Starting phenix.real_space_refine on Tue May 13 05:01:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvb_41636/05_2025/8tvb_41636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvb_41636/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tvb_41636/05_2025/8tvb_41636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvb_41636/05_2025/8tvb_41636.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvb_41636/05_2025/8tvb_41636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvb_41636/05_2025/8tvb_41636.cif" } resolution = 2.9 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B Time building chain proxies: 5.90, per 1000 atoms: 0.61 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 C 167 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS C 427 " - pdb=" SG CYS C 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 436 " distance=2.03 Simple disulfide: pdb=" SG CYS C 451 " - pdb=" SG CYS C 459 " distance=2.02 Simple disulfide: pdb=" SG CYS B 451 " - pdb=" SG CYS B 459 " distance=2.02 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 488 " distance=2.19 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 488 " distance=2.19 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 513 " distance=2.05 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.32 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: 2.90 Time building geometry restraints manager: 2.74 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.030 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.820 Find NCS groups from input model: 0.170 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- 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 (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 (0.22), 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 TRP 0.008 0.004 TRP C 404 HIS 0.005 0.002 HIS C 438 PHE 0.017 0.003 PHE C 371 TYR 0.032 0.003 TYR C 142 ARG 0.005 0.001 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.04691 ( 12) link_NAG-ASN : angle 8.33177 ( 36) hydrogen bonds : bond 0.18619 ( 413) hydrogen bonds : angle 7.65405 ( 1095) SS BOND : bond 0.07361 ( 15) SS BOND : angle 3.76994 ( 30) covalent geometry : bond 0.00960 ( 9825) covalent geometry : angle 1.21478 (13362) *********************** 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 : 0.975 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: 1.1848 time to fit residues: 274.7355 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 : 0.996 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.140565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120743 restraints weight = 10921.252| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.95 r_work: 0.3267 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9852 Z= 0.135 Angle : 0.523 6.601 13428 Z= 0.289 Chirality : 0.048 0.193 1668 Planarity : 0.004 0.030 1674 Dihedral : 4.635 29.800 1607 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.79 % Allowed : 8.16 % Favored : 90.05 % 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: 0.60 (0.23), residues: 1254 helix: -0.02 (0.25), residues: 393 sheet: 1.12 (0.29), residues: 294 loop : 0.51 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 404 HIS 0.006 0.001 HIS C 438 PHE 0.016 0.002 PHE B 371 TYR 0.017 0.001 TYR A 468 ARG 0.005 0.000 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 12) link_NAG-ASN : angle 1.94327 ( 36) hydrogen bonds : bond 0.04524 ( 413) hydrogen bonds : angle 5.20132 ( 1095) SS BOND : bond 0.00479 ( 15) SS BOND : angle 1.32010 ( 30) covalent geometry : bond 0.00301 ( 9825) covalent geometry : angle 0.51021 (13362) *********************** 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 169 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.001 Fit side-chains REVERT: A 180 ASP cc_start: 0.8341 (m-30) cc_final: 0.8098 (m-30) REVERT: A 191 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 271 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7004 (mtm) REVERT: A 296 ASP cc_start: 0.8151 (m-30) cc_final: 0.7941 (m-30) REVERT: A 305 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 125 HIS cc_start: 0.7627 (t-170) cc_final: 0.6715 (m170) REVERT: B 315 GLN cc_start: 0.7206 (mt0) cc_final: 0.6974 (mp10) REVERT: B 520 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: C 166 LYS cc_start: 0.7024 (mmmm) cc_final: 0.6163 (tttp) REVERT: C 511 GLN cc_start: 0.7558 (mt0) cc_final: 0.6977 (mm-40) outliers start: 18 outliers final: 2 residues processed: 159 average time/residue: 1.1517 time to fit residues: 196.3749 Evaluate side-chains 120 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 79 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 334 ASN B 511 GLN C 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119056 restraints weight = 10993.919| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.99 r_work: 0.3230 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3272 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= 0.110 Angle : 0.453 4.604 13428 Z= 0.250 Chirality : 0.046 0.156 1668 Planarity : 0.004 0.038 1674 Dihedral : 4.089 24.976 1605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.09 % Rotamer: Outliers : 1.59 % Allowed : 10.55 % Favored : 87.86 % 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: 0.95 (0.24), residues: 1254 helix: 0.78 (0.27), residues: 393 sheet: 1.03 (0.31), residues: 258 loop : 0.51 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 404 HIS 0.004 0.001 HIS C 438 PHE 0.013 0.002 PHE A 310 TYR 0.022 0.001 TYR A 468 ARG 0.008 0.000 ARG C 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 12) link_NAG-ASN : angle 1.43419 ( 36) hydrogen bonds : bond 0.03871 ( 413) hydrogen bonds : angle 4.77896 ( 1095) SS BOND : bond 0.00161 ( 15) SS BOND : angle 1.05572 ( 30) covalent geometry : bond 0.00249 ( 9825) covalent geometry : angle 0.44490 (13362) *********************** 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 154 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.098 Fit side-chains REVERT: A 180 ASP cc_start: 0.8490 (m-30) cc_final: 0.8264 (m-30) REVERT: A 232 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 258 GLN cc_start: 0.8585 (tp40) cc_final: 0.8366 (mm110) REVERT: A 271 MET cc_start: 0.7826 (mmm) cc_final: 0.7182 (mtm) REVERT: A 296 ASP cc_start: 0.8278 (m-30) cc_final: 0.7956 (m-30) REVERT: A 305 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 180 ASP cc_start: 0.8521 (m-30) cc_final: 0.8277 (m-30) REVERT: B 198 LYS cc_start: 0.8116 (pttt) cc_final: 0.7902 (pttp) REVERT: B 315 GLN cc_start: 0.7249 (mt0) cc_final: 0.7005 (mp10) REVERT: C 166 LYS cc_start: 0.7184 (mmmm) cc_final: 0.6482 (tttp) REVERT: C 305 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: C 315 GLN cc_start: 0.7154 (mt0) cc_final: 0.6926 (mp10) REVERT: C 334 ASN cc_start: 0.8604 (t0) cc_final: 0.8250 (t0) REVERT: C 509 ASP cc_start: 0.8402 (p0) cc_final: 0.8110 (p0) REVERT: C 511 GLN cc_start: 0.7657 (mt0) cc_final: 0.7202 (mm-40) REVERT: C 520 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: C 527 LYS cc_start: 0.8409 (tttt) cc_final: 0.8207 (ttmm) outliers start: 16 outliers final: 5 residues processed: 147 average time/residue: 1.1331 time to fit residues: 179.2936 Evaluate side-chains 122 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116546 restraints weight = 10941.700| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.97 r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9852 Z= 0.122 Angle : 0.470 5.670 13428 Z= 0.254 Chirality : 0.047 0.147 1668 Planarity : 0.004 0.037 1674 Dihedral : 4.056 19.066 1605 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.75 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 10.75 % Favored : 87.36 % 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: 0.82 (0.24), residues: 1254 helix: 0.92 (0.27), residues: 393 sheet: 0.81 (0.31), residues: 258 loop : 0.32 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 404 HIS 0.004 0.001 HIS C 438 PHE 0.015 0.002 PHE C 371 TYR 0.017 0.001 TYR A 468 ARG 0.004 0.000 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 12) link_NAG-ASN : angle 1.41557 ( 36) hydrogen bonds : bond 0.03944 ( 413) hydrogen bonds : angle 4.62680 ( 1095) SS BOND : bond 0.00248 ( 15) SS BOND : angle 1.20860 ( 30) covalent geometry : bond 0.00296 ( 9825) covalent geometry : angle 0.46186 (13362) *********************** 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 144 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.023 Fit side-chains REVERT: A 180 ASP cc_start: 0.8587 (m-30) cc_final: 0.8317 (m-30) REVERT: A 232 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 243 LEU cc_start: 0.7786 (mt) cc_final: 0.7461 (mt) REVERT: A 271 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7255 (mtm) REVERT: A 296 ASP cc_start: 0.8454 (m-30) cc_final: 0.8089 (m-30) REVERT: B 180 ASP cc_start: 0.8642 (m-30) cc_final: 0.8411 (m-30) REVERT: B 198 LYS cc_start: 0.8215 (pttt) cc_final: 0.7987 (pttp) REVERT: B 251 ASN cc_start: 0.8375 (p0) cc_final: 0.8167 (p0) REVERT: B 315 GLN cc_start: 0.7303 (mt0) cc_final: 0.7034 (mp10) REVERT: B 495 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7884 (mttp) REVERT: B 520 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: C 166 LYS cc_start: 0.7547 (mmmm) cc_final: 0.6817 (tttp) REVERT: C 305 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: C 315 GLN cc_start: 0.7213 (mt0) cc_final: 0.6935 (mp10) REVERT: C 334 ASN cc_start: 0.8773 (t0) cc_final: 0.8364 (t0) REVERT: C 509 ASP cc_start: 0.8631 (p0) cc_final: 0.8321 (p0) REVERT: C 511 GLN cc_start: 0.7708 (mt0) cc_final: 0.7232 (mm-40) outliers start: 19 outliers final: 6 residues processed: 134 average time/residue: 1.1499 time to fit residues: 165.4545 Evaluate side-chains 117 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 431 LYS 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 B residue 538 HIS Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 89 optimal weight: 0.0070 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113167 restraints weight = 11078.824| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.95 r_work: 0.3144 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9852 Z= 0.174 Angle : 0.532 5.944 13428 Z= 0.282 Chirality : 0.049 0.153 1668 Planarity : 0.004 0.038 1674 Dihedral : 4.362 27.030 1605 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.07 % Favored : 97.69 % Rotamer: Outliers : 2.49 % Allowed : 11.34 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.23), residues: 1254 helix: 0.71 (0.27), residues: 393 sheet: 0.56 (0.31), residues: 261 loop : -0.02 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 404 HIS 0.004 0.001 HIS C 369 PHE 0.018 0.002 PHE C 371 TYR 0.018 0.002 TYR A 468 ARG 0.005 0.001 ARG C 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 12) link_NAG-ASN : angle 1.59761 ( 36) hydrogen bonds : bond 0.04839 ( 413) hydrogen bonds : angle 4.80664 ( 1095) SS BOND : bond 0.00267 ( 15) SS BOND : angle 1.38849 ( 30) covalent geometry : bond 0.00435 ( 9825) covalent geometry : angle 0.52294 (13362) *********************** 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 140 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.059 Fit side-chains REVERT: A 180 ASP cc_start: 0.8687 (m-30) cc_final: 0.8471 (m-30) REVERT: A 232 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 271 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: A 296 ASP cc_start: 0.8446 (m-30) cc_final: 0.8150 (m-30) REVERT: B 180 ASP cc_start: 0.8689 (m-30) cc_final: 0.8462 (m-30) REVERT: B 251 ASN cc_start: 0.8565 (p0) cc_final: 0.8335 (p0) REVERT: B 315 GLN cc_start: 0.7429 (mt0) cc_final: 0.7129 (mp10) REVERT: B 495 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7904 (mttp) REVERT: B 511 GLN cc_start: 0.8305 (tp40) cc_final: 0.8062 (mm-40) REVERT: B 520 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: C 166 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7247 (tttp) REVERT: C 306 ILE cc_start: 0.8255 (pt) cc_final: 0.7984 (pt) REVERT: C 315 GLN cc_start: 0.7410 (mt0) cc_final: 0.7042 (mp10) REVERT: C 511 GLN cc_start: 0.7948 (mt0) cc_final: 0.7689 (mm-40) outliers start: 25 outliers final: 9 residues processed: 126 average time/residue: 1.1305 time to fit residues: 153.9216 Evaluate side-chains 115 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 150 SER 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 94 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.131891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112292 restraints weight = 11079.833| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.94 r_work: 0.3131 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9852 Z= 0.186 Angle : 0.533 5.857 13428 Z= 0.281 Chirality : 0.050 0.157 1668 Planarity : 0.004 0.038 1674 Dihedral : 4.485 25.858 1605 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.91 % Favored : 97.85 % Rotamer: Outliers : 1.79 % Allowed : 12.44 % Favored : 85.77 % 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: 0.18 (0.23), residues: 1254 helix: 0.61 (0.27), residues: 393 sheet: 0.38 (0.31), residues: 261 loop : -0.22 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 404 HIS 0.003 0.001 HIS C 438 PHE 0.018 0.002 PHE C 371 TYR 0.023 0.002 TYR C 468 ARG 0.004 0.000 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 12) link_NAG-ASN : angle 1.60964 ( 36) hydrogen bonds : bond 0.04826 ( 413) hydrogen bonds : angle 4.83869 ( 1095) SS BOND : bond 0.00277 ( 15) SS BOND : angle 1.37599 ( 30) covalent geometry : bond 0.00470 ( 9825) covalent geometry : angle 0.52399 (13362) *********************** 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: 18 poor density : 109 time to evaluate : 1.094 Fit side-chains REVERT: A 180 ASP cc_start: 0.8703 (m-30) cc_final: 0.8471 (m-30) REVERT: A 232 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 271 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7242 (mtm) REVERT: A 398 ASN cc_start: 0.8551 (t0) cc_final: 0.8345 (t0) REVERT: B 180 ASP cc_start: 0.8670 (m-30) cc_final: 0.8469 (m-30) REVERT: B 251 ASN cc_start: 0.8668 (p0) cc_final: 0.8419 (p0) REVERT: B 315 GLN cc_start: 0.7452 (mt0) cc_final: 0.7187 (mp10) REVERT: B 520 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: C 166 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7335 (tttp) REVERT: C 306 ILE cc_start: 0.8339 (pt) cc_final: 0.8067 (pt) REVERT: C 315 GLN cc_start: 0.7302 (mt0) cc_final: 0.7019 (mp10) REVERT: C 511 GLN cc_start: 0.7897 (mt0) cc_final: 0.7667 (mm-40) REVERT: C 520 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7374 (mp0) outliers start: 18 outliers final: 10 residues processed: 119 average time/residue: 1.1484 time to fit residues: 147.3796 Evaluate side-chains 116 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 520 GLU Chi-restraints excluded: chain B residue 524 SER 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 30 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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** B 347 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115723 restraints weight = 11111.375| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.95 r_work: 0.3176 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9852 Z= 0.102 Angle : 0.439 4.889 13428 Z= 0.237 Chirality : 0.046 0.141 1668 Planarity : 0.004 0.038 1674 Dihedral : 4.104 25.503 1605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.09 % Rotamer: Outliers : 1.09 % Allowed : 13.53 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.24), residues: 1254 helix: 1.06 (0.28), residues: 393 sheet: 0.48 (0.32), residues: 258 loop : -0.14 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 404 HIS 0.003 0.000 HIS C 438 PHE 0.011 0.001 PHE A 331 TYR 0.022 0.001 TYR A 468 ARG 0.005 0.000 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 12) link_NAG-ASN : angle 1.40506 ( 36) hydrogen bonds : bond 0.03609 ( 413) hydrogen bonds : angle 4.52755 ( 1095) SS BOND : bond 0.00420 ( 15) SS BOND : angle 1.04200 ( 30) covalent geometry : bond 0.00236 ( 9825) covalent geometry : angle 0.43085 (13362) *********************** 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: 11 poor density : 114 time to evaluate : 1.028 Fit side-chains REVERT: A 232 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 271 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7302 (mtm) REVERT: A 296 ASP cc_start: 0.8373 (m-30) cc_final: 0.8144 (m-30) REVERT: B 180 ASP cc_start: 0.8657 (m-30) cc_final: 0.8411 (m-30) REVERT: B 251 ASN cc_start: 0.8679 (p0) cc_final: 0.8425 (p0) REVERT: B 315 GLN cc_start: 0.7377 (mt0) cc_final: 0.7175 (mp10) REVERT: C 166 LYS cc_start: 0.8055 (mmmm) cc_final: 0.7413 (tttp) REVERT: C 306 ILE cc_start: 0.8317 (pt) cc_final: 0.8048 (pt) REVERT: C 315 GLN cc_start: 0.7295 (mt0) cc_final: 0.7056 (mp10) REVERT: C 334 ASN cc_start: 0.8867 (t0) cc_final: 0.8489 (t0) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 1.0923 time to fit residues: 141.7112 Evaluate side-chains 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET 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 C residue 433 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 532 GLN B 272 GLN C 272 GLN C 398 ASN C 532 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115556 restraints weight = 11144.415| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.94 r_work: 0.3178 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9852 Z= 0.111 Angle : 0.449 5.241 13428 Z= 0.240 Chirality : 0.047 0.140 1668 Planarity : 0.004 0.038 1674 Dihedral : 4.054 24.737 1605 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.75 % Favored : 98.01 % Rotamer: Outliers : 1.59 % Allowed : 13.53 % 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 (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: 0.53 (0.24), residues: 1254 helix: 1.18 (0.28), residues: 393 sheet: 0.50 (0.32), residues: 258 loop : -0.17 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 404 HIS 0.003 0.000 HIS C 438 PHE 0.012 0.002 PHE C 371 TYR 0.021 0.001 TYR B 468 ARG 0.006 0.000 ARG C 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 12) link_NAG-ASN : angle 1.42151 ( 36) hydrogen bonds : bond 0.03735 ( 413) hydrogen bonds : angle 4.49034 ( 1095) SS BOND : bond 0.00191 ( 15) SS BOND : angle 1.01669 ( 30) covalent geometry : bond 0.00264 ( 9825) covalent geometry : angle 0.44165 (13362) *********************** 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: 16 poor density : 106 time to evaluate : 1.129 Fit side-chains REVERT: A 232 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 271 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7242 (mtm) REVERT: A 296 ASP cc_start: 0.8336 (m-30) cc_final: 0.8108 (m-30) REVERT: B 180 ASP cc_start: 0.8651 (m-30) cc_final: 0.8404 (m-30) REVERT: B 315 GLN cc_start: 0.7423 (mt0) cc_final: 0.7177 (mp10) REVERT: C 166 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7378 (tttp) REVERT: C 306 ILE cc_start: 0.8289 (pt) cc_final: 0.8031 (pt) REVERT: C 315 GLN cc_start: 0.7299 (mt0) cc_final: 0.7053 (mp10) outliers start: 16 outliers final: 8 residues processed: 116 average time/residue: 1.1273 time to fit residues: 141.0486 Evaluate side-chains 109 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET 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 537 MET 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 111 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116090 restraints weight = 11014.413| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.94 r_work: 0.3187 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9852 Z= 0.106 Angle : 0.463 7.528 13428 Z= 0.245 Chirality : 0.047 0.145 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.034 23.733 1605 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.75 % Favored : 98.01 % Rotamer: Outliers : 1.39 % Allowed : 13.73 % 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 (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 (0.24), residues: 1254 helix: 1.25 (0.28), residues: 393 sheet: 0.47 (0.32), residues: 261 loop : -0.24 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 404 HIS 0.003 0.000 HIS C 438 PHE 0.011 0.001 PHE C 371 TYR 0.022 0.001 TYR B 468 ARG 0.006 0.000 ARG C 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 12) link_NAG-ASN : angle 1.38830 ( 36) hydrogen bonds : bond 0.03586 ( 413) hydrogen bonds : angle 4.42686 ( 1095) SS BOND : bond 0.00172 ( 15) SS BOND : angle 1.91669 ( 30) covalent geometry : bond 0.00250 ( 9825) covalent geometry : angle 0.44898 (13362) *********************** 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 120 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.146 Fit side-chains REVERT: A 232 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 271 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7233 (mtm) REVERT: A 296 ASP cc_start: 0.8323 (m-30) cc_final: 0.8094 (m-30) REVERT: A 537 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6200 (pp-130) REVERT: B 180 ASP cc_start: 0.8654 (m-30) cc_final: 0.8384 (m-30) REVERT: B 315 GLN cc_start: 0.7371 (mt0) cc_final: 0.7138 (mp10) REVERT: B 450 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7991 (mt-10) REVERT: C 166 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7400 (tttp) REVERT: C 306 ILE cc_start: 0.8263 (pt) cc_final: 0.8002 (pt) REVERT: C 315 GLN cc_start: 0.7296 (mt0) cc_final: 0.7053 (mp10) REVERT: C 506 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8616 (mtp) outliers start: 14 outliers final: 9 residues processed: 113 average time/residue: 1.1812 time to fit residues: 143.8533 Evaluate side-chains 114 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 537 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 524 SER Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 506 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** B 511 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114241 restraints weight = 11213.802| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.96 r_work: 0.3159 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9852 Z= 0.138 Angle : 0.488 6.986 13428 Z= 0.257 Chirality : 0.048 0.141 1668 Planarity : 0.004 0.040 1674 Dihedral : 4.191 23.075 1605 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.83 % Favored : 98.01 % Rotamer: Outliers : 1.59 % Allowed : 14.03 % 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 (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: 0.39 (0.24), residues: 1254 helix: 1.08 (0.28), residues: 393 sheet: 0.43 (0.31), residues: 261 loop : -0.30 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 404 HIS 0.003 0.001 HIS C 438 PHE 0.015 0.002 PHE C 371 TYR 0.022 0.001 TYR B 468 ARG 0.005 0.000 ARG C 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 12) link_NAG-ASN : angle 1.45372 ( 36) hydrogen bonds : bond 0.04091 ( 413) hydrogen bonds : angle 4.54585 ( 1095) SS BOND : bond 0.00313 ( 15) SS BOND : angle 1.38049 ( 30) covalent geometry : bond 0.00341 ( 9825) covalent geometry : angle 0.47905 (13362) ********************** 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 120 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.157 Fit side-chains REVERT: A 232 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 271 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7257 (mtm) REVERT: A 296 ASP cc_start: 0.8338 (m-30) cc_final: 0.8077 (m-30) REVERT: A 537 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6207 (pp-130) REVERT: B 180 ASP cc_start: 0.8602 (m-30) cc_final: 0.8362 (m-30) REVERT: B 315 GLN cc_start: 0.7441 (mt0) cc_final: 0.7201 (mp10) REVERT: C 166 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7421 (tttp) REVERT: C 306 ILE cc_start: 0.8318 (pt) cc_final: 0.8065 (pt) REVERT: C 315 GLN cc_start: 0.7306 (mt0) cc_final: 0.7047 (mp10) outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 1.1194 time to fit residues: 135.3062 Evaluate side-chains 111 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 537 MET Chi-restraints excluded: chain B residue 269 THR 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 524 SER Chi-restraints excluded: chain B residue 537 MET 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 8 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** 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 = 0.3547 r_free = 0.3547 target = 0.135021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115479 restraints weight = 11116.107| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.94 r_work: 0.3177 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9852 Z= 0.113 Angle : 0.461 7.457 13428 Z= 0.244 Chirality : 0.047 0.139 1668 Planarity : 0.004 0.040 1674 Dihedral : 4.072 22.222 1605 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.49 % Allowed : 14.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1254 helix: 1.19 (0.28), residues: 393 sheet: 0.45 (0.31), residues: 261 loop : -0.33 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 404 HIS 0.003 0.000 HIS C 438 PHE 0.012 0.002 PHE C 371 TYR 0.020 0.001 TYR B 468 ARG 0.006 0.000 ARG C 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 12) link_NAG-ASN : angle 1.39493 ( 36) hydrogen bonds : bond 0.03740 ( 413) hydrogen bonds : angle 4.47438 ( 1095) SS BOND : bond 0.00228 ( 15) SS BOND : angle 1.13593 ( 30) covalent geometry : bond 0.00272 ( 9825) covalent geometry : angle 0.45304 (13362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5689.47 seconds wall clock time: 98 minutes 43.92 seconds (5923.92 seconds total)