Starting phenix.real_space_refine on Fri Oct 10 23:09:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvb_41636/10_2025/8tvb_41636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvb_41636/10_2025/8tvb_41636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tvb_41636/10_2025/8tvb_41636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvb_41636/10_2025/8tvb_41636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tvb_41636/10_2025/8tvb_41636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvb_41636/10_2025/8tvb_41636.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.152 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 60 5.16 5 C 6186 2.51 5 N 1605 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9687 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3173 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C Time building chain proxies: 2.35, per 1000 atoms: 0.24 Number of scatterers: 9687 At special positions: 0 Unit cell: (108, 104, 93, 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 60 16.00 O 1836 8.00 N 1605 7.00 C 6186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 288 " distance=2.04 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 451 " - pdb=" SG CYS A 459 " distance=2.02 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 488 " distance=2.19 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 513 " distance=2.05 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 436 " distance=2.03 Simple disulfide: pdb=" SG CYS C 427 " - pdb=" SG CYS C 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 451 " - pdb=" SG CYS B 459 " distance=2.02 Simple disulfide: pdb=" SG CYS C 451 " - pdb=" SG CYS C 459 " distance=2.02 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 488 " distance=2.19 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 488 " distance=2.19 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 513 " distance=2.05 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 513 " distance=2.05 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 195 " " NAG A 902 " - " ASN A 169 " " NAG A 903 " - " ASN A 510 " " NAG A 904 " - " ASN A 160 " " NAG B 901 " - " ASN B 195 " " NAG B 902 " - " ASN B 169 " " NAG B 903 " - " ASN B 510 " " NAG B 904 " - " ASN B 160 " " NAG C 901 " - " ASN C 195 " " NAG C 902 " - " ASN C 169 " " NAG C 903 " - " ASN C 510 " " NAG C 904 " - " ASN C 160 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 447.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 37.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.878A pdb=" N ILE A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.163A pdb=" N ILE A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.758A pdb=" N GLN A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.668A pdb=" N THR A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.878A pdb=" N ILE B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.163A pdb=" N ILE B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.757A pdb=" N GLN B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 287 through 311 removed outlier: 3.667A pdb=" N THR B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.877A pdb=" N ILE C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 4.162A pdb=" N ILE C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.758A pdb=" N GLN C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 287 through 311 removed outlier: 3.668A pdb=" N THR C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 329 through 332 Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 355 Processing helix chain 'C' and resid 424 through 427 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 533 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429 removed outlier: 7.800A pdb=" N VAL A 434 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU A 141 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS A 436 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 143 " --> pdb=" O CYS A 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU A 391 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 139 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 389 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU A 141 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA A 387 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS A 143 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N SER A 385 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS A 145 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR A 383 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 411 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 422 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 12.690A pdb=" N SER A 150 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ASN A 266 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP A 152 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE A 268 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 154 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 371 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE A 365 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 373 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 359 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 322 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.545A pdb=" N LEU C 522 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 220 Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.708A pdb=" N LEU A 522 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 428 through 429 removed outlier: 7.800A pdb=" N VAL B 434 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B 141 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS B 436 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 143 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU B 391 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR B 139 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 389 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU B 141 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA B 387 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS B 143 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N SER B 385 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS B 145 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR B 383 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 411 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 422 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 258 removed outlier: 12.691A pdb=" N SER B 150 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N ASN B 266 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP B 152 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE B 268 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 154 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 371 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 365 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 373 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 359 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 322 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB2, first strand: chain 'B' and resid 506 through 508 Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.708A pdb=" N LEU B 522 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 428 through 429 removed outlier: 7.799A pdb=" N VAL C 434 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU C 141 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS C 436 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 143 " --> pdb=" O CYS C 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU C 391 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR C 139 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 389 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU C 141 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA C 387 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS C 143 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N SER C 385 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS C 145 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR C 383 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR C 411 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 422 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 258 removed outlier: 12.689A pdb=" N SER C 150 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N ASN C 266 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP C 152 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE C 268 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 154 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 371 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE C 365 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 373 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 359 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 322 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 397 through 398 413 hydrogen bonds defined for protein. 1095 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: 1.76 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1948 1.33 - 1.45: 2051 1.45 - 1.58: 5736 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9825 Sorted by residual: bond pdb=" C5 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C5 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C5 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.40e+00 bond pdb=" C5 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.10e+00 ... (remaining 9820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12064 1.81 - 3.61: 1067 3.61 - 5.42: 135 5.42 - 7.23: 78 7.23 - 9.03: 18 Bond angle restraints: 13362 Sorted by residual: angle pdb=" C TYR C 378 " pdb=" N PRO C 379 " pdb=" CA PRO C 379 " ideal model delta sigma weight residual 119.85 127.73 -7.88 1.01e+00 9.80e-01 6.09e+01 angle pdb=" C TYR B 378 " pdb=" N PRO B 379 " pdb=" CA PRO B 379 " ideal model delta sigma weight residual 119.85 127.72 -7.87 1.01e+00 9.80e-01 6.08e+01 angle pdb=" C TYR A 378 " pdb=" N PRO A 379 " pdb=" CA PRO A 379 " ideal model delta sigma weight residual 119.85 127.70 -7.85 1.01e+00 9.80e-01 6.04e+01 angle pdb=" C THR B 147 " pdb=" N PRO B 148 " pdb=" CA PRO B 148 " ideal model delta sigma weight residual 120.31 127.27 -6.96 9.80e-01 1.04e+00 5.05e+01 angle pdb=" C THR C 147 " pdb=" N PRO C 148 " pdb=" CA PRO C 148 " ideal model delta sigma weight residual 120.31 127.25 -6.94 9.80e-01 1.04e+00 5.02e+01 ... (remaining 13357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5934 17.95 - 35.90: 147 35.90 - 53.86: 36 53.86 - 71.81: 21 71.81 - 89.76: 9 Dihedral angle restraints: 6147 sinusoidal: 2442 harmonic: 3705 Sorted by residual: dihedral pdb=" CA PRO B 148 " pdb=" C PRO B 148 " pdb=" N SER B 149 " pdb=" CA SER B 149 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO A 148 " pdb=" C PRO A 148 " pdb=" N SER A 149 " pdb=" CA SER A 149 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO C 148 " pdb=" C PRO C 148 " pdb=" N SER C 149 " pdb=" CA SER C 149 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1218 0.074 - 0.147: 368 0.147 - 0.221: 67 0.221 - 0.294: 3 0.294 - 0.368: 12 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA CYS A 288 " pdb=" N CYS A 288 " pdb=" C CYS A 288 " pdb=" CB CYS A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA CYS B 288 " pdb=" N CYS B 288 " pdb=" C CYS B 288 " pdb=" CB CYS B 288 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA CYS C 288 " pdb=" N CYS C 288 " pdb=" C CYS C 288 " pdb=" CB CYS C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1665 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 239 " -0.488 9.50e-02 1.11e+02 2.19e-01 2.93e+01 pdb=" NE ARG C 239 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 239 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 239 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 239 " -0.488 9.50e-02 1.11e+02 2.19e-01 2.93e+01 pdb=" NE ARG B 239 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 239 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 239 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 239 " 0.487 9.50e-02 1.11e+02 2.18e-01 2.92e+01 pdb=" NE ARG A 239 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 239 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 239 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 239 " 0.016 2.00e-02 2.50e+03 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 4682 2.97 - 3.45: 8704 3.45 - 3.93: 15806 3.93 - 4.42: 17854 4.42 - 4.90: 29156 Nonbonded interactions: 76202 Sorted by model distance: nonbonded pdb=" NZ LYS C 151 " pdb=" O LEU C 342 " model vdw 2.487 3.120 nonbonded pdb=" NZ LYS A 151 " pdb=" O LEU A 342 " model vdw 2.487 3.120 nonbonded pdb=" NZ LYS B 151 " pdb=" O LEU B 342 " model vdw 2.487 3.120 nonbonded pdb=" N GLU C 457 " pdb=" OE1 GLU C 457 " model vdw 2.513 3.120 nonbonded pdb=" N GLU A 457 " pdb=" OE1 GLU A 457 " model vdw 2.513 3.120 ... (remaining 76197 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: 0.05 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.010 0.163 9852 Z= 0.565 Angle : 1.299 22.799 13428 Z= 0.852 Chirality : 0.075 0.368 1668 Planarity : 0.010 0.219 1674 Dihedral : 10.855 89.758 3720 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.20 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.22), residues: 1254 helix: -1.65 (0.20), residues: 363 sheet: 0.89 (0.32), residues: 252 loop : 0.56 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 461 TYR 0.032 0.003 TYR C 142 PHE 0.017 0.003 PHE C 371 TRP 0.008 0.004 TRP C 404 HIS 0.005 0.002 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00960 ( 9825) covalent geometry : angle 1.21478 (13362) SS BOND : bond 0.07361 ( 15) SS BOND : angle 3.76994 ( 30) hydrogen bonds : bond 0.18619 ( 413) hydrogen bonds : angle 7.65405 ( 1095) link_NAG-ASN : bond 0.04691 ( 12) link_NAG-ASN : angle 8.33177 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7041 (t0) cc_final: 0.6758 (t0) REVERT: A 509 ASP cc_start: 0.7452 (p0) cc_final: 0.7204 (p0) outliers start: 0 outliers final: 1 residues processed: 217 average time/residue: 0.6506 time to fit residues: 150.4134 Evaluate side-chains 132 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS B 272 GLN B 511 GLN C 482 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119805 restraints weight = 11055.269| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.98 r_work: 0.3238 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9852 Z= 0.153 Angle : 0.535 6.866 13428 Z= 0.294 Chirality : 0.048 0.190 1668 Planarity : 0.004 0.034 1674 Dihedral : 4.709 29.787 1607 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.79 % Allowed : 8.66 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.23), residues: 1254 helix: -0.06 (0.25), residues: 393 sheet: 1.06 (0.29), residues: 294 loop : 0.49 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 239 TYR 0.016 0.002 TYR A 468 PHE 0.016 0.002 PHE B 371 TRP 0.004 0.001 TRP B 404 HIS 0.006 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9825) covalent geometry : angle 0.52565 (13362) SS BOND : bond 0.01888 ( 15) SS BOND : angle 1.24670 ( 30) hydrogen bonds : bond 0.04462 ( 413) hydrogen bonds : angle 5.19959 ( 1095) link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 1.75148 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.393 Fit side-chains REVERT: A 166 LYS cc_start: 0.7175 (mttt) cc_final: 0.6971 (tttt) REVERT: A 180 ASP cc_start: 0.8392 (m-30) cc_final: 0.8138 (m-30) REVERT: A 191 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 271 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6903 (mtm) REVERT: A 296 ASP cc_start: 0.8169 (m-30) cc_final: 0.7952 (m-30) REVERT: B 125 HIS cc_start: 0.7713 (t-170) cc_final: 0.6688 (m170) REVERT: B 315 GLN cc_start: 0.7269 (mt0) cc_final: 0.7014 (mp10) REVERT: B 520 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 166 LYS cc_start: 0.7036 (mmmm) cc_final: 0.6160 (tttp) REVERT: C 511 GLN cc_start: 0.7586 (mt0) cc_final: 0.6985 (mm-40) outliers start: 18 outliers final: 4 residues processed: 156 average time/residue: 0.6188 time to fit residues: 103.0382 Evaluate side-chains 126 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 524 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.0670 chunk 85 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 511 GLN C 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.134005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113821 restraints weight = 11024.039| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.97 r_work: 0.3153 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9852 Z= 0.179 Angle : 0.554 6.852 13428 Z= 0.298 Chirality : 0.049 0.166 1668 Planarity : 0.004 0.036 1674 Dihedral : 4.625 24.794 1605 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.07 % Favored : 97.69 % Rotamer: Outliers : 1.99 % Allowed : 10.25 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.23), residues: 1254 helix: 0.24 (0.27), residues: 393 sheet: 0.77 (0.30), residues: 258 loop : 0.35 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 239 TYR 0.028 0.002 TYR A 468 PHE 0.019 0.002 PHE C 371 TRP 0.006 0.001 TRP C 404 HIS 0.004 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9825) covalent geometry : angle 0.54654 (13362) SS BOND : bond 0.00240 ( 15) SS BOND : angle 1.41601 ( 30) hydrogen bonds : bond 0.05228 ( 413) hydrogen bonds : angle 5.15343 ( 1095) link_NAG-ASN : bond 0.00235 ( 12) link_NAG-ASN : angle 1.42747 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.397 Fit side-chains REVERT: A 166 LYS cc_start: 0.7648 (mttt) cc_final: 0.7303 (tttt) REVERT: A 180 ASP cc_start: 0.8666 (m-30) cc_final: 0.8423 (m-30) REVERT: A 232 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 271 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7327 (mtm) REVERT: A 296 ASP cc_start: 0.8493 (m-30) cc_final: 0.8238 (m-30) REVERT: A 305 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 251 ASN cc_start: 0.8556 (p0) cc_final: 0.8309 (p0) REVERT: B 315 GLN cc_start: 0.7404 (mt0) cc_final: 0.7061 (mp10) REVERT: B 511 GLN cc_start: 0.8263 (tp40) cc_final: 0.7989 (mm-40) REVERT: C 166 LYS cc_start: 0.7515 (mmmm) cc_final: 0.6814 (tttp) REVERT: C 305 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: C 315 GLN cc_start: 0.7285 (mt0) cc_final: 0.7022 (mp10) REVERT: C 381 MET cc_start: 0.8676 (mmt) cc_final: 0.8334 (mmt) REVERT: C 511 GLN cc_start: 0.7820 (mt0) cc_final: 0.7461 (mt0) outliers start: 20 outliers final: 4 residues processed: 137 average time/residue: 0.6516 time to fit residues: 95.2143 Evaluate side-chains 105 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 347 ASN B 165 ASN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114960 restraints weight = 11118.175| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.98 r_work: 0.3169 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9852 Z= 0.126 Angle : 0.465 5.987 13428 Z= 0.253 Chirality : 0.047 0.150 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.208 20.504 1605 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.99 % Favored : 97.77 % Rotamer: Outliers : 2.19 % Allowed : 11.34 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.23), residues: 1254 helix: 0.67 (0.27), residues: 393 sheet: 0.66 (0.31), residues: 258 loop : 0.23 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.020 0.001 TYR A 468 PHE 0.013 0.002 PHE C 371 TRP 0.003 0.001 TRP B 404 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9825) covalent geometry : angle 0.45740 (13362) SS BOND : bond 0.00339 ( 15) SS BOND : angle 1.20417 ( 30) hydrogen bonds : bond 0.04045 ( 413) hydrogen bonds : angle 4.78461 ( 1095) link_NAG-ASN : bond 0.00165 ( 12) link_NAG-ASN : angle 1.35560 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.437 Fit side-chains REVERT: A 166 LYS cc_start: 0.7667 (mttt) cc_final: 0.7319 (tttt) REVERT: A 180 ASP cc_start: 0.8612 (m-30) cc_final: 0.8348 (m-30) REVERT: A 181 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7754 (mttt) REVERT: A 232 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 271 MET cc_start: 0.7865 (mmm) cc_final: 0.7292 (mtm) REVERT: A 296 ASP cc_start: 0.8406 (m-30) cc_final: 0.8132 (m-30) REVERT: B 180 ASP cc_start: 0.8594 (m-30) cc_final: 0.8354 (m-30) REVERT: B 271 MET cc_start: 0.7739 (mmm) cc_final: 0.7337 (mtm) REVERT: B 315 GLN cc_start: 0.7379 (mt0) cc_final: 0.7093 (mp10) REVERT: B 511 GLN cc_start: 0.8254 (tp40) cc_final: 0.8012 (mm-40) REVERT: B 520 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: C 166 LYS cc_start: 0.7622 (mmmm) cc_final: 0.6912 (tttp) REVERT: C 315 GLN cc_start: 0.7365 (mt0) cc_final: 0.7028 (mp10) REVERT: C 520 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7271 (mp0) outliers start: 22 outliers final: 8 residues processed: 129 average time/residue: 0.6371 time to fit residues: 87.7156 Evaluate side-chains 114 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.136438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116602 restraints weight = 11079.496| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.97 r_work: 0.3191 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9852 Z= 0.100 Angle : 0.433 5.312 13428 Z= 0.235 Chirality : 0.046 0.157 1668 Planarity : 0.004 0.043 1674 Dihedral : 4.094 28.808 1605 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.99 % Favored : 97.77 % Rotamer: Outliers : 1.39 % Allowed : 13.13 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.24), residues: 1254 helix: 1.03 (0.28), residues: 393 sheet: 0.67 (0.31), residues: 258 loop : 0.18 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 239 TYR 0.015 0.001 TYR A 468 PHE 0.011 0.001 PHE C 371 TRP 0.002 0.001 TRP B 404 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9825) covalent geometry : angle 0.42318 (13362) SS BOND : bond 0.00177 ( 15) SS BOND : angle 1.06956 ( 30) hydrogen bonds : bond 0.03569 ( 413) hydrogen bonds : angle 4.54909 ( 1095) link_NAG-ASN : bond 0.00183 ( 12) link_NAG-ASN : angle 1.53933 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.333 Fit side-chains REVERT: A 166 LYS cc_start: 0.7683 (mttt) cc_final: 0.7339 (tttt) REVERT: A 180 ASP cc_start: 0.8616 (m-30) cc_final: 0.8384 (m-30) REVERT: A 232 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 271 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7187 (mtm) REVERT: A 296 ASP cc_start: 0.8427 (m-30) cc_final: 0.8162 (m-30) REVERT: A 446 TYR cc_start: 0.7524 (m-80) cc_final: 0.6926 (t80) REVERT: B 150 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8764 (m) REVERT: B 180 ASP cc_start: 0.8607 (m-30) cc_final: 0.8343 (m-30) REVERT: B 271 MET cc_start: 0.7673 (mmm) cc_final: 0.7355 (mtm) REVERT: B 315 GLN cc_start: 0.7394 (mt0) cc_final: 0.7111 (mp10) REVERT: B 495 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7976 (mttp) REVERT: C 166 LYS cc_start: 0.7682 (mmmm) cc_final: 0.7025 (tttp) REVERT: C 306 ILE cc_start: 0.8194 (pt) cc_final: 0.7902 (pt) REVERT: C 315 GLN cc_start: 0.7381 (mt0) cc_final: 0.7009 (mp10) REVERT: C 334 ASN cc_start: 0.8809 (t0) cc_final: 0.8415 (t0) outliers start: 14 outliers final: 6 residues processed: 123 average time/residue: 0.6459 time to fit residues: 84.8530 Evaluate side-chains 115 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 433 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 0.0010 chunk 0 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 272 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112128 restraints weight = 11157.417| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.95 r_work: 0.3130 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9852 Z= 0.189 Angle : 0.529 5.821 13428 Z= 0.280 Chirality : 0.050 0.155 1668 Planarity : 0.004 0.043 1674 Dihedral : 4.461 28.620 1605 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.15 % Favored : 97.61 % Rotamer: Outliers : 1.89 % Allowed : 13.43 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1254 helix: 0.72 (0.27), residues: 393 sheet: 0.48 (0.31), residues: 258 loop : 0.01 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 239 TYR 0.021 0.001 TYR B 468 PHE 0.019 0.002 PHE C 371 TRP 0.006 0.002 TRP B 404 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9825) covalent geometry : angle 0.52032 (13362) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.34106 ( 30) hydrogen bonds : bond 0.04864 ( 413) hydrogen bonds : angle 4.81087 ( 1095) link_NAG-ASN : bond 0.00122 ( 12) link_NAG-ASN : angle 1.56746 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.409 Fit side-chains REVERT: A 166 LYS cc_start: 0.7829 (mttt) cc_final: 0.7428 (tttt) REVERT: A 180 ASP cc_start: 0.8666 (m-30) cc_final: 0.8442 (m-30) REVERT: A 232 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 271 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7238 (mtm) REVERT: B 180 ASP cc_start: 0.8680 (m-30) cc_final: 0.8468 (m-30) REVERT: B 315 GLN cc_start: 0.7486 (mt0) cc_final: 0.7207 (mp10) REVERT: B 495 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7924 (mttp) REVERT: B 511 GLN cc_start: 0.8351 (tp40) cc_final: 0.8090 (mm-40) REVERT: C 166 LYS cc_start: 0.7973 (mmmm) cc_final: 0.7313 (tttp) REVERT: C 306 ILE cc_start: 0.8340 (pt) cc_final: 0.8100 (pt) REVERT: C 315 GLN cc_start: 0.7299 (mt0) cc_final: 0.7025 (mp10) REVERT: C 520 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7366 (mp0) outliers start: 19 outliers final: 9 residues processed: 119 average time/residue: 0.6303 time to fit residues: 80.2851 Evaluate side-chains 114 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 272 GLN B 347 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116015 restraints weight = 10947.928| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.93 r_work: 0.3180 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9852 Z= 0.098 Angle : 0.427 5.242 13428 Z= 0.233 Chirality : 0.046 0.141 1668 Planarity : 0.004 0.042 1674 Dihedral : 4.051 27.174 1605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.52 % Favored : 98.25 % Rotamer: Outliers : 1.29 % Allowed : 13.83 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.24), residues: 1254 helix: 1.11 (0.28), residues: 393 sheet: 0.52 (0.32), residues: 258 loop : 0.01 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 239 TYR 0.017 0.001 TYR B 468 PHE 0.011 0.001 PHE C 331 TRP 0.001 0.000 TRP B 404 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9825) covalent geometry : angle 0.41904 (13362) SS BOND : bond 0.00327 ( 15) SS BOND : angle 1.04040 ( 30) hydrogen bonds : bond 0.03502 ( 413) hydrogen bonds : angle 4.47236 ( 1095) link_NAG-ASN : bond 0.00187 ( 12) link_NAG-ASN : angle 1.36958 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.481 Fit side-chains REVERT: A 166 LYS cc_start: 0.7858 (mttt) cc_final: 0.7493 (tttt) REVERT: A 232 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 271 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7265 (mtm) REVERT: A 296 ASP cc_start: 0.8345 (m-30) cc_final: 0.8135 (m-30) REVERT: B 180 ASP cc_start: 0.8645 (m-30) cc_final: 0.8400 (m-30) REVERT: B 271 MET cc_start: 0.7795 (mmm) cc_final: 0.7480 (mtm) REVERT: B 315 GLN cc_start: 0.7398 (mt0) cc_final: 0.7191 (mp10) REVERT: C 166 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7411 (tttp) REVERT: C 306 ILE cc_start: 0.8305 (pt) cc_final: 0.8044 (pt) REVERT: C 315 GLN cc_start: 0.7336 (mt0) cc_final: 0.7128 (mp10) REVERT: C 520 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7286 (mp0) outliers start: 13 outliers final: 7 residues processed: 118 average time/residue: 0.6143 time to fit residues: 77.7181 Evaluate side-chains 112 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 0.0020 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115876 restraints weight = 11027.689| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.95 r_work: 0.3183 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9852 Z= 0.102 Angle : 0.433 4.842 13428 Z= 0.234 Chirality : 0.046 0.140 1668 Planarity : 0.004 0.042 1674 Dihedral : 3.961 25.287 1605 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.91 % Favored : 97.85 % Rotamer: Outliers : 1.00 % Allowed : 14.53 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.24), residues: 1254 helix: 1.22 (0.28), residues: 393 sheet: 0.55 (0.32), residues: 258 loop : -0.02 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 239 TYR 0.017 0.001 TYR B 468 PHE 0.012 0.001 PHE C 371 TRP 0.002 0.001 TRP C 404 HIS 0.003 0.000 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9825) covalent geometry : angle 0.42521 (13362) SS BOND : bond 0.00204 ( 15) SS BOND : angle 0.98586 ( 30) hydrogen bonds : bond 0.03557 ( 413) hydrogen bonds : angle 4.41243 ( 1095) link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.38841 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.372 Fit side-chains REVERT: A 166 LYS cc_start: 0.8025 (mttt) cc_final: 0.7702 (tttt) REVERT: A 232 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 271 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7234 (mtm) REVERT: A 296 ASP cc_start: 0.8313 (m-30) cc_final: 0.8082 (m-30) REVERT: B 180 ASP cc_start: 0.8644 (m-30) cc_final: 0.8369 (m-30) REVERT: B 271 MET cc_start: 0.7740 (mmm) cc_final: 0.7465 (mtm) REVERT: B 315 GLN cc_start: 0.7364 (mt0) cc_final: 0.7140 (mp10) REVERT: B 520 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: C 166 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7386 (tttp) REVERT: C 306 ILE cc_start: 0.8265 (pt) cc_final: 0.8024 (pt) REVERT: C 315 GLN cc_start: 0.7291 (mt0) cc_final: 0.7043 (mp10) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.6098 time to fit residues: 77.1157 Evaluate side-chains 116 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 511 GLN C 272 GLN C 511 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101980 restraints weight = 11179.332| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.74 r_work: 0.2929 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9852 Z= 0.132 Angle : 0.465 5.497 13428 Z= 0.248 Chirality : 0.047 0.142 1668 Planarity : 0.004 0.041 1674 Dihedral : 4.070 24.048 1605 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.09 % Rotamer: Outliers : 1.39 % Allowed : 14.23 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1254 helix: 1.09 (0.28), residues: 393 sheet: 0.52 (0.32), residues: 258 loop : -0.09 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 239 TYR 0.021 0.001 TYR B 468 PHE 0.015 0.002 PHE C 371 TRP 0.005 0.001 TRP A 404 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9825) covalent geometry : angle 0.45797 (13362) SS BOND : bond 0.00243 ( 15) SS BOND : angle 1.07032 ( 30) hydrogen bonds : bond 0.04017 ( 413) hydrogen bonds : angle 4.50924 ( 1095) link_NAG-ASN : bond 0.00123 ( 12) link_NAG-ASN : angle 1.41575 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.419 Fit side-chains REVERT: A 166 LYS cc_start: 0.7988 (mttt) cc_final: 0.7678 (tttt) REVERT: A 232 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 271 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7278 (mtm) REVERT: A 296 ASP cc_start: 0.8401 (m-30) cc_final: 0.8175 (m-30) REVERT: B 180 ASP cc_start: 0.8610 (m-30) cc_final: 0.8365 (m-30) REVERT: B 271 MET cc_start: 0.7783 (mmm) cc_final: 0.7512 (mtm) REVERT: B 520 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 166 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7479 (tttp) REVERT: C 306 ILE cc_start: 0.8322 (pt) cc_final: 0.8080 (pt) REVERT: C 506 MET cc_start: 0.8790 (ttm) cc_final: 0.8588 (mtp) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.5936 time to fit residues: 75.0860 Evaluate side-chains 112 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 0.0040 chunk 106 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 398 ASN B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116994 restraints weight = 10953.114| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.93 r_work: 0.3199 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9852 Z= 0.088 Angle : 0.417 5.885 13428 Z= 0.225 Chirality : 0.046 0.137 1668 Planarity : 0.003 0.042 1674 Dihedral : 3.808 22.170 1605 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Rotamer: Outliers : 1.09 % Allowed : 14.63 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.24), residues: 1254 helix: 1.34 (0.28), residues: 393 sheet: 0.60 (0.32), residues: 258 loop : -0.08 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.018 0.001 TYR B 468 PHE 0.010 0.001 PHE C 331 TRP 0.001 0.001 TRP A 404 HIS 0.002 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 9825) covalent geometry : angle 0.40971 (13362) SS BOND : bond 0.00161 ( 15) SS BOND : angle 0.92280 ( 30) hydrogen bonds : bond 0.03262 ( 413) hydrogen bonds : angle 4.32088 ( 1095) link_NAG-ASN : bond 0.00170 ( 12) link_NAG-ASN : angle 1.32712 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.346 Fit side-chains REVERT: A 166 LYS cc_start: 0.7982 (mttt) cc_final: 0.7670 (tttt) REVERT: A 232 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 271 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7274 (mtm) REVERT: A 296 ASP cc_start: 0.8292 (m-30) cc_final: 0.8052 (m-30) REVERT: A 319 THR cc_start: 0.8544 (p) cc_final: 0.8294 (t) REVERT: B 180 ASP cc_start: 0.8553 (m-30) cc_final: 0.8268 (m-30) REVERT: B 520 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: C 166 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7441 (tttp) REVERT: C 171 SER cc_start: 0.7671 (p) cc_final: 0.7392 (m) REVERT: C 306 ILE cc_start: 0.8217 (pt) cc_final: 0.7984 (pt) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.5430 time to fit residues: 70.2453 Evaluate side-chains 116 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101794 restraints weight = 11339.942| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.76 r_work: 0.2914 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9852 Z= 0.148 Angle : 0.497 7.696 13428 Z= 0.261 Chirality : 0.048 0.142 1668 Planarity : 0.004 0.040 1674 Dihedral : 4.079 21.432 1605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.29 % Allowed : 14.93 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.24), residues: 1254 helix: 1.10 (0.28), residues: 393 sheet: 0.57 (0.32), residues: 258 loop : -0.14 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 239 TYR 0.019 0.001 TYR B 468 PHE 0.016 0.002 PHE C 371 TRP 0.006 0.002 TRP A 404 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9825) covalent geometry : angle 0.48409 (13362) SS BOND : bond 0.00237 ( 15) SS BOND : angle 1.96106 ( 30) hydrogen bonds : bond 0.04138 ( 413) hydrogen bonds : angle 4.53196 ( 1095) link_NAG-ASN : bond 0.00097 ( 12) link_NAG-ASN : angle 1.40443 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.74 seconds wall clock time: 52 minutes 59.77 seconds (3179.77 seconds total)