Starting phenix.real_space_refine on Sun Jun 15 08:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dws_27758/06_2025/8dws_27758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dws_27758/06_2025/8dws_27758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dws_27758/06_2025/8dws_27758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dws_27758/06_2025/8dws_27758.map" model { file = "/net/cci-nas-00/data/ceres_data/8dws_27758/06_2025/8dws_27758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dws_27758/06_2025/8dws_27758.cif" } resolution = 3.73 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= 0.049 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 156 5.16 5 C 10927 2.51 5 N 2874 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17229 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 353, 2780 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2741 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 335} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2754 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2749 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 347, 2749 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain: "G" Number of atoms: 2737 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 345, 2737 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 9, 'TRANS': 335} Chain: "H" Number of atoms: 2719 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2719 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 10.72, per 1000 atoms: 0.62 Number of scatterers: 17229 At special positions: 0 Unit cell: (73.929, 145.264, 313.874, 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 156 16.00 O 3272 8.00 N 2874 7.00 C 10927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS H 361 " distance=2.03 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: 4.19 Conformation dependent library (CDL) restraints added in 2.2 seconds 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4198 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 23 sheets defined 47.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 138 through 144 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 185 through 197 removed outlier: 3.706A pdb=" N LEU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.029A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.907A pdb=" N SER A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.810A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 314 through 333 removed outlier: 6.322A pdb=" N SER A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.570A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.077A pdb=" N VAL A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.794A pdb=" N ASP B 63 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 145 through 148 Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.575A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.750A pdb=" N TYR B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.512A pdb=" N SER B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.315A pdb=" N VAL B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.964A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.923A pdb=" N SER D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.543A pdb=" N VAL D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.619A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 4.109A pdb=" N GLN D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 removed outlier: 4.124A pdb=" N CYS E 44 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 removed outlier: 3.825A pdb=" N LEU E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.543A pdb=" N ASP E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.846A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 259 removed outlier: 4.670A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 4.113A pdb=" N ALA E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 328 through 333 removed outlier: 3.560A pdb=" N VAL E 332 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 333' Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.808A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 359 removed outlier: 3.669A pdb=" N VAL E 349 " --> pdb=" O HIS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.865A pdb=" N ASP F 63 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 81 removed outlier: 3.843A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 81' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 145 through 148 Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.518A pdb=" N ASP F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.958A pdb=" N LEU F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 222 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.534A pdb=" N MET F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 247 through 261 Processing helix chain 'F' and resid 265 through 268 removed outlier: 3.752A pdb=" N LYS F 268 " --> pdb=" O ASN F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.523A pdb=" N SER F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 314 through 328 Processing helix chain 'F' and resid 328 through 333 Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.548A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 356 removed outlier: 3.613A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 150 through 154 removed outlier: 3.609A pdb=" N ASP G 153 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 197 removed outlier: 4.006A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 222 removed outlier: 3.846A pdb=" N LEU G 218 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 230 removed outlier: 3.582A pdb=" N MET G 228 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.807A pdb=" N ASN G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 265 through 268 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.624A pdb=" N SER G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 314 through 333 removed outlier: 6.230A pdb=" N SER G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 removed outlier: 4.178A pdb=" N LYS G 339 " --> pdb=" O THR G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.900A pdb=" N VAL G 349 " --> pdb=" O HIS G 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 44 removed outlier: 3.579A pdb=" N PHE H 43 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.644A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 3.709A pdb=" N ASN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.230A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.678A pdb=" N GLU H 230 " --> pdb=" O SER H 226 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.927A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 269 through 281 removed outlier: 3.609A pdb=" N LEU H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.504A pdb=" N SER H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 313 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 328 through 333 removed outlier: 3.911A pdb=" N LEU H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 345 Processing helix chain 'H' and resid 345 through 358 removed outlier: 4.153A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.660A pdb=" N ILE A 38 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 155 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 101 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 104 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 117 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.631A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 213 removed outlier: 8.804A pdb=" N ILE A 243 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS A 205 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.647A pdb=" N ILE B 137 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 86 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS B 135 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 213 removed outlier: 3.878A pdb=" N VAL B 241 " --> pdb=" O CYS B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 23 through 25 removed outlier: 6.489A pdb=" N CYS E 23 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 155 " --> pdb=" O ILE G 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AB1, first strand: chain 'E' and resid 115 through 118 removed outlier: 3.846A pdb=" N LYS E 101 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N CYS F 23 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET E 35 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 66 through 72 removed outlier: 7.132A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS E 68 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N AARG E 70 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 211 through 213 removed outlier: 6.350A pdb=" N CYS E 203 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 28 through 29 removed outlier: 4.024A pdb=" N LYS F 28 " --> pdb=" O GLN F 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN F 165 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 164 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 57 through 59 removed outlier: 4.162A pdb=" N SER F 59 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU F 65 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 91 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N AARG F 70 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE F 137 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU F 86 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS F 135 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 88 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE F 133 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 206 Processing sheet with id=AB8, first strand: chain 'G' and resid 28 through 33 removed outlier: 4.372A pdb=" N LYS G 28 " --> pdb=" O GLN G 165 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG G 99 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 100 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 123 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.562A pdb=" N VAL G 71 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 89 " --> pdb=" O CYS G 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N AARG G 70 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 85 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AC2, first strand: chain 'H' and resid 29 through 35 removed outlier: 4.713A pdb=" N PHE H 158 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER H 105 " --> pdb=" O PHE H 158 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE H 102 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU H 118 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE H 104 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA H 116 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 106 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 66 through 72 removed outlier: 7.277A pdb=" N LYS H 66 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN H 72 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER H 85 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 86 " --> pdb=" O PHE H 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AC5, first strand: chain 'H' and resid 205 through 206 697 hydrogen bonds defined for protein. 1926 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: 5.27 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5578 1.34 - 1.46: 3961 1.46 - 1.59: 7797 1.59 - 1.71: 0 1.71 - 1.83: 231 Bond restraints: 17567 Sorted by residual: bond pdb=" N SER G 171 " pdb=" CA SER G 171 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N GLN G 173 " pdb=" CA GLN G 173 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ILE G 170 " pdb=" CA ILE G 170 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.35e-02 5.49e+03 9.09e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N ASP G 166 " pdb=" CA ASP G 166 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.25e-02 6.40e+03 7.90e+00 ... (remaining 17562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 23583 4.09 - 8.18: 104 8.18 - 12.27: 4 12.27 - 16.36: 0 16.36 - 20.45: 1 Bond angle restraints: 23692 Sorted by residual: angle pdb=" C MET B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 121.54 141.99 -20.45 1.91e+00 2.74e-01 1.15e+02 angle pdb=" C ASP G 166 " pdb=" CA ASP G 166 " pdb=" CB ASP G 166 " ideal model delta sigma weight residual 109.64 118.86 -9.22 1.77e+00 3.19e-01 2.71e+01 angle pdb=" CA ILE G 170 " pdb=" C ILE G 170 " pdb=" O ILE G 170 " ideal model delta sigma weight residual 121.98 116.42 5.56 1.21e+00 6.83e-01 2.11e+01 angle pdb=" C VAL D 342 " pdb=" N VAL D 343 " pdb=" CA VAL D 343 " ideal model delta sigma weight residual 121.97 130.03 -8.06 1.80e+00 3.09e-01 2.00e+01 angle pdb=" C VAL B 168 " pdb=" N ASN B 169 " pdb=" CA ASN B 169 " ideal model delta sigma weight residual 121.70 129.48 -7.78 1.80e+00 3.09e-01 1.87e+01 ... (remaining 23687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9678 17.97 - 35.94: 834 35.94 - 53.91: 139 53.91 - 71.88: 30 71.88 - 89.85: 18 Dihedral angle restraints: 10699 sinusoidal: 4269 harmonic: 6430 Sorted by residual: dihedral pdb=" CA SER G 171 " pdb=" C SER G 171 " pdb=" N GLY G 172 " pdb=" CA GLY G 172 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA SER G 167 " pdb=" C SER G 167 " pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta harmonic sigma weight residual 180.00 138.67 41.33 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA GLN H 360 " pdb=" C GLN H 360 " pdb=" N CYS H 361 " pdb=" CA CYS H 361 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 10696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2498 0.099 - 0.199: 113 0.199 - 0.298: 4 0.298 - 0.397: 2 0.397 - 0.497: 2 Chirality restraints: 2619 Sorted by residual: chirality pdb=" CA ARG E 198 " pdb=" N ARG E 198 " pdb=" C ARG E 198 " pdb=" CB ARG E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LYS E 47 " pdb=" N LYS E 47 " pdb=" C LYS E 47 " pdb=" CB LYS E 47 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 2616 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 43 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE E 43 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE E 43 " -0.027 2.00e-02 2.50e+03 pdb=" N CYS E 44 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 52 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ILE E 52 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE E 52 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS E 53 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 169 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C ASN G 169 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN G 169 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE G 170 " 0.016 2.00e-02 2.50e+03 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.17: 15273 3.17 - 3.75: 26430 3.75 - 4.32: 34497 4.32 - 4.90: 57045 Nonbonded interactions: 133409 Sorted by model distance: nonbonded pdb=" OG SER G 21 " pdb=" O MET H 35 " model vdw 2.013 3.040 nonbonded pdb=" OG1 THR G 25 " pdb=" O THR H 37 " model vdw 2.061 3.040 nonbonded pdb=" OG SER F 54 " pdb=" O LEU F 69 " model vdw 2.063 3.040 nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.084 3.040 nonbonded pdb=" O VAL D 332 " pdb=" OG1 THR D 335 " model vdw 2.091 3.040 ... (remaining 133404 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 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'B' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'E' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 361)) selection = (chain 'F' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'G' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'H' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 39.480 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4530 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 : 0.004 0.052 17569 Z= 0.207 Angle : 0.789 20.445 23696 Z= 0.433 Chirality : 0.047 0.497 2619 Planarity : 0.004 0.065 3037 Dihedral : 14.369 89.853 6495 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.16 % Favored : 91.24 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.47 (0.18), residues: 2168 helix: 0.34 (0.18), residues: 826 sheet: -1.48 (0.28), residues: 345 loop : -1.92 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 67 HIS 0.005 0.001 HIS E 347 PHE 0.029 0.002 PHE E 136 TYR 0.026 0.002 TYR A 259 ARG 0.005 0.001 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.19643 ( 693) hydrogen bonds : angle 7.53851 ( 1926) SS BOND : bond 0.00472 ( 2) SS BOND : angle 2.34532 ( 4) covalent geometry : bond 0.00435 (17567) covalent geometry : angle 0.78824 (23692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 254 MET cc_start: 0.7340 (ttp) cc_final: 0.7110 (ttm) REVERT: G 353 TYR cc_start: 0.0306 (t80) cc_final: -0.1649 (m-80) REVERT: H 178 MET cc_start: 0.2555 (pmm) cc_final: 0.2133 (pmm) outliers start: 6 outliers final: 1 residues processed: 130 average time/residue: 0.2984 time to fit residues: 60.3017 Evaluate side-chains 98 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 328 HIS E 231 HIS E 326 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.079939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.049064 restraints weight = 164319.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048440 restraints weight = 123544.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048264 restraints weight = 118821.814| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17569 Z= 0.296 Angle : 0.796 11.909 23696 Z= 0.416 Chirality : 0.045 0.178 2619 Planarity : 0.005 0.079 3037 Dihedral : 5.865 50.148 2316 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.14 % Rotamer: Outliers : 0.42 % Allowed : 7.75 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.39 (0.18), residues: 2168 helix: 0.45 (0.17), residues: 845 sheet: -1.56 (0.29), residues: 310 loop : -1.92 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 36 HIS 0.007 0.001 HIS F 312 PHE 0.027 0.002 PHE F 257 TYR 0.035 0.002 TYR H 24 ARG 0.007 0.001 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 693) hydrogen bonds : angle 5.98596 ( 1926) SS BOND : bond 0.00299 ( 2) SS BOND : angle 2.04709 ( 4) covalent geometry : bond 0.00617 (17567) covalent geometry : angle 0.79568 (23692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.6229 (tmm) cc_final: 0.5811 (tmm) REVERT: B 228 MET cc_start: 0.8709 (ptm) cc_final: 0.8470 (ptm) REVERT: B 341 MET cc_start: 0.8878 (tmm) cc_final: 0.8664 (tmm) REVERT: F 176 MET cc_start: 0.7767 (mmt) cc_final: 0.7391 (mpp) REVERT: G 117 MET cc_start: 0.8291 (ppp) cc_final: 0.8006 (ppp) REVERT: G 173 GLN cc_start: 0.9594 (mp10) cc_final: 0.9324 (tp40) REVERT: G 254 MET cc_start: 0.6629 (ptp) cc_final: 0.6427 (ptm) REVERT: G 341 MET cc_start: 0.4634 (tmm) cc_final: 0.4269 (tmm) REVERT: H 176 MET cc_start: 0.4090 (tmm) cc_final: 0.3781 (mmp) REVERT: H 233 MET cc_start: 0.6268 (ppp) cc_final: 0.5904 (ppp) REVERT: H 288 MET cc_start: 0.9594 (ppp) cc_final: 0.9345 (ppp) outliers start: 8 outliers final: 5 residues processed: 108 average time/residue: 0.2806 time to fit residues: 49.5092 Evaluate side-chains 97 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain H residue 361 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 210 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 213 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 176 optimal weight: 50.0000 chunk 92 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.080778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.048532 restraints weight = 162163.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048017 restraints weight = 99527.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.048172 restraints weight = 74808.296| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17569 Z= 0.135 Angle : 0.620 12.176 23696 Z= 0.326 Chirality : 0.042 0.181 2619 Planarity : 0.003 0.058 3037 Dihedral : 5.366 48.750 2316 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.47 % Favored : 92.02 % Rotamer: Outliers : 1.05 % Allowed : 10.02 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.99 (0.18), residues: 2168 helix: 0.99 (0.18), residues: 850 sheet: -1.30 (0.30), residues: 303 loop : -1.93 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 36 HIS 0.003 0.001 HIS B 231 PHE 0.018 0.001 PHE F 257 TYR 0.017 0.001 TYR E 280 ARG 0.004 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 693) hydrogen bonds : angle 5.30308 ( 1926) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.63391 ( 4) covalent geometry : bond 0.00288 (17567) covalent geometry : angle 0.61957 (23692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8437 (t80) REVERT: A 117 MET cc_start: 0.6417 (ptt) cc_final: 0.6165 (pmm) REVERT: A 233 MET cc_start: 0.6415 (tmm) cc_final: 0.5941 (tmm) REVERT: B 228 MET cc_start: 0.8760 (ptm) cc_final: 0.8388 (ptm) REVERT: B 341 MET cc_start: 0.9058 (tmm) cc_final: 0.8763 (tmm) REVERT: E 250 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8871 (p) REVERT: F 83 TYR cc_start: 0.9548 (OUTLIER) cc_final: 0.9348 (t80) REVERT: F 269 MET cc_start: 0.6184 (ptm) cc_final: 0.5874 (ptm) REVERT: G 173 GLN cc_start: 0.9344 (mp-120) cc_final: 0.9140 (tp40) REVERT: G 178 MET cc_start: 0.8683 (tpp) cc_final: 0.8453 (tmm) REVERT: H 48 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8487 (mmp) REVERT: H 255 MET cc_start: 0.8609 (mmm) cc_final: 0.8226 (mmm) REVERT: H 269 MET cc_start: 0.7466 (ppp) cc_final: 0.7034 (ppp) REVERT: H 288 MET cc_start: 0.9626 (ppp) cc_final: 0.9348 (ppp) outliers start: 20 outliers final: 7 residues processed: 110 average time/residue: 0.2786 time to fit residues: 49.1773 Evaluate side-chains 105 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 361 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 HIS ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN ** H 347 HIS ** 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 = 0.4404 r_free = 0.4404 target = 0.081070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049443 restraints weight = 163432.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.050068 restraints weight = 112221.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.049208 restraints weight = 84744.902| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17569 Z= 0.120 Angle : 0.602 11.414 23696 Z= 0.314 Chirality : 0.041 0.250 2619 Planarity : 0.003 0.052 3037 Dihedral : 5.138 50.830 2316 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.70 % Favored : 91.79 % Rotamer: Outliers : 1.21 % Allowed : 12.08 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.77 (0.18), residues: 2168 helix: 1.25 (0.18), residues: 851 sheet: -1.33 (0.28), residues: 329 loop : -1.84 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 22 HIS 0.014 0.001 HIS D 328 PHE 0.017 0.001 PHE F 257 TYR 0.014 0.001 TYR B 280 ARG 0.003 0.000 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 693) hydrogen bonds : angle 4.99671 ( 1926) SS BOND : bond 0.00252 ( 2) SS BOND : angle 1.43883 ( 4) covalent geometry : bond 0.00257 (17567) covalent geometry : angle 0.60168 (23692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.5608 (pmm) REVERT: A 233 MET cc_start: 0.6484 (tmm) cc_final: 0.5971 (tmm) REVERT: B 176 MET cc_start: 0.8005 (mpp) cc_final: 0.7020 (tmm) REVERT: B 228 MET cc_start: 0.8727 (ptm) cc_final: 0.8194 (ttt) REVERT: B 341 MET cc_start: 0.9198 (tmm) cc_final: 0.8910 (tmm) REVERT: F 176 MET cc_start: 0.7357 (mmt) cc_final: 0.6922 (mpp) REVERT: F 269 MET cc_start: 0.6263 (ptm) cc_final: 0.6023 (ptm) REVERT: G 115 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5710 (pttm) REVERT: G 176 MET cc_start: 0.6776 (ppp) cc_final: 0.5807 (tpp) REVERT: G 255 MET cc_start: 0.8289 (mmp) cc_final: 0.7866 (mmm) REVERT: H 48 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (mmp) REVERT: H 176 MET cc_start: 0.4486 (mmp) cc_final: 0.3443 (tmm) REVERT: H 178 MET cc_start: 0.8298 (pmm) cc_final: 0.7810 (pmm) REVERT: H 233 MET cc_start: 0.6026 (ppp) cc_final: 0.5739 (ppp) REVERT: H 250 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.8855 (p) REVERT: H 255 MET cc_start: 0.8667 (mmm) cc_final: 0.8109 (mmm) REVERT: H 269 MET cc_start: 0.7725 (ppp) cc_final: 0.7106 (ppp) REVERT: H 288 MET cc_start: 0.9661 (ppp) cc_final: 0.9371 (ppp) outliers start: 23 outliers final: 10 residues processed: 110 average time/residue: 0.2746 time to fit residues: 48.1811 Evaluate side-chains 105 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 74 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 166 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.078821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047918 restraints weight = 168081.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047982 restraints weight = 125015.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.047348 restraints weight = 123358.023| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17569 Z= 0.209 Angle : 0.683 13.622 23696 Z= 0.355 Chirality : 0.042 0.213 2619 Planarity : 0.004 0.049 3037 Dihedral : 5.326 45.233 2316 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.81 % Favored : 90.73 % Rotamer: Outliers : 1.58 % Allowed : 13.66 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.94 (0.18), residues: 2168 helix: 1.06 (0.18), residues: 858 sheet: -1.32 (0.28), residues: 329 loop : -1.95 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 36 HIS 0.008 0.001 HIS D 345 PHE 0.025 0.002 PHE F 257 TYR 0.041 0.002 TYR F 83 ARG 0.004 0.001 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 693) hydrogen bonds : angle 5.30930 ( 1926) SS BOND : bond 0.00119 ( 2) SS BOND : angle 1.30756 ( 4) covalent geometry : bond 0.00444 (17567) covalent geometry : angle 0.68295 (23692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5854 (pmm) REVERT: A 233 MET cc_start: 0.6883 (tmm) cc_final: 0.6667 (tmm) REVERT: B 176 MET cc_start: 0.8032 (mpp) cc_final: 0.7086 (tmm) REVERT: B 178 MET cc_start: 0.7504 (tpp) cc_final: 0.7271 (tpp) REVERT: B 341 MET cc_start: 0.8848 (tmm) cc_final: 0.8620 (tmm) REVERT: E 157 LEU cc_start: 0.9326 (tp) cc_final: 0.9095 (tp) REVERT: F 176 MET cc_start: 0.6984 (mmt) cc_final: 0.6452 (mpp) REVERT: G 255 MET cc_start: 0.8499 (mmp) cc_final: 0.8091 (mmm) REVERT: H 176 MET cc_start: 0.4959 (mmp) cc_final: 0.3743 (tmm) REVERT: H 233 MET cc_start: 0.6020 (ppp) cc_final: 0.5796 (ppp) REVERT: H 269 MET cc_start: 0.7892 (ppp) cc_final: 0.7242 (ppp) outliers start: 30 outliers final: 15 residues processed: 117 average time/residue: 0.2703 time to fit residues: 50.8878 Evaluate side-chains 107 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain H residue 361 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 0.0670 chunk 49 optimal weight: 50.0000 chunk 9 optimal weight: 0.0000 chunk 195 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.080482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.049120 restraints weight = 165223.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.049887 restraints weight = 110250.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.048839 restraints weight = 82872.129| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17569 Z= 0.111 Angle : 0.623 11.557 23696 Z= 0.322 Chirality : 0.041 0.192 2619 Planarity : 0.003 0.049 3037 Dihedral : 5.018 53.264 2316 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.07 % Favored : 91.56 % Rotamer: Outliers : 1.05 % Allowed : 14.35 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.73 (0.19), residues: 2168 helix: 1.29 (0.18), residues: 857 sheet: -1.16 (0.28), residues: 330 loop : -1.90 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 22 HIS 0.009 0.001 HIS D 347 PHE 0.016 0.001 PHE F 257 TYR 0.031 0.001 TYR A 83 ARG 0.003 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.02710 ( 693) hydrogen bonds : angle 4.82242 ( 1926) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.08325 ( 4) covalent geometry : bond 0.00237 (17567) covalent geometry : angle 0.62255 (23692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9099 (tt) REVERT: A 117 MET cc_start: 0.6564 (ptt) cc_final: 0.6244 (pmm) REVERT: A 233 MET cc_start: 0.7041 (tmm) cc_final: 0.6601 (tmm) REVERT: B 176 MET cc_start: 0.7845 (mpp) cc_final: 0.6891 (tmm) REVERT: B 288 MET cc_start: 0.9214 (mtm) cc_final: 0.8993 (mtm) REVERT: B 341 MET cc_start: 0.8999 (tmm) cc_final: 0.8766 (tmm) REVERT: F 176 MET cc_start: 0.7097 (mmt) cc_final: 0.6680 (mpp) REVERT: F 269 MET cc_start: 0.6044 (ptm) cc_final: 0.5695 (ptm) REVERT: G 35 MET cc_start: 0.8204 (mmp) cc_final: 0.7981 (mmp) REVERT: G 178 MET cc_start: 0.8663 (tpp) cc_final: 0.8285 (tmm) REVERT: H 48 MET cc_start: 0.8499 (mmp) cc_final: 0.8278 (mmp) REVERT: H 176 MET cc_start: 0.4352 (mmp) cc_final: 0.3045 (tmm) REVERT: H 269 MET cc_start: 0.7827 (ppp) cc_final: 0.7610 (ppp) REVERT: H 288 MET cc_start: 0.9657 (ppp) cc_final: 0.9414 (ppp) REVERT: H 341 MET cc_start: 0.8929 (tmm) cc_final: 0.8702 (tmm) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 0.2757 time to fit residues: 49.2028 Evaluate side-chains 107 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 241 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 166 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 100 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.079920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.047221 restraints weight = 163831.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.045676 restraints weight = 101900.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.045910 restraints weight = 79089.298| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17569 Z= 0.123 Angle : 0.633 11.081 23696 Z= 0.321 Chirality : 0.041 0.235 2619 Planarity : 0.003 0.039 3037 Dihedral : 4.923 51.733 2316 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.70 % Favored : 91.97 % Rotamer: Outliers : 1.37 % Allowed : 14.93 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.64 (0.19), residues: 2168 helix: 1.36 (0.18), residues: 860 sheet: -1.11 (0.28), residues: 335 loop : -1.86 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 194 HIS 0.014 0.001 HIS B 231 PHE 0.017 0.001 PHE F 257 TYR 0.015 0.001 TYR A 83 ARG 0.004 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.02709 ( 693) hydrogen bonds : angle 4.81846 ( 1926) SS BOND : bond 0.00458 ( 2) SS BOND : angle 0.50443 ( 4) covalent geometry : bond 0.00265 (17567) covalent geometry : angle 0.63305 (23692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6666 (pmm) REVERT: A 233 MET cc_start: 0.6260 (tmm) cc_final: 0.5793 (tmm) REVERT: A 255 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8980 (ptm) REVERT: B 176 MET cc_start: 0.7724 (mpp) cc_final: 0.6728 (tmm) REVERT: B 178 MET cc_start: 0.7501 (tpp) cc_final: 0.7152 (tpp) REVERT: B 288 MET cc_start: 0.9196 (mtm) cc_final: 0.8974 (mtm) REVERT: B 341 MET cc_start: 0.9236 (tmm) cc_final: 0.8910 (tmm) REVERT: E 50 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: F 176 MET cc_start: 0.7090 (mmt) cc_final: 0.6561 (mpp) REVERT: H 48 MET cc_start: 0.8326 (mmp) cc_final: 0.7947 (mmp) REVERT: H 176 MET cc_start: 0.4218 (mmp) cc_final: 0.2937 (tmm) REVERT: H 341 MET cc_start: 0.9048 (tmm) cc_final: 0.8722 (tmm) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.2729 time to fit residues: 47.3531 Evaluate side-chains 105 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 156 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.079944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.048584 restraints weight = 162776.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.047818 restraints weight = 107302.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.047619 restraints weight = 77538.981| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17569 Z= 0.116 Angle : 0.652 14.812 23696 Z= 0.326 Chirality : 0.041 0.265 2619 Planarity : 0.003 0.046 3037 Dihedral : 4.892 52.578 2316 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.89 % Favored : 91.79 % Rotamer: Outliers : 1.37 % Allowed : 15.40 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.59 (0.19), residues: 2168 helix: 1.43 (0.18), residues: 859 sheet: -1.06 (0.29), residues: 333 loop : -1.86 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 36 HIS 0.006 0.001 HIS G 345 PHE 0.017 0.001 PHE F 257 TYR 0.030 0.001 TYR F 83 ARG 0.003 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.02627 ( 693) hydrogen bonds : angle 4.75099 ( 1926) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.71618 ( 4) covalent geometry : bond 0.00251 (17567) covalent geometry : angle 0.65174 (23692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8788 (tt) REVERT: A 117 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.6087 (pmm) REVERT: A 233 MET cc_start: 0.6388 (tmm) cc_final: 0.6021 (tmm) REVERT: A 255 MET cc_start: 0.9488 (tpp) cc_final: 0.8915 (ptm) REVERT: B 176 MET cc_start: 0.7836 (mpp) cc_final: 0.6916 (tmm) REVERT: B 178 MET cc_start: 0.7558 (tpp) cc_final: 0.7222 (tpp) REVERT: B 288 MET cc_start: 0.9194 (mtm) cc_final: 0.8922 (mtm) REVERT: B 341 MET cc_start: 0.9098 (tmm) cc_final: 0.8813 (tmm) REVERT: D 341 MET cc_start: 0.8083 (tmm) cc_final: 0.7768 (ppp) REVERT: E 50 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: F 176 MET cc_start: 0.7177 (mmt) cc_final: 0.6610 (mpp) REVERT: G 255 MET cc_start: 0.8563 (mmp) cc_final: 0.8252 (mmm) REVERT: H 48 MET cc_start: 0.8301 (mmp) cc_final: 0.7998 (mmp) REVERT: H 176 MET cc_start: 0.4256 (mmp) cc_final: 0.2972 (tmm) REVERT: H 269 MET cc_start: 0.8868 (ppp) cc_final: 0.8417 (ppp) outliers start: 26 outliers final: 13 residues processed: 112 average time/residue: 0.2797 time to fit residues: 50.7391 Evaluate side-chains 104 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 41 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.077868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.043830 restraints weight = 165140.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.043615 restraints weight = 107874.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.043615 restraints weight = 84400.881| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17569 Z= 0.237 Angle : 0.780 13.383 23696 Z= 0.392 Chirality : 0.044 0.268 2619 Planarity : 0.004 0.053 3037 Dihedral : 5.252 46.323 2316 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.90 % Favored : 90.73 % Rotamer: Outliers : 1.37 % Allowed : 15.56 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.90 (0.18), residues: 2168 helix: 1.08 (0.18), residues: 858 sheet: -1.30 (0.28), residues: 340 loop : -1.92 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 338 HIS 0.010 0.002 HIS B 231 PHE 0.023 0.002 PHE F 257 TYR 0.019 0.002 TYR F 83 ARG 0.008 0.001 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 693) hydrogen bonds : angle 5.30556 ( 1926) SS BOND : bond 0.00629 ( 2) SS BOND : angle 3.61100 ( 4) covalent geometry : bond 0.00501 (17567) covalent geometry : angle 0.77884 (23692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.6992 (tmm) cc_final: 0.6544 (tmm) REVERT: B 176 MET cc_start: 0.7517 (mpp) cc_final: 0.6594 (tmm) REVERT: B 288 MET cc_start: 0.9252 (mtm) cc_final: 0.8991 (mtm) REVERT: B 341 MET cc_start: 0.8921 (tmm) cc_final: 0.8638 (tmm) REVERT: F 269 MET cc_start: 0.6366 (ptm) cc_final: 0.5935 (ptm) REVERT: G 255 MET cc_start: 0.8769 (mmp) cc_final: 0.8471 (mmm) REVERT: H 176 MET cc_start: 0.4336 (mmp) cc_final: 0.2964 (tmm) REVERT: H 291 ASP cc_start: 0.9371 (OUTLIER) cc_final: 0.8910 (m-30) outliers start: 26 outliers final: 19 residues processed: 112 average time/residue: 0.3296 time to fit residues: 60.4906 Evaluate side-chains 108 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 123 optimal weight: 0.0000 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.9686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.078913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047770 restraints weight = 163990.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.045088 restraints weight = 107932.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045147 restraints weight = 82020.462| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17569 Z= 0.122 Angle : 0.708 14.467 23696 Z= 0.352 Chirality : 0.043 0.295 2619 Planarity : 0.003 0.056 3037 Dihedral : 5.016 52.301 2316 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.07 % Favored : 91.56 % Rotamer: Outliers : 0.95 % Allowed : 15.98 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.66 (0.19), residues: 2168 helix: 1.35 (0.18), residues: 851 sheet: -1.14 (0.29), residues: 334 loop : -1.84 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 338 HIS 0.007 0.001 HIS H 214 PHE 0.017 0.001 PHE E 257 TYR 0.014 0.001 TYR E 280 ARG 0.004 0.000 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.02641 ( 693) hydrogen bonds : angle 4.92735 ( 1926) SS BOND : bond 0.00432 ( 2) SS BOND : angle 2.66470 ( 4) covalent geometry : bond 0.00266 (17567) covalent geometry : angle 0.70748 (23692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.6468 (tmm) cc_final: 0.6240 (tmm) REVERT: A 255 MET cc_start: 0.9323 (tpp) cc_final: 0.9013 (ptm) REVERT: B 176 MET cc_start: 0.8010 (mpp) cc_final: 0.7287 (tmm) REVERT: B 178 MET cc_start: 0.7535 (tpp) cc_final: 0.6475 (tmm) REVERT: B 341 MET cc_start: 0.9087 (tmm) cc_final: 0.8785 (tmm) REVERT: F 176 MET cc_start: 0.6787 (mmt) cc_final: 0.6179 (mpp) REVERT: G 255 MET cc_start: 0.8689 (mmp) cc_final: 0.8471 (mmm) REVERT: H 48 MET cc_start: 0.7749 (mmp) cc_final: 0.7461 (mmp) REVERT: H 176 MET cc_start: 0.3795 (mmp) cc_final: 0.2483 (tmm) REVERT: H 291 ASP cc_start: 0.9349 (OUTLIER) cc_final: 0.8900 (m-30) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.2841 time to fit residues: 48.1722 Evaluate side-chains 104 residues out of total 1899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 25 optimal weight: 0.0070 chunk 186 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.078858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.047268 restraints weight = 164820.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.046393 restraints weight = 104540.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.045830 restraints weight = 76035.893| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17569 Z= 0.125 Angle : 0.701 14.801 23696 Z= 0.346 Chirality : 0.042 0.299 2619 Planarity : 0.003 0.057 3037 Dihedral : 4.923 51.444 2316 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.80 % Favored : 91.88 % Rotamer: Outliers : 0.90 % Allowed : 16.14 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.56 (0.19), residues: 2168 helix: 1.46 (0.19), residues: 850 sheet: -1.10 (0.29), residues: 338 loop : -1.81 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 338 HIS 0.009 0.001 HIS B 231 PHE 0.018 0.001 PHE F 257 TYR 0.012 0.001 TYR E 280 ARG 0.005 0.000 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.02557 ( 693) hydrogen bonds : angle 4.83708 ( 1926) SS BOND : bond 0.00371 ( 2) SS BOND : angle 1.96153 ( 4) covalent geometry : bond 0.00272 (17567) covalent geometry : angle 0.70052 (23692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11235.03 seconds wall clock time: 194 minutes 9.40 seconds (11649.40 seconds total)