Starting phenix.real_space_refine on Wed Feb 4 19:38:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9llc_63197/02_2026/9llc_63197.cif Found real_map, /net/cci-nas-00/data/ceres_data/9llc_63197/02_2026/9llc_63197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9llc_63197/02_2026/9llc_63197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9llc_63197/02_2026/9llc_63197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9llc_63197/02_2026/9llc_63197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9llc_63197/02_2026/9llc_63197.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 15 5.49 5 Mg 5 5.21 5 S 65 5.16 5 C 7907 2.51 5 N 2106 2.21 5 O 2401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12499 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 3 Chain: "B" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2231 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Chain: "C" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2266 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "D" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2308 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "E" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2297 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.16, per 1000 atoms: 0.25 Number of scatterers: 12499 At special positions: 0 Unit cell: (84.87, 137.76, 127.1, 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 65 16.00 P 15 15.00 Mg 5 11.99 O 2401 8.00 N 2106 7.00 C 7907 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: 1.03 Conformation dependent library (CDL) restraints added in 557.0 milliseconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2984 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 6 sheets defined 59.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.726A pdb=" N LEU A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.765A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'B' and resid 48 through 61 removed outlier: 3.569A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.736A pdb=" N THR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.580A pdb=" N LEU B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.620A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.864A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.518A pdb=" N ARG B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.299A pdb=" N ASP B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 340 through 348 removed outlier: 4.037A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.504A pdb=" N ILE C 86 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 116 through 120 removed outlier: 4.220A pdb=" N ASN C 119 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 120 " --> pdb=" O TYR C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.065A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.899A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.513A pdb=" N ILE D 93 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 113 through 118 removed outlier: 4.240A pdb=" N TYR D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.952A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.121A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.643A pdb=" N ARG D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 294 through 308 Processing helix chain 'D' and resid 310 through 318 Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.510A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.656A pdb=" N ILE E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.663A pdb=" N ILE E 93 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.695A pdb=" N SER E 118 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN E 119 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER E 120 " --> pdb=" O TYR E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 115 through 120' Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.501A pdb=" N SER E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.186A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 Processing helix chain 'E' and resid 294 through 318 removed outlier: 5.331A pdb=" N GLU E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.519A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 96 through 112 removed outlier: 5.409A pdb=" N TYR F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 113 through 118 removed outlier: 4.297A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.673A pdb=" N ILE F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 removed outlier: 3.702A pdb=" N LYS F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.694A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 224 removed outlier: 3.675A pdb=" N ASP F 221 " --> pdb=" O MET F 217 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY F 222 " --> pdb=" O THR F 218 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 224 " --> pdb=" O TRP F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.607A pdb=" N ARG F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.798A pdb=" N THR F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 340 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.716A pdb=" N ILE A 155 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.818A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE B 157 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.712A pdb=" N CYS C 187 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE C 232 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 189 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA C 234 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 191 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.080A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D 187 " --> pdb=" O MET D 230 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE D 232 " --> pdb=" O CYS D 187 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 189 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA D 234 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE D 191 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL D 129 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR D 235 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU D 131 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 3.990A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS E 187 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE E 232 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE E 189 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA E 234 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE E 191 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 154 removed outlier: 6.121A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET F 230 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1626 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: 2.01 Time building geometry restraints manager: 1.35 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: 3385 1.33 - 1.46: 2236 1.46 - 1.58: 6952 1.58 - 1.70: 14 1.70 - 1.82: 114 Bond restraints: 12701 Sorted by residual: bond pdb=" C SER C 120 " pdb=" N PRO C 121 " ideal model delta sigma weight residual 1.335 1.363 -0.028 9.40e-03 1.13e+04 9.10e+00 bond pdb=" C ARG B 337 " pdb=" N PRO B 338 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.27e-02 6.20e+03 8.41e+00 bond pdb=" N MET B 112 " pdb=" CA MET B 112 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.83e+00 bond pdb=" N ARG E 60 " pdb=" CA ARG E 60 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.31e+00 bond pdb=" N SER B 150 " pdb=" CA SER B 150 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.17e+00 ... (remaining 12696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16568 2.02 - 4.04: 474 4.04 - 6.05: 74 6.05 - 8.07: 30 8.07 - 10.09: 12 Bond angle restraints: 17158 Sorted by residual: angle pdb=" O TYR B 109 " pdb=" C TYR B 109 " pdb=" N PRO B 110 " ideal model delta sigma weight residual 121.32 116.40 4.92 1.15e+00 7.56e-01 1.83e+01 angle pdb=" CD1 LEU C 276 " pdb=" CG LEU C 276 " pdb=" CD2 LEU C 276 " ideal model delta sigma weight residual 110.80 101.49 9.31 2.20e+00 2.07e-01 1.79e+01 angle pdb=" CG MET C 163 " pdb=" SD MET C 163 " pdb=" CE MET C 163 " ideal model delta sigma weight residual 100.90 109.56 -8.66 2.20e+00 2.07e-01 1.55e+01 angle pdb=" O SER E 120 " pdb=" C SER E 120 " pdb=" N PRO E 121 " ideal model delta sigma weight residual 121.66 118.12 3.54 9.40e-01 1.13e+00 1.42e+01 angle pdb=" CA LYS C 59 " pdb=" CB LYS C 59 " pdb=" CG LYS C 59 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 ... (remaining 17153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 6553 18.33 - 36.67: 1046 36.67 - 55.00: 269 55.00 - 73.33: 66 73.33 - 91.66: 19 Dihedral angle restraints: 7953 sinusoidal: 3381 harmonic: 4572 Sorted by residual: dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N GLN D 185 " pdb=" CA GLN D 185 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU E 184 " pdb=" C LEU E 184 " pdb=" N GLN E 185 " pdb=" CA GLN E 185 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL F 107 " pdb=" C VAL F 107 " pdb=" N ILE F 108 " pdb=" CA ILE F 108 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1531 0.052 - 0.104: 360 0.104 - 0.155: 71 0.155 - 0.207: 4 0.207 - 0.259: 4 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CB ILE F 157 " pdb=" CA ILE F 157 " pdb=" CG1 ILE F 157 " pdb=" CG2 ILE F 157 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB VAL F 269 " pdb=" CA VAL F 269 " pdb=" CG1 VAL F 269 " pdb=" CG2 VAL F 269 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR F 218 " pdb=" CA THR F 218 " pdb=" OG1 THR F 218 " pdb=" CG2 THR F 218 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1967 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 111 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C LEU B 111 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 111 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 112 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 82 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 83 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 83 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 83 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 273 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ASP F 273 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP F 273 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F 274 " 0.011 2.00e-02 2.50e+03 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 103 2.54 - 3.13: 9453 3.13 - 3.72: 21124 3.72 - 4.31: 28258 4.31 - 4.90: 47118 Nonbonded interactions: 106056 Sorted by model distance: nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 401 " model vdw 1.951 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 401 " model vdw 1.971 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G ATP D 402 " model vdw 1.975 2.170 nonbonded pdb="MG MG F 401 " pdb=" O3G ATP F 402 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 401 " model vdw 2.004 2.170 ... (remaining 106051 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 47 through 348 or resid 401 through 402)) selection = (chain 'C' and (resid 47 through 316 or resid 337 through 348 or resid 401 throu \ gh 402)) selection = (chain 'D' and (resid 47 through 316 or resid 337 through 348 or resid 401 throu \ gh 402)) selection = (chain 'E' and (resid 47 through 316 or resid 337 through 348 or resid 401 throu \ gh 402)) selection = (chain 'F' and (resid 47 through 316 or resid 337 through 402)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 8.960 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: 0.730 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.005 0.076 12701 Z= 0.238 Angle : 0.856 10.088 17158 Z= 0.437 Chirality : 0.046 0.259 1970 Planarity : 0.005 0.070 2149 Dihedral : 19.301 91.663 4969 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.22 % Allowed : 29.83 % Favored : 69.95 % 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: -0.86 (0.21), residues: 1526 helix: -0.22 (0.18), residues: 803 sheet: -0.94 (0.51), residues: 99 loop : -0.79 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 158 TYR 0.021 0.002 TYR B 167 PHE 0.019 0.002 PHE C 281 TRP 0.010 0.001 TRP D 54 HIS 0.006 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00523 (12701) covalent geometry : angle 0.85610 (17158) hydrogen bonds : bond 0.18526 ( 550) hydrogen bonds : angle 6.46769 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.519 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 240 average time/residue: 0.1168 time to fit residues: 40.5616 Evaluate side-chains 233 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 91 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.169843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130809 restraints weight = 17978.719| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.53 r_work: 0.3402 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12701 Z= 0.126 Angle : 0.579 7.355 17158 Z= 0.284 Chirality : 0.041 0.147 1970 Planarity : 0.004 0.044 2149 Dihedral : 11.825 89.170 1841 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.70 % Allowed : 27.13 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.21), residues: 1526 helix: 0.23 (0.18), residues: 852 sheet: -0.64 (0.50), residues: 107 loop : -0.40 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.011 0.001 TYR F 313 PHE 0.009 0.001 PHE C 281 TRP 0.005 0.001 TRP D 220 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00282 (12701) covalent geometry : angle 0.57944 (17158) hydrogen bonds : bond 0.04017 ( 550) hydrogen bonds : angle 4.73689 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7728 (mm110) REVERT: B 200 GLU cc_start: 0.7987 (tp30) cc_final: 0.7673 (tp30) REVERT: C 112 MET cc_start: 0.8906 (mmm) cc_final: 0.8690 (mmm) REVERT: C 291 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7385 (tptp) REVERT: C 298 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7787 (mp) REVERT: D 60 ARG cc_start: 0.7737 (tpp-160) cc_final: 0.7450 (ttt-90) REVERT: D 311 LYS cc_start: 0.8242 (tmtt) cc_final: 0.7821 (pttt) outliers start: 37 outliers final: 16 residues processed: 279 average time/residue: 0.1144 time to fit residues: 46.3749 Evaluate side-chains 245 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 0.0020 chunk 124 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 145 optimal weight: 0.4980 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 226 ASN C 236 ASN E 171 ASN E 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129696 restraints weight = 18243.750| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.43 r_work: 0.3394 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12701 Z= 0.131 Angle : 0.563 8.447 17158 Z= 0.272 Chirality : 0.041 0.143 1970 Planarity : 0.003 0.044 2149 Dihedral : 11.594 87.996 1839 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 27.72 % Favored : 69.37 % 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: 0.18 (0.22), residues: 1526 helix: 0.57 (0.18), residues: 860 sheet: -0.38 (0.52), residues: 107 loop : -0.30 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 158 TYR 0.011 0.001 TYR F 313 PHE 0.012 0.001 PHE E 178 TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00306 (12701) covalent geometry : angle 0.56278 (17158) hydrogen bonds : bond 0.03577 ( 550) hydrogen bonds : angle 4.47154 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7893 (tp30) cc_final: 0.7625 (tp30) REVERT: B 124 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7823 (mm110) REVERT: B 146 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8495 (mm) REVERT: B 200 GLU cc_start: 0.8218 (tp30) cc_final: 0.7936 (tp30) REVERT: C 291 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7437 (tptp) REVERT: C 298 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7941 (mp) REVERT: D 311 LYS cc_start: 0.8300 (tmtt) cc_final: 0.7914 (pttt) REVERT: E 284 GLN cc_start: 0.8524 (mm110) cc_final: 0.8089 (mm-40) REVERT: F 273 ASP cc_start: 0.7622 (t0) cc_final: 0.7361 (t0) outliers start: 40 outliers final: 21 residues processed: 269 average time/residue: 0.1109 time to fit residues: 43.0431 Evaluate side-chains 248 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 71 optimal weight: 0.0370 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN C 236 ASN D 91 GLN E 236 ASN F 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126223 restraints weight = 18202.619| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.63 r_work: 0.3351 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12701 Z= 0.161 Angle : 0.571 8.226 17158 Z= 0.276 Chirality : 0.041 0.155 1970 Planarity : 0.003 0.033 2149 Dihedral : 11.414 86.615 1839 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.67 % Allowed : 26.77 % Favored : 68.56 % 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: 0.30 (0.22), residues: 1526 helix: 0.72 (0.18), residues: 869 sheet: -0.41 (0.51), residues: 107 loop : -0.34 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 158 TYR 0.012 0.001 TYR F 313 PHE 0.013 0.001 PHE E 178 TRP 0.009 0.001 TRP D 220 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00387 (12701) covalent geometry : angle 0.57110 (17158) hydrogen bonds : bond 0.03395 ( 550) hydrogen bonds : angle 4.39098 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7888 (tp30) cc_final: 0.7639 (tp30) REVERT: B 124 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7915 (mm110) REVERT: B 146 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8409 (mm) REVERT: B 200 GLU cc_start: 0.8274 (tp30) cc_final: 0.8065 (tp30) REVERT: B 285 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6110 (tp) REVERT: C 291 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7447 (tptp) REVERT: C 298 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7880 (mp) REVERT: C 346 LYS cc_start: 0.8394 (pttp) cc_final: 0.7991 (pptt) REVERT: E 74 ARG cc_start: 0.8364 (tpt170) cc_final: 0.8022 (tpt170) REVERT: E 237 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7563 (ptt90) REVERT: E 284 GLN cc_start: 0.8652 (mm110) cc_final: 0.8293 (mm-40) REVERT: F 44 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7295 (mtp180) REVERT: F 53 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8752 (mp10) REVERT: F 113 MET cc_start: 0.7762 (ptt) cc_final: 0.7330 (ppp) REVERT: F 273 ASP cc_start: 0.7778 (t0) cc_final: 0.7570 (t0) outliers start: 64 outliers final: 32 residues processed: 273 average time/residue: 0.1071 time to fit residues: 42.5875 Evaluate side-chains 259 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN D 236 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121895 restraints weight = 18191.621| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.52 r_work: 0.3300 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12701 Z= 0.196 Angle : 0.600 8.056 17158 Z= 0.289 Chirality : 0.042 0.157 1970 Planarity : 0.004 0.044 2149 Dihedral : 11.326 86.855 1839 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.89 % Allowed : 27.21 % Favored : 67.91 % 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 (0.22), residues: 1526 helix: 0.83 (0.18), residues: 854 sheet: -0.53 (0.49), residues: 113 loop : -0.42 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 74 TYR 0.012 0.001 TYR F 313 PHE 0.014 0.002 PHE E 178 TRP 0.013 0.001 TRP D 220 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00474 (12701) covalent geometry : angle 0.59993 (17158) hydrogen bonds : bond 0.03433 ( 550) hydrogen bonds : angle 4.46107 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.564 Fit side-chains REVERT: B 124 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8063 (mm110) REVERT: B 200 GLU cc_start: 0.8111 (tp30) cc_final: 0.7909 (tp30) REVERT: B 285 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6094 (tp) REVERT: C 205 ASP cc_start: 0.8268 (m-30) cc_final: 0.7998 (t0) REVERT: C 291 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7478 (ttpt) REVERT: C 298 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7812 (mp) REVERT: D 50 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: E 74 ARG cc_start: 0.8247 (tpt170) cc_final: 0.7932 (tpt170) REVERT: E 237 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7548 (ptt90) REVERT: E 284 GLN cc_start: 0.8527 (mm110) cc_final: 0.8189 (mm-40) outliers start: 67 outliers final: 40 residues processed: 271 average time/residue: 0.1155 time to fit residues: 45.3086 Evaluate side-chains 262 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 307 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 6 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 102 optimal weight: 0.0070 chunk 72 optimal weight: 0.6980 chunk 115 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN D 236 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129266 restraints weight = 18065.260| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.65 r_work: 0.3393 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12701 Z= 0.107 Angle : 0.563 8.083 17158 Z= 0.268 Chirality : 0.040 0.166 1970 Planarity : 0.003 0.032 2149 Dihedral : 11.142 88.551 1839 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.79 % Allowed : 27.94 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.22), residues: 1526 helix: 0.96 (0.18), residues: 858 sheet: -0.52 (0.49), residues: 107 loop : -0.35 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 74 TYR 0.014 0.001 TYR F 313 PHE 0.010 0.001 PHE C 197 TRP 0.006 0.001 TRP D 54 HIS 0.003 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00247 (12701) covalent geometry : angle 0.56337 (17158) hydrogen bonds : bond 0.03028 ( 550) hydrogen bonds : angle 4.27364 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 124 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7974 (mm110) REVERT: B 200 GLU cc_start: 0.8041 (tp30) cc_final: 0.7763 (tp30) REVERT: C 205 ASP cc_start: 0.8252 (m-30) cc_final: 0.7950 (t0) REVERT: C 298 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7703 (mp) REVERT: D 350 MET cc_start: 0.7706 (tmm) cc_final: 0.6773 (ptm) REVERT: E 158 ARG cc_start: 0.7226 (mtp-110) cc_final: 0.6550 (mtp-110) REVERT: E 237 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7616 (ptt90) REVERT: E 284 GLN cc_start: 0.8469 (mm110) cc_final: 0.7998 (mm-40) REVERT: F 47 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8350 (mmtt) outliers start: 52 outliers final: 35 residues processed: 272 average time/residue: 0.1147 time to fit residues: 45.3194 Evaluate side-chains 258 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN D 91 GLN D 236 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 316 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122858 restraints weight = 18258.485| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.51 r_work: 0.3324 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12701 Z= 0.181 Angle : 0.599 9.198 17158 Z= 0.286 Chirality : 0.042 0.171 1970 Planarity : 0.004 0.050 2149 Dihedral : 11.130 87.686 1839 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.01 % Allowed : 28.74 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1526 helix: 0.97 (0.18), residues: 864 sheet: -0.40 (0.48), residues: 112 loop : -0.36 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 74 TYR 0.014 0.001 TYR E 313 PHE 0.014 0.001 PHE E 178 TRP 0.011 0.001 TRP D 220 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00440 (12701) covalent geometry : angle 0.59907 (17158) hydrogen bonds : bond 0.03234 ( 550) hydrogen bonds : angle 4.31184 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: B 285 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5965 (tp) REVERT: C 91 GLN cc_start: 0.8287 (mp10) cc_final: 0.8034 (mp10) REVERT: C 298 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 350 MET cc_start: 0.7697 (tmm) cc_final: 0.6769 (ptm) REVERT: E 158 ARG cc_start: 0.7326 (mtp-110) cc_final: 0.6586 (mtp-110) REVERT: E 237 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7628 (ptt90) REVERT: E 284 GLN cc_start: 0.8491 (mm110) cc_final: 0.8022 (mm-40) REVERT: F 113 MET cc_start: 0.7699 (ptt) cc_final: 0.7278 (ppp) outliers start: 55 outliers final: 35 residues processed: 257 average time/residue: 0.1124 time to fit residues: 41.7402 Evaluate side-chains 251 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN E 50 GLN ** E 171 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 = 0.4002 r_free = 0.4002 target = 0.168129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128438 restraints weight = 17971.628| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.66 r_work: 0.3376 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12701 Z= 0.117 Angle : 0.580 8.424 17158 Z= 0.276 Chirality : 0.041 0.174 1970 Planarity : 0.003 0.049 2149 Dihedral : 10.981 88.106 1839 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.36 % Allowed : 28.96 % Favored : 67.69 % 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: 0.56 (0.22), residues: 1526 helix: 1.01 (0.18), residues: 858 sheet: -0.48 (0.49), residues: 107 loop : -0.32 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 74 TYR 0.014 0.001 TYR F 313 PHE 0.008 0.001 PHE D 178 TRP 0.005 0.001 TRP D 54 HIS 0.003 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00275 (12701) covalent geometry : angle 0.57953 (17158) hydrogen bonds : bond 0.03043 ( 550) hydrogen bonds : angle 4.23667 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: B 99 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6960 (tt) REVERT: B 285 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5978 (tp) REVERT: C 91 GLN cc_start: 0.8271 (mp10) cc_final: 0.7987 (mp10) REVERT: C 205 ASP cc_start: 0.8227 (m-30) cc_final: 0.7949 (t0) REVERT: C 298 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7662 (mp) REVERT: E 158 ARG cc_start: 0.7205 (mtp-110) cc_final: 0.6394 (mtp-110) REVERT: E 175 ASP cc_start: 0.8912 (t70) cc_final: 0.8636 (t0) REVERT: E 237 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7552 (ptt90) REVERT: E 284 GLN cc_start: 0.8508 (mm110) cc_final: 0.8097 (mm-40) outliers start: 46 outliers final: 32 residues processed: 261 average time/residue: 0.1015 time to fit residues: 38.9620 Evaluate side-chains 259 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 HIS D 91 GLN D 236 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127787 restraints weight = 18128.813| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.66 r_work: 0.3339 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12701 Z= 0.161 Angle : 0.605 8.563 17158 Z= 0.286 Chirality : 0.042 0.225 1970 Planarity : 0.003 0.035 2149 Dihedral : 10.992 88.889 1839 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.21 % Allowed : 29.32 % Favored : 67.47 % 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: 0.54 (0.22), residues: 1526 helix: 1.01 (0.18), residues: 858 sheet: -0.37 (0.46), residues: 120 loop : -0.38 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 74 TYR 0.016 0.001 TYR E 313 PHE 0.014 0.001 PHE E 178 TRP 0.009 0.001 TRP D 220 HIS 0.005 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00392 (12701) covalent geometry : angle 0.60489 (17158) hydrogen bonds : bond 0.03115 ( 550) hydrogen bonds : angle 4.30059 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: B 99 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7040 (tt) REVERT: B 124 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7929 (mm110) REVERT: B 285 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5943 (tp) REVERT: C 298 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7770 (mp) REVERT: E 158 ARG cc_start: 0.7301 (mtp-110) cc_final: 0.6539 (mtp-110) REVERT: E 175 ASP cc_start: 0.8901 (t70) cc_final: 0.8646 (t0) REVERT: E 237 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7577 (ptt90) REVERT: E 284 GLN cc_start: 0.8464 (mm110) cc_final: 0.8044 (mm-40) REVERT: F 113 MET cc_start: 0.7719 (ptt) cc_final: 0.7252 (ppp) REVERT: F 185 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8183 (tp40) outliers start: 44 outliers final: 37 residues processed: 254 average time/residue: 0.1186 time to fit residues: 43.5357 Evaluate side-chains 258 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN D 236 ASN D 289 ASN ** E 171 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 = 0.3996 r_free = 0.3996 target = 0.168055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129032 restraints weight = 18226.160| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.57 r_work: 0.3353 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12701 Z= 0.124 Angle : 0.607 10.708 17158 Z= 0.286 Chirality : 0.041 0.190 1970 Planarity : 0.004 0.059 2149 Dihedral : 10.929 89.381 1839 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.21 % Allowed : 29.61 % Favored : 67.18 % 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: 0.55 (0.22), residues: 1526 helix: 1.04 (0.18), residues: 854 sheet: -0.46 (0.49), residues: 108 loop : -0.38 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 74 TYR 0.015 0.001 TYR E 313 PHE 0.009 0.001 PHE E 178 TRP 0.005 0.001 TRP D 54 HIS 0.003 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00296 (12701) covalent geometry : angle 0.60726 (17158) hydrogen bonds : bond 0.03013 ( 550) hydrogen bonds : angle 4.28342 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.603 Fit side-chains REVERT: B 99 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7027 (tt) REVERT: B 124 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7972 (mm110) REVERT: B 285 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.5939 (tp) REVERT: C 91 GLN cc_start: 0.8263 (mp10) cc_final: 0.8051 (mp10) REVERT: C 298 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7797 (mp) REVERT: D 50 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7283 (mp-120) REVERT: E 158 ARG cc_start: 0.7185 (mtp-110) cc_final: 0.6453 (mtp-110) REVERT: E 175 ASP cc_start: 0.8865 (t70) cc_final: 0.8597 (t0) REVERT: E 237 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7575 (ptt90) REVERT: E 284 GLN cc_start: 0.8461 (mm110) cc_final: 0.8052 (mm-40) REVERT: F 113 MET cc_start: 0.7655 (ptt) cc_final: 0.7225 (ppp) REVERT: F 185 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8166 (tp40) outliers start: 44 outliers final: 36 residues processed: 249 average time/residue: 0.1106 time to fit residues: 40.3347 Evaluate side-chains 263 residues out of total 1371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN D 91 GLN D 289 ASN ** E 171 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 = 0.3991 r_free = 0.3991 target = 0.167133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128625 restraints weight = 18334.618| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.61 r_work: 0.3337 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12701 Z= 0.146 Angle : 0.617 10.036 17158 Z= 0.291 Chirality : 0.042 0.204 1970 Planarity : 0.003 0.042 2149 Dihedral : 10.918 89.508 1839 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.06 % Allowed : 30.20 % Favored : 66.74 % 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: 0.56 (0.22), residues: 1526 helix: 1.06 (0.18), residues: 854 sheet: -0.44 (0.46), residues: 120 loop : -0.39 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 74 TYR 0.015 0.001 TYR E 313 PHE 0.011 0.001 PHE E 178 TRP 0.007 0.001 TRP D 220 HIS 0.004 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00356 (12701) covalent geometry : angle 0.61667 (17158) hydrogen bonds : bond 0.03051 ( 550) hydrogen bonds : angle 4.28258 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.88 seconds wall clock time: 63 minutes 51.24 seconds (3831.24 seconds total)