.635 7.870 11886 Z= 0.310 Chirality : 0.042 0.149 1411 Planarity : 0.003 0.034 1476 Dihedral : 5.315 49.786 1151 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 0.86 % Allowed : 5.72 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1115 helix: 0.28 (0.22), residues: 587 sheet: -1.13 (0.67), residues: 53 loop : -1.69 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.011 0.001 TYR C 37 PHE 0.013 0.001 PHE D 180 TRP 0.010 0.001 TRP A 271 HIS 0.019 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8786) covalent geometry : angle 0.63477 / 0.31 (11886) hydrogen bonds : bond 0.04050 / 2.80 ( 361) hydrogen bonds : angle 4.29517 / 2.90 ( 1071) Misc. bond : bond 0.00555 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9311 (tt) cc_final: 0.9054 (pp) REVERT: B 162 ASP cc_start: 0.7436 (p0) cc_final: 0.6890 (p0) REVERT: D 180 PHE cc_start: 0.8801 (m-80) cc_final: 0.8601 (m-80) outliers start: 8 outliers final: 8 residues processed: 105 average time/residue: 0.0693 time to fit residues: 11.0224 Evaluate side-chains 84 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 0.0020 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 154 HIS ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.094800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.078080 restraints weight = 54673.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.079605 restraints weight = 40127.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.080735 restraints weight = 32211.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.081510 restraints weight = 27357.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.082025 restraints weight = 24365.023| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8787 Z= 0.108 Angle : 0.617 8.263 11886 Z= 0.299 Chirality : 0.041 0.147 1411 Planarity : 0.003 0.033 1476 Dihedral : 5.116 46.385 1151 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 0.97 % Allowed : 5.08 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1115 helix: 0.62 (0.22), residues: 586 sheet: -1.19 (0.67), residues: 53 loop : -1.62 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.010 0.001 TYR C 37 PHE 0.012 0.001 PHE D 180 TRP 0.010 0.001 TRP A 271 HIS 0.020 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 8786) covalent geometry : angle 0.61657 / 0.30 (11886) hydrogen bonds : bond 0.03651 / 2.51 ( 361) hydrogen bonds : angle 4.09216 / 2.76 ( 1071) Misc. bond : bond 0.00661 / 0.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9326 (tt) cc_final: 0.9065 (pp) REVERT: B 162 ASP cc_start: 0.7381 (p0) cc_final: 0.6851 (p0) REVERT: D 180 PHE cc_start: 0.8826 (m-80) cc_final: 0.8610 (m-80) outliers start: 9 outliers final: 9 residues processed: 104 average time/residue: 0.0676 time to fit residues: 10.8674 Evaluate side-chains 86 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.0170 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 282 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.094294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.077637 restraints weight = 54922.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.079160 restraints weight = 40547.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.080285 restraints weight = 32569.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.081072 restraints weight = 27658.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.081488 restraints weight = 24586.833| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8787 Z= 0.111 Angle : 0.635 8.018 11886 Z= 0.306 Chirality : 0.041 0.168 1411 Planarity : 0.003 0.034 1476 Dihedral : 5.078 44.038 1151 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 1.08 % Allowed : 5.29 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 1115 helix: 0.76 (0.22), residues: 586 sheet: -1.40 (0.63), residues: 63 loop : -1.46 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.010 0.001 TYR C 37 PHE 0.027 0.001 PHE C 53 TRP 0.008 0.001 TRP A 271 HIS 0.014 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8786) covalent geometry : angle 0.63475 / 0.31 (11886) hydrogen bonds : bond 0.03547 / 2.44 ( 361) hydrogen bonds : angle 4.07930 / 2.75 ( 1071) Misc. bond : bond 0.00331 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.7354 (p0) cc_final: 0.6809 (p0) REVERT: C 53 PHE cc_start: 0.7575 (m-80) cc_final: 0.7342 (m-80) REVERT: C 82 ASN cc_start: 0.4117 (OUTLIER) cc_final: 0.3867 (t0) outliers start: 10 outliers final: 9 residues processed: 105 average time/residue: 0.0677 time to fit residues: 11.0346 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 188 GLN C 82 ASN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.091744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.075182 restraints weight = 56250.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.076614 restraints weight = 41769.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.077651 restraints weight = 33722.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.078439 restraints weight = 28824.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.078984 restraints weight = 25637.430| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8787 Z= 0.155 Angle : 0.682 8.312 11886 Z= 0.335 Chirality : 0.044 0.171 1411 Planarity : 0.003 0.032 1476 Dihedral : 5.198 42.850 1151 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 0.97 % Allowed : 4.43 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.26), residues: 1115 helix: 0.65 (0.22), residues: 590 sheet: -1.69 (0.66), residues: 53 loop : -1.46 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.010 0.002 TYR A 292 PHE 0.024 0.002 PHE C 53 TRP 0.007 0.001 TRP A 271 HIS 0.030 0.002 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 8786) covalent geometry : angle 0.68216 / 0.34 (11886) hydrogen bonds : bond 0.03996 / 2.75 ( 361) hydrogen bonds : angle 4.30639 / 2.89 ( 1071) Misc. bond : bond 0.00402 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 162 ASP cc_start: 0.7515 (p0) cc_final: 0.6922 (p0) REVERT: C 38 LEU cc_start: 0.8067 (tp) cc_final: 0.7834 (tp) REVERT: C 53 PHE cc_start: 0.7625 (m-80) cc_final: 0.7358 (m-80) outliers start: 9 outliers final: 9 residues processed: 102 average time/residue: 0.0660 time to fit residues: 10.4063 Evaluate side-chains 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.0000 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS C 82 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.093518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.076784 restraints weight = 54467.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.078241 restraints weight = 40354.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.079342 restraints weight = 32557.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.080135 restraints weight = 27747.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.080703 restraints weight = 24718.336| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8787 Z= 0.110 Angle : 0.656 8.522 11886 Z= 0.311 Chirality : 0.042 0.149 1411 Planarity : 0.003 0.046 1476 Dihedral : 4.986 40.011 1151 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 1.08 % Allowed : 3.78 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1115 helix: 0.90 (0.22), residues: 590 sheet: -1.64 (0.63), residues: 65 loop : -1.48 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 99 TYR 0.010 0.001 TYR C 37 PHE 0.021 0.001 PHE C 53 TRP 0.010 0.001 TRP A 271 HIS 0.021 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8786) covalent geometry : angle 0.65639 / 0.31 (11886) hydrogen bonds : bond 0.03545 / 2.44 ( 361) hydrogen bonds : angle 4.09000 / 2.76 ( 1071) Misc. bond : bond 0.00427 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.347 Fit side-chains REVERT: B 123 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 38 LEU cc_start: 0.8054 (tp) cc_final: 0.7800 (tp) REVERT: C 53 PHE cc_start: 0.7586 (m-80) cc_final: 0.7289 (m-80) REVERT: D 180 PHE cc_start: 0.9060 (m-80) cc_final: 0.8739 (m-80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.0664 time to fit residues: 10.8603 Evaluate side-chains 85 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 37 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.093759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.076942 restraints weight = 53883.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.078485 restraints weight = 39723.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.079624 restraints weight = 31822.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.080439 restraints weight = 27024.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.081007 restraints weight = 23915.763| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8787 Z= 0.110 Angle : 0.661 8.643 11886 Z= 0.315 Chirality : 0.042 0.156 1411 Planarity : 0.003 0.032 1476 Dihedral : 4.952 41.554 1151 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 1.08 % Allowed : 2.59 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1115 helix: 0.93 (0.22), residues: 589 sheet: -1.56 (0.63), residues: 65 loop : -1.46 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.010 0.001 TYR C 37 PHE 0.020 0.001 PHE C 53 TRP 0.017 0.001 TRP C 322 HIS 0.015 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8786) covalent geometry : angle 0.66074 / 0.32 (11886) hydrogen bonds : bond 0.03393 / 2.32 ( 361) hydrogen bonds : angle 4.00981 / 2.70 ( 1071) Misc. bond : bond 0.00309 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 123 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7878 (mm-30) REVERT: C 38 LEU cc_start: 0.8039 (tp) cc_final: 0.7791 (tp) REVERT: C 53 PHE cc_start: 0.7555 (m-80) cc_final: 0.7283 (m-80) REVERT: D 180 PHE cc_start: 0.9044 (m-80) cc_final: 0.8696 (m-80) outliers start: 10 outliers final: 10 residues processed: 107 average time/residue: 0.0647 time to fit residues: 10.7718 Evaluate side-chains 89 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.0070 chunk 102 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.093349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.076518 restraints weight = 54592.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.078012 restraints weight = 40055.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.079095 restraints weight = 32113.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.079917 restraints weight = 27352.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.080246 restraints weight = 24258.729| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8787 Z= 0.117 Angle : 0.678 8.895 11886 Z= 0.325 Chirality : 0.043 0.152 1411 Planarity : 0.003 0.032 1476 Dihedral : 4.971 40.811 1151 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1115 helix: 0.97 (0.22), residues: 589 sheet: -1.55 (0.62), residues: 65 loop : -1.43 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.010 0.001 TYR C 37 PHE 0.020 0.001 PHE C 53 TRP 0.020 0.001 TRP C 318 HIS 0.014 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8786) covalent geometry : angle 0.67766 / 0.33 (11886) hydrogen bonds : bond 0.03445 / 2.34 ( 361) hydrogen bonds : angle 4.02334 / 2.72 ( 1071) Misc. bond : bond 0.00327 / 0.17 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 123 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 38 LEU cc_start: 0.8060 (tp) cc_final: 0.7806 (tp) REVERT: C 53 PHE cc_start: 0.7650 (m-80) cc_final: 0.7350 (m-80) REVERT: C 66 MET cc_start: 0.4220 (tpt) cc_final: 0.3994 (tpt) REVERT: D 180 PHE cc_start: 0.9029 (m-80) cc_final: 0.8661 (m-80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.0631 time to fit residues: 10.2915 Evaluate side-chains 89 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.094218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.077447 restraints weight = 54082.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.078981 restraints weight = 39655.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.080115 restraints weight = 31681.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.080953 restraints weight = 26780.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.081548 restraints weight = 23643.825| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8787 Z= 0.108 Angle : 0.661 8.788 11886 Z= 0.314 Chirality : 0.042 0.156 1411 Planarity : 0.003 0.032 1476 Dihedral : 4.901 41.647 1151 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 1.08 % Allowed : 2.27 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1115 helix: 1.12 (0.22), residues: 589 sheet: -1.52 (0.62), residues: 65 loop : -1.41 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.010 0.001 TYR C 37 PHE 0.020 0.001 PHE C 53 TRP 0.022 0.001 TRP C 318 HIS 0.012 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 8786) covalent geometry : angle 0.66052 / 0.31 (11886) hydrogen bonds : bond 0.03230 / 2.20 ( 361) hydrogen bonds : angle 3.98838 / 2.71 ( 1071) Misc. bond : bond 0.00266 / 0.14 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.12 seconds wall clock time: 29 minutes 11.19 seconds (1751.19 seconds total)