Starting phenix.real_space_refine on Wed Jul 30 15:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gf0_51308/07_2025/9gf0_51308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gf0_51308/07_2025/9gf0_51308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gf0_51308/07_2025/9gf0_51308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gf0_51308/07_2025/9gf0_51308.map" model { file = "/net/cci-nas-00/data/ceres_data/9gf0_51308/07_2025/9gf0_51308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gf0_51308/07_2025/9gf0_51308.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7869 2.51 5 N 2105 2.21 5 O 2600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12619 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 bond proxies already assigned to first conformer: 2543 Chain: "C" Number of atoms: 2536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2524 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 325} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 333, 2524 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 325} Chain breaks: 1 bond proxies already assigned to first conformer: 2559 Chain: "D" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2516 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 324} Chain breaks: 1 Chain: "E" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2504 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR B 127 " occ=0.70 ... (22 atoms not shown) pdb=" OH BTYR B 127 " occ=0.30 residue: pdb=" N ATYR C 127 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 127 " occ=0.50 Time building chain proxies: 13.14, per 1000 atoms: 1.04 Number of scatterers: 12619 At special positions: 0 Unit cell: (75.985, 111.89, 116.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2600 8.00 N 2105 7.00 C 7869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 2.8 seconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 9.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.740A pdb=" N MET A 28 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.728A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 23 through 29 removed outlier: 3.679A pdb=" N MET B 28 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 82 removed outlier: 3.534A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 23 through 29 removed outlier: 3.639A pdb=" N PHE C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.661A pdb=" N SER C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.644A pdb=" N MET D 28 " --> pdb=" O TYR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 25 through 30 removed outlier: 3.791A pdb=" N ALA E 29 " --> pdb=" O TYR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.764A pdb=" N SER E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.546A pdb=" N ALA A 64 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 114 " --> pdb=" O TRP A 121 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 141 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 144 " --> pdb=" O PHE A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 155 through 164 current: chain 'A' and resid 175 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 175 through 178 current: chain 'A' and resid 197 through 211 removed outlier: 6.953A pdb=" N PHE A 239 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 238 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 266 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU A 285 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 261 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 283 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET A 263 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLN A 281 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL A 265 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL A 279 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS A 267 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ALA A 277 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 288 " --> pdb=" O THR A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 296 through 298 current: chain 'A' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 321 current: chain 'B' and resid 49 through 55 removed outlier: 3.509A pdb=" N TRP B 119 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 140 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 167 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 142 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY B 165 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 144 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP B 155 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR B 190 " --> pdb=" O TRP B 155 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 157 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 188 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 159 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 186 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 161 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 184 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE B 163 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY B 182 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY B 165 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 178 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP B 210 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER B 180 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 208 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 182 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 231 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE B 239 " --> pdb=" O LEU B 231 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 258 current: chain 'B' and resid 273 through 282 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 282 current: chain 'B' and resid 315 through 321 removed outlier: 6.835A pdb=" N VAL B 316 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 340 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP B 318 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 338 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 297 through 298 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 297 through 298 current: chain 'C' and resid 49 through 55 removed outlier: 3.553A pdb=" N ALA C 64 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 138 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C 169 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS C 140 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER C 167 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 142 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY C 165 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA C 144 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 183 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR C 164 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS C 181 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS C 166 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU C 179 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU C 168 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU C 177 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS C 206 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 183 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET C 204 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN C 185 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 202 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 187 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY C 200 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 189 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 198 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE C 239 " --> pdb=" O LEU C 231 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 254 through 258 current: chain 'C' and resid 275 through 282 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 275 through 282 current: chain 'C' and resid 296 through 298 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 296 through 298 current: chain 'C' and resid 315 through 321 removed outlier: 6.786A pdb=" N VAL C 316 " --> pdb=" O TYR C 340 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR C 340 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP C 318 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 338 " --> pdb=" O ASP C 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 335 through 343 current: chain 'D' and resid 49 through 53 removed outlier: 3.650A pdb=" N ALA D 64 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS D 140 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER D 167 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 142 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY D 165 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 144 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 183 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR D 164 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LYS D 181 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS D 166 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU D 179 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU D 168 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU D 177 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP D 170 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR D 175 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS D 206 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 183 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET D 204 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN D 185 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 202 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 187 " --> pdb=" O GLY D 200 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY D 200 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY D 189 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 198 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS D 191 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N MET D 196 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU D 255 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU D 287 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 257 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU D 285 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU D 259 " --> pdb=" O VAL D 283 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 296 through 298 current: chain 'D' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 321 current: chain 'E' and resid 49 through 55 removed outlier: 3.760A pdb=" N TRP E 119 " --> pdb=" O MET E 116 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY E 138 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 169 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS E 140 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER E 167 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 142 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY E 165 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA E 144 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU E 183 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N THR E 164 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LYS E 181 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS E 166 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 179 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU E 168 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU E 177 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP E 170 " --> pdb=" O THR E 175 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR E 175 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL E 178 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASP E 210 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER E 180 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU E 208 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY E 182 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 206 " --> pdb=" O GLY E 182 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 199 " --> pdb=" O GLY E 226 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 239 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN E 238 " --> pdb=" O GLU E 266 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU E 266 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU E 255 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU E 287 " --> pdb=" O GLU E 255 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU E 257 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU E 285 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU E 259 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA E 306 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 316 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR E 340 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP E 318 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL E 338 " --> pdb=" O ASP E 318 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2489 1.32 - 1.45: 3287 1.45 - 1.57: 6966 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12832 Sorted by residual: bond pdb=" C PRO B 194 " pdb=" N GLU B 195 " ideal model delta sigma weight residual 1.333 1.457 -0.124 1.26e-02 6.30e+03 9.68e+01 bond pdb=" C GLU B 195 " pdb=" N MET B 196 " ideal model delta sigma weight residual 1.329 1.242 0.088 1.36e-02 5.41e+03 4.15e+01 bond pdb=" C ARG E 69 " pdb=" N SER E 70 " ideal model delta sigma weight residual 1.330 1.413 -0.082 1.30e-02 5.92e+03 4.01e+01 bond pdb=" C GLY A 226 " pdb=" N MET A 227 " ideal model delta sigma weight residual 1.330 1.418 -0.088 1.41e-02 5.03e+03 3.86e+01 bond pdb=" C VAL E 174 " pdb=" N THR E 175 " ideal model delta sigma weight residual 1.331 1.400 -0.070 1.34e-02 5.57e+03 2.71e+01 ... (remaining 12827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 16523 2.34 - 4.68: 791 4.68 - 7.03: 67 7.03 - 9.37: 11 9.37 - 11.71: 2 Bond angle restraints: 17394 Sorted by residual: angle pdb=" N ASN A 132 " pdb=" CA ASN A 132 " pdb=" C ASN A 132 " ideal model delta sigma weight residual 114.62 106.50 8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" N ASN D 152 " pdb=" CA ASN D 152 " pdb=" C ASN D 152 " ideal model delta sigma weight residual 110.46 101.07 9.39 1.48e+00 4.57e-01 4.03e+01 angle pdb=" O PRO B 194 " pdb=" C PRO B 194 " pdb=" N GLU B 195 " ideal model delta sigma weight residual 122.22 130.36 -8.14 1.29e+00 6.01e-01 3.98e+01 angle pdb=" C ARG E 69 " pdb=" N SER E 70 " pdb=" CA SER E 70 " ideal model delta sigma weight residual 121.06 109.35 11.71 1.88e+00 2.83e-01 3.88e+01 angle pdb=" N PHE D 17 " pdb=" CA PHE D 17 " pdb=" C PHE D 17 " ideal model delta sigma weight residual 113.23 105.85 7.38 1.24e+00 6.50e-01 3.54e+01 ... (remaining 17389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6404 17.76 - 35.52: 766 35.52 - 53.28: 227 53.28 - 71.05: 54 71.05 - 88.81: 27 Dihedral angle restraints: 7478 sinusoidal: 2762 harmonic: 4716 Sorted by residual: dihedral pdb=" C PHE A 111 " pdb=" N PHE A 111 " pdb=" CA PHE A 111 " pdb=" CB PHE A 111 " ideal model delta harmonic sigma weight residual -122.60 -111.64 -10.96 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" CA PHE C 66 " pdb=" C PHE C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 16 " pdb=" CB ASP A 16 " pdb=" CG ASP A 16 " pdb=" OD1 ASP A 16 " ideal model delta sinusoidal sigma weight residual -30.00 -89.01 59.01 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 7475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1353 0.054 - 0.107: 345 0.107 - 0.161: 171 0.161 - 0.214: 39 0.214 - 0.268: 11 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CA PHE C 103 " pdb=" N PHE C 103 " pdb=" C PHE C 103 " pdb=" CB PHE C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA TYR B 223 " pdb=" N TYR B 223 " pdb=" C TYR B 223 " pdb=" CB TYR B 223 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LYS E 206 " pdb=" N LYS E 206 " pdb=" C LYS E 206 " pdb=" CB LYS E 206 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1916 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTYR C 127 " 0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C BTYR C 127 " -0.084 2.00e-02 2.50e+03 pdb=" O BTYR C 127 " 0.031 2.00e-02 2.50e+03 pdb=" N SER C 128 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 343 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C THR D 343 " 0.080 2.00e-02 2.50e+03 pdb=" O THR D 343 " -0.031 2.00e-02 2.50e+03 pdb=" N PHE D 344 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 343 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C THR A 343 " -0.077 2.00e-02 2.50e+03 pdb=" O THR A 343 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A 344 " 0.026 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 669 2.71 - 3.26: 11116 3.26 - 3.81: 19748 3.81 - 4.35: 26440 4.35 - 4.90: 46901 Nonbonded interactions: 104874 Sorted by model distance: nonbonded pdb=" O ASN B 332 " pdb=" OD1 ASN B 332 " model vdw 2.163 3.040 nonbonded pdb=" O ASN C 152 " pdb=" OD1 ASN C 152 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 301 " pdb=" ND2 ASN E 106 " model vdw 2.221 3.120 nonbonded pdb=" OD2 ASP A 318 " pdb=" O HOH A 401 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR E 199 " pdb=" OE2 GLU E 244 " model vdw 2.262 3.040 ... (remaining 104869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'B' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'C' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'D' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'E' and (resid 1 through 126 or resid 128 through 344)) } 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=0.30 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: 2.630 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.640 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 12832 Z= 0.536 Angle : 1.011 11.709 17394 Z= 0.697 Chirality : 0.063 0.268 1919 Planarity : 0.006 0.115 2290 Dihedral : 18.171 88.806 4470 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.74 % Favored : 94.01 % Rotamer: Outliers : 4.11 % Allowed : 26.39 % Favored : 69.51 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1643 helix: -1.61 (0.40), residues: 143 sheet: 0.09 (0.17), residues: 974 loop : -2.03 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 121 HIS 0.004 0.001 HIS C 191 PHE 0.023 0.002 PHE A 111 TYR 0.023 0.002 TYR E 241 ARG 0.003 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.21888 ( 557) hydrogen bonds : angle 8.63883 ( 1553) covalent geometry : bond 0.00789 (12832) covalent geometry : angle 1.01111 (17394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 1.382 Fit side-chains REVERT: A 111 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 140 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7388 (ttpm) REVERT: B 238 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7614 (t0) REVERT: C 330 ASN cc_start: 0.7525 (p0) cc_final: 0.7322 (p0) REVERT: D 134 ASP cc_start: 0.8039 (t70) cc_final: 0.7083 (p0) REVERT: D 234 SER cc_start: 0.5250 (OUTLIER) cc_final: 0.4592 (m) REVERT: D 249 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7671 (tttp) REVERT: E 217 GLU cc_start: 0.6784 (tt0) cc_final: 0.6499 (tt0) outliers start: 52 outliers final: 28 residues processed: 224 average time/residue: 1.1926 time to fit residues: 291.9431 Evaluate side-chains 169 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 132 ASN B 332 ASN C 152 ASN C 332 ASN C 333 ASN E 33 GLN E 171 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125770 restraints weight = 34032.996| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.11 r_work: 0.3197 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12832 Z= 0.110 Angle : 0.527 6.341 17394 Z= 0.299 Chirality : 0.044 0.144 1919 Planarity : 0.004 0.065 2290 Dihedral : 6.219 59.780 1811 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.11 % Allowed : 27.98 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1643 helix: -1.08 (0.40), residues: 145 sheet: 0.42 (0.17), residues: 972 loop : -1.62 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 121 HIS 0.009 0.001 HIS A 56 PHE 0.011 0.001 PHE C 111 TYR 0.009 0.001 TYR A 223 ARG 0.003 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 557) hydrogen bonds : angle 5.68441 ( 1553) covalent geometry : bond 0.00235 (12832) covalent geometry : angle 0.52676 (17394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 2.351 Fit side-chains REVERT: A 132 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7613 (t0) REVERT: A 168 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7276 (mp0) REVERT: A 217 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7944 (mm-30) REVERT: A 227 MET cc_start: 0.7951 (ppp) cc_final: 0.7715 (ppp) REVERT: A 249 LYS cc_start: 0.7448 (ttmp) cc_final: 0.7075 (mtpp) REVERT: A 258 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8032 (mt) REVERT: D 227 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8068 (tmt) REVERT: D 249 LYS cc_start: 0.7612 (tttt) cc_final: 0.7101 (tttp) REVERT: D 303 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7458 (ptp-170) REVERT: E 179 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: E 195 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: E 217 GLU cc_start: 0.7015 (tt0) cc_final: 0.6413 (tt0) outliers start: 52 outliers final: 22 residues processed: 192 average time/residue: 1.2887 time to fit residues: 271.2079 Evaluate side-chains 159 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 109 ASN C 333 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118331 restraints weight = 31480.269| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.76 r_work: 0.3173 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12832 Z= 0.186 Angle : 0.569 5.660 17394 Z= 0.322 Chirality : 0.045 0.154 1919 Planarity : 0.004 0.063 2290 Dihedral : 5.183 48.450 1765 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.80 % Allowed : 28.14 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1643 helix: -1.19 (0.41), residues: 145 sheet: 0.32 (0.17), residues: 992 loop : -1.51 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 121 HIS 0.009 0.001 HIS A 56 PHE 0.015 0.002 PHE D 73 TYR 0.011 0.001 TYR C 241 ARG 0.004 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 557) hydrogen bonds : angle 5.43205 ( 1553) covalent geometry : bond 0.00434 (12832) covalent geometry : angle 0.56855 (17394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 1.443 Fit side-chains REVERT: A 192 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7408 (mpp) REVERT: A 249 LYS cc_start: 0.7370 (ttmp) cc_final: 0.7023 (mtpp) REVERT: B 219 GLU cc_start: 0.7407 (tt0) cc_final: 0.6479 (tm-30) REVERT: D 159 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7503 (tp) REVERT: D 179 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: D 227 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8150 (tmm) REVERT: D 249 LYS cc_start: 0.7628 (tttt) cc_final: 0.7118 (tttp) REVERT: D 303 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7431 (ptp-170) REVERT: E 116 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5486 (pp-130) REVERT: E 179 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: E 217 GLU cc_start: 0.7061 (tt0) cc_final: 0.6313 (tt0) outliers start: 48 outliers final: 25 residues processed: 172 average time/residue: 1.1922 time to fit residues: 224.1236 Evaluate side-chains 163 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 6.9990 chunk 163 optimal weight: 0.0060 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 0.0070 chunk 79 optimal weight: 10.0000 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS B 332 ASN C 152 ASN D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124937 restraints weight = 33230.709| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.92 r_work: 0.3203 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12832 Z= 0.098 Angle : 0.481 5.218 17394 Z= 0.274 Chirality : 0.043 0.141 1919 Planarity : 0.003 0.062 2290 Dihedral : 4.533 38.370 1758 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.35 % Allowed : 27.98 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1643 helix: -0.82 (0.41), residues: 151 sheet: 0.45 (0.17), residues: 984 loop : -1.25 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 PHE 0.013 0.001 PHE C 111 TYR 0.008 0.001 TYR D 223 ARG 0.006 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 557) hydrogen bonds : angle 5.05139 ( 1553) covalent geometry : bond 0.00214 (12832) covalent geometry : angle 0.48111 (17394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 1.469 Fit side-chains REVERT: A 55 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7910 (mtt180) REVERT: A 168 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7376 (mp0) REVERT: A 249 LYS cc_start: 0.7349 (ttmp) cc_final: 0.6992 (mtpp) REVERT: B 219 GLU cc_start: 0.7405 (tt0) cc_final: 0.6574 (tm-30) REVERT: D 140 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7673 (tttm) REVERT: D 227 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8060 (tmt) REVERT: D 249 LYS cc_start: 0.7698 (tttt) cc_final: 0.7254 (tttp) REVERT: D 303 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7461 (ptp-170) REVERT: E 116 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5701 (pp-130) REVERT: E 217 GLU cc_start: 0.7070 (tt0) cc_final: 0.6351 (tt0) outliers start: 42 outliers final: 18 residues processed: 168 average time/residue: 1.1967 time to fit residues: 220.1767 Evaluate side-chains 157 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 15 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 238 ASN E 152 ASN E 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121732 restraints weight = 28402.020| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.18 r_work: 0.3196 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12832 Z= 0.191 Angle : 0.557 5.432 17394 Z= 0.314 Chirality : 0.045 0.156 1919 Planarity : 0.004 0.061 2290 Dihedral : 4.834 36.801 1758 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.11 % Allowed : 27.83 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1643 helix: -1.11 (0.40), residues: 151 sheet: 0.41 (0.17), residues: 986 loop : -1.30 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 PHE 0.016 0.002 PHE D 73 TYR 0.012 0.001 TYR C 241 ARG 0.004 0.001 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 557) hydrogen bonds : angle 5.19041 ( 1553) covalent geometry : bond 0.00445 (12832) covalent geometry : angle 0.55692 (17394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 1.305 Fit side-chains REVERT: A 168 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7330 (mp0) REVERT: A 249 LYS cc_start: 0.7446 (ttmp) cc_final: 0.7094 (mtpp) REVERT: B 219 GLU cc_start: 0.7371 (tt0) cc_final: 0.6531 (tm-30) REVERT: C 236 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: D 140 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7704 (tttm) REVERT: D 159 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7535 (tp) REVERT: D 179 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: D 227 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8179 (tmm) REVERT: D 249 LYS cc_start: 0.7802 (tttt) cc_final: 0.7309 (tttp) REVERT: E 116 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5823 (pp-130) REVERT: E 179 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: E 217 GLU cc_start: 0.7033 (tt0) cc_final: 0.6285 (tt0) outliers start: 52 outliers final: 28 residues processed: 167 average time/residue: 1.2475 time to fit residues: 227.3358 Evaluate side-chains 163 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122520 restraints weight = 27881.810| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.07 r_work: 0.3218 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12832 Z= 0.145 Angle : 0.517 5.090 17394 Z= 0.293 Chirality : 0.044 0.149 1919 Planarity : 0.004 0.061 2290 Dihedral : 4.688 32.158 1758 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.88 % Allowed : 27.45 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1643 helix: -0.95 (0.41), residues: 145 sheet: 0.40 (0.16), residues: 988 loop : -1.15 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 PHE 0.016 0.001 PHE A 21 TYR 0.015 0.001 TYR C 241 ARG 0.004 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 557) hydrogen bonds : angle 5.07905 ( 1553) covalent geometry : bond 0.00335 (12832) covalent geometry : angle 0.51684 (17394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.492 Fit side-chains REVERT: A 249 LYS cc_start: 0.7459 (ttmp) cc_final: 0.7140 (mtpp) REVERT: B 204 MET cc_start: 0.7896 (mmm) cc_final: 0.7616 (mmm) REVERT: B 219 GLU cc_start: 0.7444 (tt0) cc_final: 0.6577 (tm-30) REVERT: D 140 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7773 (tttm) REVERT: D 159 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7542 (tp) REVERT: D 179 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: D 227 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: D 249 LYS cc_start: 0.7725 (tttt) cc_final: 0.7144 (tttp) REVERT: E 116 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5828 (pp-130) REVERT: E 179 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: E 217 GLU cc_start: 0.7084 (tt0) cc_final: 0.6286 (tt0) outliers start: 49 outliers final: 26 residues processed: 167 average time/residue: 1.7925 time to fit residues: 325.8461 Evaluate side-chains 158 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 238 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.158747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125952 restraints weight = 28253.239| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.20 r_work: 0.3262 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12832 Z= 0.085 Angle : 0.456 4.464 17394 Z= 0.259 Chirality : 0.043 0.138 1919 Planarity : 0.004 0.089 2290 Dihedral : 4.238 22.476 1758 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.74 % Allowed : 28.75 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1643 helix: -0.41 (0.43), residues: 145 sheet: 0.50 (0.17), residues: 988 loop : -0.95 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 PHE 0.014 0.001 PHE A 21 TYR 0.015 0.001 TYR C 241 ARG 0.003 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.02533 ( 557) hydrogen bonds : angle 4.78496 ( 1553) covalent geometry : bond 0.00181 (12832) covalent geometry : angle 0.45587 (17394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.352 Fit side-chains REVERT: A 55 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7744 (mtt180) REVERT: A 168 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7195 (mp0) REVERT: A 249 LYS cc_start: 0.7302 (ttmp) cc_final: 0.7022 (mtpp) REVERT: B 204 MET cc_start: 0.7877 (mmm) cc_final: 0.7584 (mmm) REVERT: B 219 GLU cc_start: 0.7318 (tt0) cc_final: 0.6481 (tm-30) REVERT: D 75 GLU cc_start: 0.7746 (tt0) cc_final: 0.7407 (tt0) REVERT: D 140 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7722 (tttm) REVERT: D 159 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7474 (tp) REVERT: D 179 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: D 208 GLU cc_start: 0.7119 (tp30) cc_final: 0.6404 (mm-30) REVERT: D 249 LYS cc_start: 0.7705 (tttt) cc_final: 0.7185 (tttp) REVERT: E 45 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8340 (t0) REVERT: E 217 GLU cc_start: 0.6995 (tt0) cc_final: 0.6260 (tt0) outliers start: 34 outliers final: 17 residues processed: 165 average time/residue: 1.2092 time to fit residues: 218.2086 Evaluate side-chains 149 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123211 restraints weight = 35977.783| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.28 r_work: 0.3132 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12832 Z= 0.148 Angle : 0.520 5.165 17394 Z= 0.294 Chirality : 0.044 0.159 1919 Planarity : 0.004 0.079 2290 Dihedral : 4.492 24.707 1758 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.81 % Allowed : 29.05 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1643 helix: -0.70 (0.42), residues: 145 sheet: 0.52 (0.17), residues: 978 loop : -1.11 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 PHE 0.013 0.001 PHE D 73 TYR 0.015 0.001 TYR C 241 ARG 0.006 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 557) hydrogen bonds : angle 4.89577 ( 1553) covalent geometry : bond 0.00342 (12832) covalent geometry : angle 0.51953 (17394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.414 Fit side-chains REVERT: A 249 LYS cc_start: 0.7369 (ttmp) cc_final: 0.7048 (mtpp) REVERT: B 204 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (mmm) REVERT: B 219 GLU cc_start: 0.7397 (tt0) cc_final: 0.6545 (tm-30) REVERT: D 140 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7763 (tttm) REVERT: D 159 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7531 (tp) REVERT: D 179 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: D 249 LYS cc_start: 0.7708 (tttt) cc_final: 0.7130 (tttp) REVERT: D 252 ASP cc_start: 0.6376 (m-30) cc_final: 0.6151 (t0) REVERT: E 217 GLU cc_start: 0.7079 (tt0) cc_final: 0.6266 (tt0) outliers start: 35 outliers final: 25 residues processed: 153 average time/residue: 1.1811 time to fit residues: 197.9086 Evaluate side-chains 154 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS B 286 ASN C 26 GLN C 106 ASN D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123173 restraints weight = 19022.628| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.21 r_work: 0.3286 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12832 Z= 0.120 Angle : 0.498 5.376 17394 Z= 0.283 Chirality : 0.044 0.160 1919 Planarity : 0.004 0.075 2290 Dihedral : 4.408 24.427 1758 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.74 % Allowed : 29.28 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1643 helix: -0.67 (0.41), residues: 151 sheet: 0.52 (0.17), residues: 980 loop : -1.04 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 PHE 0.016 0.001 PHE B 163 TYR 0.017 0.001 TYR C 241 ARG 0.007 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 557) hydrogen bonds : angle 4.84224 ( 1553) covalent geometry : bond 0.00271 (12832) covalent geometry : angle 0.49767 (17394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.675 Fit side-chains REVERT: A 55 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7909 (mtt180) REVERT: A 249 LYS cc_start: 0.7435 (ttmp) cc_final: 0.7108 (mtpp) REVERT: B 204 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7727 (mmm) REVERT: B 219 GLU cc_start: 0.7465 (tt0) cc_final: 0.6614 (tm-30) REVERT: D 140 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7776 (tttm) REVERT: D 159 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7546 (tp) REVERT: D 179 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: D 208 GLU cc_start: 0.7209 (tp30) cc_final: 0.6817 (mm-30) REVERT: D 249 LYS cc_start: 0.7727 (tttt) cc_final: 0.7138 (tttp) REVERT: E 217 GLU cc_start: 0.7092 (tt0) cc_final: 0.6304 (tt0) outliers start: 34 outliers final: 26 residues processed: 152 average time/residue: 1.8393 time to fit residues: 307.5731 Evaluate side-chains 154 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 137 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN C 26 GLN C 106 ASN D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122007 restraints weight = 26148.389| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.85 r_work: 0.3193 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12832 Z= 0.193 Angle : 0.562 5.788 17394 Z= 0.317 Chirality : 0.046 0.156 1919 Planarity : 0.004 0.075 2290 Dihedral : 4.715 27.951 1758 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.66 % Allowed : 29.20 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1643 helix: -0.98 (0.40), residues: 151 sheet: 0.43 (0.16), residues: 984 loop : -1.18 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 121 HIS 0.002 0.001 HIS E 13 PHE 0.016 0.002 PHE D 73 TYR 0.016 0.002 TYR C 241 ARG 0.007 0.001 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 557) hydrogen bonds : angle 5.03106 ( 1553) covalent geometry : bond 0.00452 (12832) covalent geometry : angle 0.56218 (17394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.324 Fit side-chains REVERT: A 249 LYS cc_start: 0.7503 (ttmp) cc_final: 0.7180 (mtpp) REVERT: B 204 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7674 (mmm) REVERT: B 219 GLU cc_start: 0.7411 (tt0) cc_final: 0.6574 (tm-30) REVERT: C 333 ASN cc_start: 0.8509 (m110) cc_final: 0.8188 (m110) REVERT: D 140 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7829 (tttm) REVERT: D 159 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7546 (tp) REVERT: D 179 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: D 208 GLU cc_start: 0.7262 (tp30) cc_final: 0.6867 (mm-30) REVERT: D 249 LYS cc_start: 0.7758 (tttt) cc_final: 0.7200 (tttp) REVERT: E 159 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7958 (tt) REVERT: E 179 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: E 217 GLU cc_start: 0.7019 (tt0) cc_final: 0.6228 (tt0) outliers start: 33 outliers final: 24 residues processed: 151 average time/residue: 1.1720 time to fit residues: 194.6659 Evaluate side-chains 151 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 0.1980 chunk 159 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN C 26 GLN C 106 ASN D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124034 restraints weight = 26089.436| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.88 r_work: 0.3248 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12832 Z= 0.096 Angle : 0.479 6.542 17394 Z= 0.272 Chirality : 0.043 0.161 1919 Planarity : 0.004 0.073 2290 Dihedral : 4.341 24.547 1758 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.98 % Allowed : 29.81 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1643 helix: -0.47 (0.42), residues: 145 sheet: 0.48 (0.17), residues: 990 loop : -0.86 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 121 HIS 0.002 0.000 HIS E 267 PHE 0.017 0.001 PHE B 163 TYR 0.018 0.001 TYR C 241 ARG 0.007 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.02656 ( 557) hydrogen bonds : angle 4.80201 ( 1553) covalent geometry : bond 0.00212 (12832) covalent geometry : angle 0.47914 (17394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9690.00 seconds wall clock time: 171 minutes 59.14 seconds (10319.14 seconds total)