Starting phenix.real_space_refine on Sat Dec 9 00:11:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p4i_13193/12_2023/7p4i_13193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p4i_13193/12_2023/7p4i_13193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p4i_13193/12_2023/7p4i_13193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p4i_13193/12_2023/7p4i_13193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p4i_13193/12_2023/7p4i_13193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p4i_13193/12_2023/7p4i_13193.pdb" } resolution = 4.2 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= 0.023 sd= 0.073 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 48 5.16 5 C 6198 2.51 5 N 1572 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9510 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3170 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 1 Chain: "B" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3170 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 1 Chain: "C" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3170 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 1 Time building chain proxies: 5.38, per 1000 atoms: 0.57 Number of scatterers: 9510 At special positions: 0 Unit cell: (120.146, 119.294, 86.9142, 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 48 16.00 O 1692 8.00 N 1572 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 79.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.664A pdb=" N ARG A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A 89 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 140 removed outlier: 4.054A pdb=" N ALA A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.587A pdb=" N LEU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 223 through 240 removed outlier: 4.257A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 285 removed outlier: 3.996A pdb=" N ILE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.109A pdb=" N MET A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 322 removed outlier: 5.087A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.528A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.869A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.653A pdb=" N CYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 378 removed outlier: 4.082A pdb=" N THR A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.655A pdb=" N ILE A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 427 through 439 removed outlier: 3.569A pdb=" N ILE A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 removed outlier: 4.369A pdb=" N ASP A 444 " --> pdb=" O PRO A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.156A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 480 removed outlier: 3.948A pdb=" N VAL A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG A 457 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.663A pdb=" N ARG B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 140 removed outlier: 4.053A pdb=" N ALA B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.588A pdb=" N LEU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 223 through 240 removed outlier: 4.257A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 244 through 285 removed outlier: 3.996A pdb=" N ILE B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 4.109A pdb=" N MET B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 322 removed outlier: 5.088A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.528A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.869A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.653A pdb=" N CYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 378 removed outlier: 4.081A pdb=" N THR B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 398 removed outlier: 3.655A pdb=" N ILE B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.570A pdb=" N ILE B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 444 removed outlier: 4.370A pdb=" N ASP B 444 " --> pdb=" O PRO B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.157A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 480 removed outlier: 3.949A pdb=" N VAL B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG B 457 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.665A pdb=" N ARG C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 4.053A pdb=" N ALA C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.587A pdb=" N LEU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 223 through 240 removed outlier: 4.258A pdb=" N LEU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 285 removed outlier: 3.997A pdb=" N ILE C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Proline residue: C 270 - end of helix removed outlier: 4.108A pdb=" N MET C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 322 removed outlier: 5.087A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Proline residue: C 314 - end of helix removed outlier: 3.527A pdb=" N PHE C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.870A pdb=" N LEU C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 330' Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.652A pdb=" N CYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 378 removed outlier: 4.081A pdb=" N THR C 376 " --> pdb=" O PRO C 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 398 removed outlier: 3.656A pdb=" N ILE C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 427 through 439 removed outlier: 3.568A pdb=" N ILE C 438 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 removed outlier: 4.369A pdb=" N ASP C 444 " --> pdb=" O PRO C 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.156A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 480 removed outlier: 3.948A pdb=" N VAL C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG C 457 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 189 through 196 Processing sheet with id=AA3, first strand: chain 'C' and resid 189 through 196 594 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 4.51 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: 2999 1.34 - 1.46: 1178 1.46 - 1.57: 5414 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9672 Sorted by residual: bond pdb=" C PHE B 77 " pdb=" N PRO B 78 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.26e+00 bond pdb=" C PHE C 77 " pdb=" N PRO C 78 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.12e+00 bond pdb=" C PHE A 77 " pdb=" N PRO A 78 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" C ALA A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.46e+00 bond pdb=" C ALA C 334 " pdb=" N PRO C 335 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.39e+00 ... (remaining 9667 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.50: 225 106.50 - 113.37: 5538 113.37 - 120.24: 3559 120.24 - 127.10: 3758 127.10 - 133.97: 78 Bond angle restraints: 13158 Sorted by residual: angle pdb=" C ALA B 76 " pdb=" N PHE B 77 " pdb=" CA PHE B 77 " ideal model delta sigma weight residual 120.26 124.54 -4.28 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA A 76 " pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta sigma weight residual 120.26 124.53 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA C 76 " pdb=" N PHE C 77 " pdb=" CA PHE C 77 " ideal model delta sigma weight residual 120.26 124.53 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" CA LEU B 313 " pdb=" CB LEU B 313 " pdb=" CG LEU B 313 " ideal model delta sigma weight residual 116.30 126.48 -10.18 3.50e+00 8.16e-02 8.46e+00 angle pdb=" CA LEU C 313 " pdb=" CB LEU C 313 " pdb=" CG LEU C 313 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 ... (remaining 13153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 4786 11.89 - 23.79: 625 23.79 - 35.68: 226 35.68 - 47.57: 57 47.57 - 59.46: 15 Dihedral angle restraints: 5709 sinusoidal: 2082 harmonic: 3627 Sorted by residual: dihedral pdb=" CA LEU B 62 " pdb=" C LEU B 62 " pdb=" N ARG B 63 " pdb=" CA ARG B 63 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU C 62 " pdb=" C LEU C 62 " pdb=" N ARG C 63 " pdb=" CA ARG C 63 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 62 " pdb=" C LEU A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual -180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 5706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1018 0.032 - 0.064: 460 0.064 - 0.096: 137 0.096 - 0.128: 41 0.128 - 0.160: 3 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA LEU C 313 " pdb=" N LEU C 313 " pdb=" C LEU C 313 " pdb=" CB LEU C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA LEU A 313 " pdb=" N LEU A 313 " pdb=" C LEU A 313 " pdb=" CB LEU A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA LEU B 313 " pdb=" N LEU B 313 " pdb=" C LEU B 313 " pdb=" CB LEU B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 1656 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 334 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO B 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 334 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 334 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " -0.022 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 364 2.71 - 3.26: 10712 3.26 - 3.81: 15044 3.81 - 4.35: 18140 4.35 - 4.90: 28741 Nonbonded interactions: 73001 Sorted by model distance: nonbonded pdb=" O VAL B 260 " pdb=" OG SER B 263 " model vdw 2.168 2.440 nonbonded pdb=" O VAL A 260 " pdb=" OG SER A 263 " model vdw 2.168 2.440 nonbonded pdb=" O VAL C 260 " pdb=" OG SER C 263 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR C 167 " pdb=" OH TYR C 195 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 167 " pdb=" OH TYR A 195 " model vdw 2.232 2.440 ... (remaining 72996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.020 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.990 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.003 0.031 9672 Z= 0.179 Angle : 0.765 10.183 13158 Z= 0.410 Chirality : 0.039 0.160 1659 Planarity : 0.004 0.039 1626 Dihedral : 13.104 59.464 3381 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1272 helix: 0.56 (0.19), residues: 780 sheet: -2.19 (0.48), residues: 48 loop : -1.74 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 267 HIS 0.004 0.001 HIS C 476 PHE 0.007 0.001 PHE C 250 TYR 0.011 0.001 TYR A 191 ARG 0.003 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1930 time to fit residues: 10.6108 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 32 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 50.0000 chunk 38 optimal weight: 0.0070 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9672 Z= 0.187 Angle : 0.629 9.182 13158 Z= 0.316 Chirality : 0.039 0.145 1659 Planarity : 0.004 0.037 1626 Dihedral : 4.600 29.403 1344 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.29 % Allowed : 7.87 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1272 helix: 0.91 (0.19), residues: 804 sheet: -1.89 (0.56), residues: 48 loop : -1.89 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 267 HIS 0.003 0.001 HIS A 476 PHE 0.010 0.001 PHE A 250 TYR 0.009 0.001 TYR B 74 ARG 0.001 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.107 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.1858 time to fit residues: 11.2644 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.0070 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 91 optimal weight: 0.1980 overall best weight: 2.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9672 Z= 0.150 Angle : 0.644 9.349 13158 Z= 0.312 Chirality : 0.040 0.150 1659 Planarity : 0.003 0.034 1626 Dihedral : 4.416 28.120 1344 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1272 helix: 1.14 (0.19), residues: 786 sheet: -1.89 (0.50), residues: 48 loop : -1.55 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 453 HIS 0.002 0.001 HIS A 476 PHE 0.021 0.001 PHE A 250 TYR 0.011 0.001 TYR B 191 ARG 0.001 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1885 time to fit residues: 10.4140 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9672 Z= 0.152 Angle : 0.633 9.309 13158 Z= 0.307 Chirality : 0.039 0.150 1659 Planarity : 0.003 0.032 1626 Dihedral : 4.343 26.732 1344 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1272 helix: 1.12 (0.19), residues: 801 sheet: -2.64 (0.50), residues: 60 loop : -1.44 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 453 HIS 0.002 0.001 HIS C 476 PHE 0.020 0.001 PHE A 250 TYR 0.009 0.001 TYR B 191 ARG 0.001 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.308 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2579 time to fit residues: 13.7208 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 1 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9672 Z= 0.181 Angle : 0.640 8.710 13158 Z= 0.313 Chirality : 0.040 0.148 1659 Planarity : 0.003 0.028 1626 Dihedral : 4.367 25.530 1344 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1272 helix: 1.05 (0.19), residues: 822 sheet: -2.69 (0.50), residues: 60 loop : -1.26 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 264 HIS 0.002 0.001 HIS B 475 PHE 0.017 0.001 PHE A 250 TYR 0.008 0.001 TYR C 74 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1907 time to fit residues: 10.5293 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9672 Z= 0.193 Angle : 0.662 8.578 13158 Z= 0.325 Chirality : 0.040 0.147 1659 Planarity : 0.003 0.027 1626 Dihedral : 4.448 28.267 1344 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.25), residues: 1272 helix: 1.01 (0.19), residues: 819 sheet: -2.76 (0.49), residues: 60 loop : -1.12 (0.35), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 267 HIS 0.002 0.001 HIS B 475 PHE 0.017 0.001 PHE A 250 TYR 0.008 0.001 TYR B 74 ARG 0.002 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1844 time to fit residues: 10.2651 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 8.9990 chunk 69 optimal weight: 0.0670 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9672 Z= 0.150 Angle : 0.654 9.202 13158 Z= 0.312 Chirality : 0.040 0.168 1659 Planarity : 0.003 0.026 1626 Dihedral : 4.381 28.169 1344 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1272 helix: 1.29 (0.19), residues: 801 sheet: -2.66 (0.50), residues: 60 loop : -1.00 (0.35), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 453 HIS 0.002 0.001 HIS C 476 PHE 0.019 0.001 PHE A 250 TYR 0.008 0.001 TYR B 191 ARG 0.001 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1854 time to fit residues: 10.7004 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 95 optimal weight: 0.2980 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9672 Z= 0.193 Angle : 0.674 9.314 13158 Z= 0.327 Chirality : 0.040 0.154 1659 Planarity : 0.003 0.024 1626 Dihedral : 4.472 28.896 1344 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1272 helix: 1.13 (0.19), residues: 816 sheet: -2.75 (0.50), residues: 60 loop : -0.84 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 267 HIS 0.002 0.001 HIS B 475 PHE 0.015 0.001 PHE A 250 TYR 0.008 0.001 TYR C 74 ARG 0.002 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1950 time to fit residues: 10.9039 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 50.0000 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.0870 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 209 HIS B 397 ASN C 209 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9672 Z= 0.157 Angle : 0.676 9.450 13158 Z= 0.320 Chirality : 0.040 0.156 1659 Planarity : 0.003 0.024 1626 Dihedral : 4.406 28.819 1344 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1272 helix: 1.22 (0.19), residues: 816 sheet: -2.68 (0.50), residues: 60 loop : -0.77 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 267 HIS 0.002 0.001 HIS B 308 PHE 0.019 0.001 PHE A 250 TYR 0.008 0.001 TYR C 191 ARG 0.001 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1970 time to fit residues: 10.8921 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9672 Z= 0.201 Angle : 0.679 8.874 13158 Z= 0.333 Chirality : 0.040 0.154 1659 Planarity : 0.003 0.023 1626 Dihedral : 4.499 29.735 1344 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1272 helix: 1.17 (0.19), residues: 828 sheet: -2.71 (0.51), residues: 60 loop : -0.75 (0.37), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 267 HIS 0.003 0.001 HIS B 475 PHE 0.015 0.001 PHE A 250 TYR 0.008 0.001 TYR A 74 ARG 0.003 0.000 ARG B 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1967 time to fit residues: 10.7326 Evaluate side-chains 33 residues out of total 1017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.035721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026716 restraints weight = 127640.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027289 restraints weight = 88262.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.027700 restraints weight = 68383.188| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9672 Z= 0.175 Angle : 0.671 9.337 13158 Z= 0.325 Chirality : 0.040 0.155 1659 Planarity : 0.003 0.023 1626 Dihedral : 4.497 29.773 1344 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1272 helix: 1.22 (0.19), residues: 828 sheet: -2.73 (0.51), residues: 60 loop : -0.74 (0.37), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 267 HIS 0.001 0.001 HIS C 475 PHE 0.017 0.001 PHE A 250 TYR 0.009 0.001 TYR C 74 ARG 0.002 0.000 ARG C 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1554.92 seconds wall clock time: 29 minutes 38.68 seconds (1778.68 seconds total)