Starting phenix.real_space_refine on Tue Nov 18 14:03:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfx_23308/11_2025/7lfx_23308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfx_23308/11_2025/7lfx_23308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lfx_23308/11_2025/7lfx_23308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfx_23308/11_2025/7lfx_23308.map" model { file = "/net/cci-nas-00/data/ceres_data/7lfx_23308/11_2025/7lfx_23308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfx_23308/11_2025/7lfx_23308_neut.cif" } resolution = 3.1 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 9684 2.51 5 N 2396 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 3.85, per 1000 atoms: 0.26 Number of scatterers: 14846 At special positions: 0 Unit cell: (94.185, 94.185, 115.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 76 16.00 P 4 15.00 O 2684 8.00 N 2396 7.00 C 9684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 662.6 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 66.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.259A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.536A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 591 through 605 removed outlier: 3.642A pdb=" N LYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.261A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.840A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.253A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.536A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.586A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.642A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.253A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.537A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.840A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 591 through 605 removed outlier: 3.642A pdb=" N LYS D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.495A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 7.057A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.493A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.495A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 7.059A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2652 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: 2.68 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4304 1.34 - 1.45: 2412 1.45 - 1.57: 8344 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15196 Sorted by residual: bond pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O1A PCG C 701 " pdb=" PA PCG C 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1' PCG D 701 " pdb=" O4' PCG D 701 " ideal model delta sigma weight residual 1.409 1.477 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 20207 1.85 - 3.71: 282 3.71 - 5.56: 71 5.56 - 7.42: 24 7.42 - 9.27: 24 Bond angle restraints: 20608 Sorted by residual: angle pdb=" N ARG C 291 " pdb=" CA ARG C 291 " pdb=" C ARG C 291 " ideal model delta sigma weight residual 112.89 119.23 -6.34 1.24e+00 6.50e-01 2.61e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.20 -6.31 1.24e+00 6.50e-01 2.59e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.17 -6.28 1.24e+00 6.50e-01 2.56e+01 angle pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " pdb=" O3' PCG B 701 " ideal model delta sigma weight residual 100.83 110.10 -9.27 3.00e+00 1.11e-01 9.56e+00 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 8794 28.99 - 57.98: 286 57.98 - 86.97: 8 86.97 - 115.96: 4 115.96 - 144.95: 12 Dihedral angle restraints: 9104 sinusoidal: 3788 harmonic: 5316 Sorted by residual: dihedral pdb=" C3' PCG B 701 " pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O1A PCG B 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.64 -144.95 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG A 701 " pdb=" O3' PCG A 701 " pdb=" PA PCG A 701 " pdb=" O1A PCG A 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.66 -144.93 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG C 701 " pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O1A PCG C 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.66 -144.93 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2276 0.131 - 0.262: 28 0.262 - 0.392: 4 0.392 - 0.523: 0 0.523 - 0.654: 4 Chirality restraints: 2312 Sorted by residual: chirality pdb=" PA PCG B 701 " pdb=" O2A PCG B 701 " pdb=" O3' PCG B 701 " pdb=" O5' PCG B 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" PA PCG C 701 " pdb=" O2A PCG C 701 " pdb=" O3' PCG C 701 " pdb=" O5' PCG C 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" PA PCG D 701 " pdb=" O2A PCG D 701 " pdb=" O3' PCG D 701 " pdb=" O5' PCG D 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 2309 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 526 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C VAL D 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL D 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL D 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C VAL C 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL C 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 526 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL A 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2635 2.76 - 3.30: 15662 3.30 - 3.83: 26894 3.83 - 4.37: 32518 4.37 - 4.90: 53443 Nonbonded interactions: 131152 Sorted by model distance: nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.227 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 3.040 nonbonded pdb=" O THR D 357 " pdb=" OG1 THR D 361 " model vdw 2.319 3.040 ... (remaining 131147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 701) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.660 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.350 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.005 0.104 15196 Z= 0.231 Angle : 0.697 9.274 20608 Z= 0.370 Chirality : 0.052 0.654 2312 Planarity : 0.003 0.028 2540 Dihedral : 14.964 144.946 5696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.25 % Allowed : 2.65 % Favored : 97.10 % 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 are not related in a simple way. whole: -1.18 (0.19), residues: 1792 helix: -0.53 (0.14), residues: 1080 sheet: -1.27 (0.82), residues: 56 loop : -0.92 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 561 TYR 0.015 0.001 TYR A 349 PHE 0.014 0.002 PHE C 389 TRP 0.024 0.002 TRP C 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00482 (15196) covalent geometry : angle 0.69657 (20608) hydrogen bonds : bond 0.12174 ( 904) hydrogen bonds : angle 6.69147 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8512 (mt) cc_final: 0.8307 (mt) REVERT: A 594 MET cc_start: 0.4708 (ppp) cc_final: 0.3440 (ttt) REVERT: B 387 LEU cc_start: 0.8518 (mt) cc_final: 0.8310 (mt) REVERT: B 594 MET cc_start: 0.4704 (ppp) cc_final: 0.3432 (ttt) REVERT: C 220 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7463 (mmt90) REVERT: C 387 LEU cc_start: 0.8529 (mt) cc_final: 0.8322 (mt) REVERT: C 594 MET cc_start: 0.4702 (ppp) cc_final: 0.3429 (ttt) REVERT: D 387 LEU cc_start: 0.8510 (mt) cc_final: 0.8305 (mt) REVERT: D 407 ARG cc_start: 0.7295 (ttt90) cc_final: 0.7031 (tpt170) REVERT: D 594 MET cc_start: 0.4692 (ppp) cc_final: 0.3433 (ttt) outliers start: 4 outliers final: 0 residues processed: 370 average time/residue: 0.1474 time to fit residues: 77.1365 Evaluate side-chains 214 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 302 ASN A 395 ASN A 422 HIS A 468 ASN A 496 GLN A 534 GLN B 238 ASN B 302 ASN B 395 ASN B 422 HIS B 444 ASN B 468 ASN B 496 GLN B 534 GLN C 238 ASN C 302 ASN C 395 ASN C 422 HIS C 468 ASN C 496 GLN C 534 GLN D 238 ASN D 302 ASN D 395 ASN D 411 GLN D 422 HIS D 444 ASN D 468 ASN D 496 GLN D 534 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121722 restraints weight = 18541.671| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.67 r_work: 0.3300 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.129 Angle : 0.519 6.170 20608 Z= 0.276 Chirality : 0.040 0.146 2312 Planarity : 0.004 0.036 2540 Dihedral : 12.763 148.979 2120 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.35 % Allowed : 10.06 % Favored : 87.59 % 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 are not related in a simple way. whole: 0.25 (0.21), residues: 1792 helix: 0.74 (0.16), residues: 1092 sheet: -0.71 (0.65), residues: 56 loop : -0.61 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 413 TYR 0.011 0.001 TYR D 349 PHE 0.010 0.001 PHE C 574 TRP 0.017 0.002 TRP C 168 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00283 (15196) covalent geometry : angle 0.51892 (20608) hydrogen bonds : bond 0.03957 ( 904) hydrogen bonds : angle 4.88813 ( 2652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7791 (m-30) cc_final: 0.7552 (m-30) REVERT: A 395 ASN cc_start: 0.7123 (m-40) cc_final: 0.6531 (t0) REVERT: A 498 GLN cc_start: 0.7649 (mt0) cc_final: 0.7324 (mt0) REVERT: A 594 MET cc_start: 0.5246 (ppp) cc_final: 0.3545 (ttt) REVERT: B 204 ASP cc_start: 0.7766 (m-30) cc_final: 0.7531 (m-30) REVERT: B 395 ASN cc_start: 0.7172 (m-40) cc_final: 0.6592 (t0) REVERT: B 450 GLU cc_start: 0.6655 (pt0) cc_final: 0.6360 (pm20) REVERT: B 498 GLN cc_start: 0.7674 (mt0) cc_final: 0.7354 (mt0) REVERT: B 594 MET cc_start: 0.5288 (ppp) cc_final: 0.3462 (ttt) REVERT: C 204 ASP cc_start: 0.7802 (m-30) cc_final: 0.7570 (m-30) REVERT: C 395 ASN cc_start: 0.7172 (m-40) cc_final: 0.6598 (t0) REVERT: C 464 GLU cc_start: 0.7069 (tp30) cc_final: 0.6704 (tt0) REVERT: C 498 GLN cc_start: 0.7625 (mt0) cc_final: 0.7315 (mt0) REVERT: C 594 MET cc_start: 0.5284 (ppp) cc_final: 0.3447 (ttt) REVERT: D 204 ASP cc_start: 0.7785 (m-30) cc_final: 0.7551 (m-30) REVERT: D 395 ASN cc_start: 0.7132 (m-40) cc_final: 0.6560 (t0) REVERT: D 464 GLU cc_start: 0.7083 (tp30) cc_final: 0.6759 (tt0) REVERT: D 498 GLN cc_start: 0.7650 (mt0) cc_final: 0.7324 (mt0) REVERT: D 594 MET cc_start: 0.5233 (ppp) cc_final: 0.3517 (ttt) outliers start: 38 outliers final: 14 residues processed: 278 average time/residue: 0.1212 time to fit residues: 50.9319 Evaluate side-chains 214 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 82 optimal weight: 0.0010 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN B 444 ASN C 338 ASN D 444 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119209 restraints weight = 18554.797| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.73 r_work: 0.3287 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.119 Angle : 0.490 4.829 20608 Z= 0.262 Chirality : 0.040 0.150 2312 Planarity : 0.004 0.029 2540 Dihedral : 12.601 149.507 2120 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.42 % Allowed : 14.01 % Favored : 84.57 % 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 are not related in a simple way. whole: 1.04 (0.21), residues: 1792 helix: 1.31 (0.16), residues: 1060 sheet: 0.14 (0.68), residues: 56 loop : -0.14 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 433 TYR 0.009 0.001 TYR B 375 PHE 0.010 0.001 PHE A 298 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00265 (15196) covalent geometry : angle 0.49007 (20608) hydrogen bonds : bond 0.03730 ( 904) hydrogen bonds : angle 4.54727 ( 2652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7757 (m-30) cc_final: 0.7113 (m-30) REVERT: A 205 TYR cc_start: 0.6123 (m-10) cc_final: 0.5618 (t80) REVERT: A 450 GLU cc_start: 0.6677 (pt0) cc_final: 0.6427 (pm20) REVERT: A 498 GLN cc_start: 0.7913 (mt0) cc_final: 0.7586 (mt0) REVERT: A 594 MET cc_start: 0.5271 (ppp) cc_final: 0.3987 (tpt) REVERT: B 204 ASP cc_start: 0.7747 (m-30) cc_final: 0.7102 (m-30) REVERT: B 205 TYR cc_start: 0.6082 (m-10) cc_final: 0.5606 (t80) REVERT: B 286 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7491 (mt0) REVERT: B 429 ASP cc_start: 0.8289 (t70) cc_final: 0.8021 (t70) REVERT: B 450 GLU cc_start: 0.6703 (pt0) cc_final: 0.6445 (pm20) REVERT: B 498 GLN cc_start: 0.7952 (mt0) cc_final: 0.7621 (mt0) REVERT: B 594 MET cc_start: 0.5214 (ppp) cc_final: 0.3947 (tpt) REVERT: C 204 ASP cc_start: 0.7754 (m-30) cc_final: 0.7028 (m-30) REVERT: C 205 TYR cc_start: 0.5533 (m-10) cc_final: 0.5289 (t80) REVERT: C 286 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7509 (mt0) REVERT: C 450 GLU cc_start: 0.6689 (pt0) cc_final: 0.6468 (pm20) REVERT: C 498 GLN cc_start: 0.7913 (mt0) cc_final: 0.7585 (mt0) REVERT: C 594 MET cc_start: 0.5225 (ppp) cc_final: 0.3964 (tpt) REVERT: D 204 ASP cc_start: 0.7733 (m-30) cc_final: 0.7085 (m-30) REVERT: D 205 TYR cc_start: 0.5533 (m-10) cc_final: 0.5279 (t80) REVERT: D 286 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7513 (mt0) REVERT: D 407 ARG cc_start: 0.8241 (tpt170) cc_final: 0.8032 (tpt170) REVERT: D 429 ASP cc_start: 0.8288 (t70) cc_final: 0.8038 (t70) REVERT: D 450 GLU cc_start: 0.6732 (pt0) cc_final: 0.6479 (pm20) REVERT: D 498 GLN cc_start: 0.7899 (mt0) cc_final: 0.7573 (mt0) REVERT: D 594 MET cc_start: 0.5240 (ppp) cc_final: 0.3966 (tpt) outliers start: 23 outliers final: 11 residues processed: 239 average time/residue: 0.1215 time to fit residues: 44.3212 Evaluate side-chains 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 6.9990 chunk 131 optimal weight: 0.0970 chunk 174 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 155 optimal weight: 0.0000 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 468 ASN C 444 ASN C 468 ASN D 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120006 restraints weight = 18583.015| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.73 r_work: 0.3302 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15196 Z= 0.108 Angle : 0.473 5.685 20608 Z= 0.250 Chirality : 0.039 0.151 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.547 151.086 2120 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.60 % Allowed : 14.38 % Favored : 84.01 % 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 are not related in a simple way. whole: 1.22 (0.21), residues: 1792 helix: 1.45 (0.16), residues: 1060 sheet: 0.37 (0.64), residues: 56 loop : -0.07 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.008 0.001 TYR C 375 PHE 0.009 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00238 (15196) covalent geometry : angle 0.47314 (20608) hydrogen bonds : bond 0.03511 ( 904) hydrogen bonds : angle 4.42834 ( 2652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7697 (m-30) cc_final: 0.7117 (m-30) REVERT: A 286 GLN cc_start: 0.8573 (tm-30) cc_final: 0.7593 (mt0) REVERT: A 407 ARG cc_start: 0.8208 (tpt170) cc_final: 0.8004 (tpt90) REVERT: A 429 ASP cc_start: 0.8159 (t70) cc_final: 0.7881 (t70) REVERT: A 450 GLU cc_start: 0.6685 (pt0) cc_final: 0.6480 (pm20) REVERT: A 498 GLN cc_start: 0.8069 (mt0) cc_final: 0.7818 (mt0) REVERT: A 594 MET cc_start: 0.5230 (ppp) cc_final: 0.4050 (tpt) REVERT: B 204 ASP cc_start: 0.7673 (m-30) cc_final: 0.7091 (m-30) REVERT: B 286 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7430 (mt0) REVERT: B 430 MET cc_start: 0.8534 (tpp) cc_final: 0.8237 (tpt) REVERT: B 498 GLN cc_start: 0.8103 (mt0) cc_final: 0.7841 (mt0) REVERT: B 571 SER cc_start: 0.8968 (m) cc_final: 0.8755 (p) REVERT: B 594 MET cc_start: 0.5200 (ppp) cc_final: 0.3999 (tpt) REVERT: C 204 ASP cc_start: 0.7662 (m-30) cc_final: 0.7048 (m-30) REVERT: C 286 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7564 (mt0) REVERT: C 430 MET cc_start: 0.8494 (tpp) cc_final: 0.8222 (tpt) REVERT: C 450 GLU cc_start: 0.6691 (pt0) cc_final: 0.6478 (pm20) REVERT: C 498 GLN cc_start: 0.8097 (mt0) cc_final: 0.7844 (mt0) REVERT: C 571 SER cc_start: 0.8973 (m) cc_final: 0.8756 (p) REVERT: C 594 MET cc_start: 0.5226 (ppp) cc_final: 0.4032 (tpt) REVERT: D 204 ASP cc_start: 0.7701 (m-30) cc_final: 0.7092 (m-30) REVERT: D 286 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7574 (mt0) REVERT: D 407 ARG cc_start: 0.8279 (tpt170) cc_final: 0.8049 (tpt90) REVERT: D 429 ASP cc_start: 0.8234 (t70) cc_final: 0.7910 (t70) REVERT: D 498 GLN cc_start: 0.8078 (mt0) cc_final: 0.7830 (mt0) REVERT: D 594 MET cc_start: 0.5188 (ppp) cc_final: 0.4012 (tpt) outliers start: 26 outliers final: 11 residues processed: 263 average time/residue: 0.1154 time to fit residues: 46.5453 Evaluate side-chains 231 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 314 ASN C 314 ASN D 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115460 restraints weight = 18433.298| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.71 r_work: 0.3178 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15196 Z= 0.127 Angle : 0.490 5.057 20608 Z= 0.258 Chirality : 0.040 0.152 2312 Planarity : 0.003 0.032 2540 Dihedral : 12.541 151.638 2120 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.22 % Allowed : 15.06 % Favored : 82.72 % 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 are not related in a simple way. whole: 1.14 (0.20), residues: 1792 helix: 1.34 (0.16), residues: 1084 sheet: 0.26 (0.61), residues: 56 loop : -0.07 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 220 TYR 0.010 0.001 TYR B 351 PHE 0.011 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00291 (15196) covalent geometry : angle 0.48957 (20608) hydrogen bonds : bond 0.03634 ( 904) hydrogen bonds : angle 4.41378 ( 2652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7632 (m-30) cc_final: 0.7081 (m-30) REVERT: A 286 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7626 (mt0) REVERT: A 430 MET cc_start: 0.8557 (tpp) cc_final: 0.8243 (tpp) REVERT: A 498 GLN cc_start: 0.8165 (mt0) cc_final: 0.7924 (mt0) REVERT: A 594 MET cc_start: 0.5273 (ppp) cc_final: 0.4042 (tpt) REVERT: B 204 ASP cc_start: 0.7607 (m-30) cc_final: 0.7056 (m-30) REVERT: B 286 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7419 (mt0) REVERT: B 498 GLN cc_start: 0.8069 (mt0) cc_final: 0.7702 (mt0) REVERT: B 547 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6900 (mp) REVERT: B 594 MET cc_start: 0.5348 (ppp) cc_final: 0.4149 (tpt) REVERT: C 204 ASP cc_start: 0.7621 (m-30) cc_final: 0.7030 (m-30) REVERT: C 286 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7453 (mt0) REVERT: C 450 GLU cc_start: 0.6834 (pt0) cc_final: 0.6505 (pm20) REVERT: C 494 LYS cc_start: 0.7950 (mppt) cc_final: 0.7111 (mtmm) REVERT: C 498 GLN cc_start: 0.8182 (mt0) cc_final: 0.7934 (mt0) REVERT: C 547 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6901 (mp) REVERT: C 594 MET cc_start: 0.5262 (ppp) cc_final: 0.4056 (tpt) REVERT: D 204 ASP cc_start: 0.7653 (m-30) cc_final: 0.7060 (m-30) REVERT: D 286 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7542 (mt0) REVERT: D 498 GLN cc_start: 0.8066 (mt0) cc_final: 0.7701 (mt0) REVERT: D 547 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6896 (mp) REVERT: D 594 MET cc_start: 0.5253 (ppp) cc_final: 0.3999 (tpt) outliers start: 36 outliers final: 17 residues processed: 243 average time/residue: 0.1148 time to fit residues: 43.3603 Evaluate side-chains 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118564 restraints weight = 18104.530| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.62 r_work: 0.3196 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15196 Z= 0.116 Angle : 0.484 6.867 20608 Z= 0.252 Chirality : 0.040 0.149 2312 Planarity : 0.003 0.031 2540 Dihedral : 12.507 151.228 2120 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.79 % Allowed : 16.36 % Favored : 81.85 % 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 are not related in a simple way. whole: 1.19 (0.20), residues: 1792 helix: 1.37 (0.16), residues: 1084 sheet: 0.27 (0.61), residues: 56 loop : -0.03 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 344 TYR 0.009 0.001 TYR D 456 PHE 0.009 0.001 PHE A 298 TRP 0.017 0.001 TRP D 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00263 (15196) covalent geometry : angle 0.48377 (20608) hydrogen bonds : bond 0.03558 ( 904) hydrogen bonds : angle 4.37568 ( 2652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7601 (m-30) cc_final: 0.7016 (m-30) REVERT: A 286 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7591 (mt0) REVERT: A 297 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8171 (mm) REVERT: A 450 GLU cc_start: 0.6888 (pt0) cc_final: 0.6462 (pp20) REVERT: A 498 GLN cc_start: 0.8125 (mt0) cc_final: 0.7918 (mt0) REVERT: A 594 MET cc_start: 0.5269 (ppp) cc_final: 0.4063 (tpt) REVERT: B 204 ASP cc_start: 0.7569 (m-30) cc_final: 0.7024 (m-30) REVERT: B 286 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7352 (mt0) REVERT: B 297 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8179 (mm) REVERT: B 498 GLN cc_start: 0.8133 (mt0) cc_final: 0.7817 (mt0) REVERT: B 538 LEU cc_start: 0.7247 (mt) cc_final: 0.7044 (mt) REVERT: B 547 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6967 (mp) REVERT: B 594 MET cc_start: 0.5369 (ppp) cc_final: 0.4189 (tpt) REVERT: C 204 ASP cc_start: 0.7566 (m-30) cc_final: 0.6984 (m-30) REVERT: C 286 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7514 (mt0) REVERT: C 498 GLN cc_start: 0.8140 (mt0) cc_final: 0.7938 (mt0) REVERT: C 538 LEU cc_start: 0.7253 (mt) cc_final: 0.7044 (mt) REVERT: C 547 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6959 (mp) REVERT: C 594 MET cc_start: 0.5360 (ppp) cc_final: 0.4182 (tpt) REVERT: D 204 ASP cc_start: 0.7610 (m-30) cc_final: 0.6995 (m-30) REVERT: D 286 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7525 (mt0) REVERT: D 306 TYR cc_start: 0.8388 (m-10) cc_final: 0.8168 (m-10) REVERT: D 498 GLN cc_start: 0.8119 (mt0) cc_final: 0.7828 (mt0) REVERT: D 594 MET cc_start: 0.5260 (ppp) cc_final: 0.4044 (tpt) outliers start: 29 outliers final: 11 residues processed: 231 average time/residue: 0.1142 time to fit residues: 41.3094 Evaluate side-chains 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.0050 chunk 95 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 468 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118595 restraints weight = 18125.626| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.62 r_work: 0.3266 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15196 Z= 0.113 Angle : 0.485 6.924 20608 Z= 0.252 Chirality : 0.040 0.154 2312 Planarity : 0.003 0.031 2540 Dihedral : 12.485 151.180 2120 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.30 % Allowed : 17.47 % Favored : 81.23 % 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 are not related in a simple way. whole: 1.26 (0.20), residues: 1792 helix: 1.44 (0.16), residues: 1084 sheet: 0.17 (0.61), residues: 56 loop : -0.00 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.010 0.001 TYR B 456 PHE 0.009 0.001 PHE C 298 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00256 (15196) covalent geometry : angle 0.48517 (20608) hydrogen bonds : bond 0.03483 ( 904) hydrogen bonds : angle 4.29843 ( 2652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7576 (m-30) cc_final: 0.7046 (m-30) REVERT: A 286 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7532 (mt0) REVERT: A 297 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 306 TYR cc_start: 0.8407 (m-10) cc_final: 0.8199 (m-10) REVERT: A 430 MET cc_start: 0.8621 (tpp) cc_final: 0.8170 (tpp) REVERT: A 450 GLU cc_start: 0.6950 (pt0) cc_final: 0.6546 (pp20) REVERT: A 594 MET cc_start: 0.5174 (ppp) cc_final: 0.4001 (tpt) REVERT: B 204 ASP cc_start: 0.7586 (m-30) cc_final: 0.7001 (m-30) REVERT: B 286 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7477 (mt0) REVERT: B 303 LEU cc_start: 0.8736 (mt) cc_final: 0.8529 (mp) REVERT: B 498 GLN cc_start: 0.8097 (mt0) cc_final: 0.7837 (mt0) REVERT: B 594 MET cc_start: 0.5208 (ppp) cc_final: 0.4029 (tpt) REVERT: C 204 ASP cc_start: 0.7600 (m-30) cc_final: 0.7015 (m-30) REVERT: C 286 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7553 (mt0) REVERT: C 303 LEU cc_start: 0.8701 (mt) cc_final: 0.8500 (mp) REVERT: C 494 LYS cc_start: 0.7869 (mppt) cc_final: 0.7089 (mtmm) REVERT: C 594 MET cc_start: 0.5181 (ppp) cc_final: 0.4022 (tpt) REVERT: D 204 ASP cc_start: 0.7601 (m-30) cc_final: 0.7067 (m-30) REVERT: D 286 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7561 (mt0) REVERT: D 305 MET cc_start: 0.8048 (ttm) cc_final: 0.7796 (ttp) REVERT: D 498 GLN cc_start: 0.8081 (mt0) cc_final: 0.7844 (mt0) REVERT: D 556 LYS cc_start: 0.2595 (OUTLIER) cc_final: 0.1767 (tptt) REVERT: D 594 MET cc_start: 0.5208 (ppp) cc_final: 0.4049 (tpt) outliers start: 21 outliers final: 9 residues processed: 221 average time/residue: 0.1138 time to fit residues: 38.6845 Evaluate side-chains 203 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 0.0980 chunk 122 optimal weight: 0.0370 chunk 157 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125297 restraints weight = 18020.847| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.60 r_work: 0.3274 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15196 Z= 0.099 Angle : 0.468 6.762 20608 Z= 0.244 Chirality : 0.039 0.154 2312 Planarity : 0.003 0.035 2540 Dihedral : 12.419 150.229 2120 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 17.10 % Favored : 81.42 % 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 are not related in a simple way. whole: 1.32 (0.20), residues: 1792 helix: 1.54 (0.16), residues: 1084 sheet: 0.16 (0.62), residues: 56 loop : -0.08 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 407 TYR 0.009 0.001 TYR B 456 PHE 0.008 0.001 PHE D 410 TRP 0.017 0.001 TRP D 442 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00217 (15196) covalent geometry : angle 0.46764 (20608) hydrogen bonds : bond 0.03326 ( 904) hydrogen bonds : angle 4.22874 ( 2652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7522 (m-30) cc_final: 0.7114 (m-30) REVERT: A 286 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7525 (mt0) REVERT: A 297 ILE cc_start: 0.8410 (mt) cc_final: 0.8094 (mm) REVERT: A 305 MET cc_start: 0.8082 (ttm) cc_final: 0.7842 (ttp) REVERT: A 331 THR cc_start: 0.8737 (p) cc_final: 0.8512 (p) REVERT: A 430 MET cc_start: 0.8630 (tpp) cc_final: 0.8168 (tpp) REVERT: A 450 GLU cc_start: 0.6932 (pt0) cc_final: 0.6525 (pp20) REVERT: A 498 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: A 556 LYS cc_start: 0.2614 (OUTLIER) cc_final: 0.2228 (mtmm) REVERT: A 594 MET cc_start: 0.5167 (ppp) cc_final: 0.4007 (tpt) REVERT: B 204 ASP cc_start: 0.7471 (m-30) cc_final: 0.7059 (m-30) REVERT: B 286 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7459 (mt0) REVERT: B 297 ILE cc_start: 0.8423 (mt) cc_final: 0.8112 (mm) REVERT: B 303 LEU cc_start: 0.8659 (mt) cc_final: 0.8445 (mp) REVERT: B 305 MET cc_start: 0.8128 (ttm) cc_final: 0.7863 (ttp) REVERT: B 331 THR cc_start: 0.8732 (p) cc_final: 0.8509 (p) REVERT: B 498 GLN cc_start: 0.8106 (mt0) cc_final: 0.7839 (mt0) REVERT: B 556 LYS cc_start: 0.2666 (OUTLIER) cc_final: 0.2199 (mptt) REVERT: B 594 MET cc_start: 0.5208 (ppp) cc_final: 0.4059 (tpt) REVERT: C 204 ASP cc_start: 0.7515 (m-30) cc_final: 0.7095 (m-30) REVERT: C 286 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7409 (mt0) REVERT: C 297 ILE cc_start: 0.8429 (mt) cc_final: 0.8120 (mm) REVERT: C 305 MET cc_start: 0.8089 (ttm) cc_final: 0.7837 (ttp) REVERT: C 331 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 494 LYS cc_start: 0.7795 (mppt) cc_final: 0.7028 (mtmm) REVERT: C 498 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: C 556 LYS cc_start: 0.2651 (OUTLIER) cc_final: 0.2202 (mptt) REVERT: C 594 MET cc_start: 0.5210 (ppp) cc_final: 0.4057 (tpt) REVERT: D 204 ASP cc_start: 0.7543 (m-30) cc_final: 0.7128 (m-30) REVERT: D 286 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7499 (mt0) REVERT: D 297 ILE cc_start: 0.8428 (mt) cc_final: 0.8125 (mm) REVERT: D 305 MET cc_start: 0.8025 (ttm) cc_final: 0.7777 (ttp) REVERT: D 331 THR cc_start: 0.8727 (p) cc_final: 0.8500 (p) REVERT: D 498 GLN cc_start: 0.8127 (mt0) cc_final: 0.7878 (mt0) REVERT: D 594 MET cc_start: 0.5168 (ppp) cc_final: 0.4007 (tpt) outliers start: 24 outliers final: 12 residues processed: 250 average time/residue: 0.1038 time to fit residues: 41.3326 Evaluate side-chains 233 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.0870 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125536 restraints weight = 18077.466| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.47 r_work: 0.3242 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15196 Z= 0.111 Angle : 0.468 6.224 20608 Z= 0.246 Chirality : 0.039 0.149 2312 Planarity : 0.004 0.064 2540 Dihedral : 12.410 150.592 2120 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.60 % Allowed : 17.35 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1792 helix: 1.56 (0.16), residues: 1084 sheet: 0.03 (0.62), residues: 56 loop : -0.14 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 407 TYR 0.010 0.001 TYR A 306 PHE 0.012 0.001 PHE C 389 TRP 0.015 0.001 TRP B 168 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00252 (15196) covalent geometry : angle 0.46811 (20608) hydrogen bonds : bond 0.03414 ( 904) hydrogen bonds : angle 4.26744 ( 2652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7579 (m-30) cc_final: 0.7063 (m-30) REVERT: A 286 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7582 (mt0) REVERT: A 305 MET cc_start: 0.8108 (ttm) cc_final: 0.7876 (ttp) REVERT: A 331 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 450 GLU cc_start: 0.6930 (pt0) cc_final: 0.6518 (pp20) REVERT: A 543 TYR cc_start: 0.7010 (p90) cc_final: 0.6634 (p90) REVERT: A 556 LYS cc_start: 0.2505 (OUTLIER) cc_final: 0.2207 (mtmm) REVERT: A 594 MET cc_start: 0.5234 (ppp) cc_final: 0.4074 (tpt) REVERT: B 204 ASP cc_start: 0.7535 (m-30) cc_final: 0.7011 (m-30) REVERT: B 297 ILE cc_start: 0.8443 (mt) cc_final: 0.8099 (mm) REVERT: B 331 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 498 GLN cc_start: 0.8133 (mt0) cc_final: 0.7863 (mt0) REVERT: B 543 TYR cc_start: 0.7028 (p90) cc_final: 0.6676 (p90) REVERT: B 556 LYS cc_start: 0.2581 (OUTLIER) cc_final: 0.1929 (mptt) REVERT: B 594 MET cc_start: 0.5227 (ppp) cc_final: 0.4078 (tpt) REVERT: C 204 ASP cc_start: 0.7596 (m-30) cc_final: 0.7074 (m-30) REVERT: C 286 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7396 (mt0) REVERT: C 297 ILE cc_start: 0.8443 (mt) cc_final: 0.8095 (mm) REVERT: C 331 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 494 LYS cc_start: 0.7805 (mppt) cc_final: 0.7037 (mtmm) REVERT: C 543 TYR cc_start: 0.7003 (p90) cc_final: 0.6646 (p90) REVERT: C 556 LYS cc_start: 0.2431 (OUTLIER) cc_final: 0.1868 (mptt) REVERT: C 594 MET cc_start: 0.5228 (ppp) cc_final: 0.4074 (tpt) REVERT: D 204 ASP cc_start: 0.7601 (m-30) cc_final: 0.7091 (m-30) REVERT: D 286 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7416 (mt0) REVERT: D 297 ILE cc_start: 0.8381 (mt) cc_final: 0.8036 (mm) REVERT: D 331 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8461 (p) REVERT: D 498 GLN cc_start: 0.8136 (mt0) cc_final: 0.7886 (mt0) REVERT: D 543 TYR cc_start: 0.7021 (p90) cc_final: 0.6647 (p90) REVERT: D 556 LYS cc_start: 0.2369 (OUTLIER) cc_final: 0.2141 (mtmm) REVERT: D 594 MET cc_start: 0.5214 (ppp) cc_final: 0.4062 (tpt) outliers start: 26 outliers final: 12 residues processed: 239 average time/residue: 0.1064 time to fit residues: 39.9612 Evaluate side-chains 233 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.0470 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN D 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113790 restraints weight = 18397.657| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.69 r_work: 0.3151 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15196 Z= 0.140 Angle : 0.494 6.370 20608 Z= 0.259 Chirality : 0.040 0.151 2312 Planarity : 0.004 0.044 2540 Dihedral : 12.441 150.179 2120 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.60 % Allowed : 17.35 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1792 helix: 1.45 (0.16), residues: 1084 sheet: -0.24 (0.60), residues: 56 loop : -0.10 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 424 TYR 0.011 0.001 TYR C 349 PHE 0.013 0.001 PHE A 285 TRP 0.017 0.001 TRP A 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00323 (15196) covalent geometry : angle 0.49359 (20608) hydrogen bonds : bond 0.03661 ( 904) hydrogen bonds : angle 4.41675 ( 2652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7636 (m-30) cc_final: 0.7120 (m-30) REVERT: A 286 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7624 (mt0) REVERT: A 331 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 450 GLU cc_start: 0.7043 (pt0) cc_final: 0.6660 (pp20) REVERT: A 460 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7622 (tptp) REVERT: A 498 GLN cc_start: 0.8017 (mt0) cc_final: 0.7812 (mp10) REVERT: A 509 LYS cc_start: 0.6281 (mttt) cc_final: 0.5841 (mtpp) REVERT: A 543 TYR cc_start: 0.7165 (p90) cc_final: 0.6759 (p90) REVERT: A 594 MET cc_start: 0.5240 (ppp) cc_final: 0.4192 (tpt) REVERT: B 204 ASP cc_start: 0.7583 (m-30) cc_final: 0.7055 (m-30) REVERT: B 331 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 498 GLN cc_start: 0.8202 (mt0) cc_final: 0.7933 (mt0) REVERT: B 509 LYS cc_start: 0.6260 (mttt) cc_final: 0.5802 (mtpp) REVERT: B 543 TYR cc_start: 0.7188 (p90) cc_final: 0.6811 (p90) REVERT: B 556 LYS cc_start: 0.2320 (OUTLIER) cc_final: 0.1675 (mtmm) REVERT: B 594 MET cc_start: 0.5144 (ppp) cc_final: 0.4139 (tpt) REVERT: C 204 ASP cc_start: 0.7652 (m-30) cc_final: 0.7129 (m-30) REVERT: C 286 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7458 (mt0) REVERT: C 331 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 494 LYS cc_start: 0.7908 (mppt) cc_final: 0.7114 (mtmm) REVERT: C 498 GLN cc_start: 0.8023 (mt0) cc_final: 0.7790 (mp10) REVERT: C 509 LYS cc_start: 0.6234 (mttt) cc_final: 0.5773 (mtpp) REVERT: C 543 TYR cc_start: 0.7211 (p90) cc_final: 0.6854 (p90) REVERT: C 556 LYS cc_start: 0.2330 (OUTLIER) cc_final: 0.2014 (mtmm) REVERT: C 594 MET cc_start: 0.5191 (ppp) cc_final: 0.4193 (tpt) REVERT: D 204 ASP cc_start: 0.7624 (m-30) cc_final: 0.7093 (m-30) REVERT: D 286 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7467 (mt0) REVERT: D 297 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8175 (mm) REVERT: D 331 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8543 (p) REVERT: D 498 GLN cc_start: 0.8175 (mt0) cc_final: 0.7910 (mt0) REVERT: D 509 LYS cc_start: 0.6234 (mttt) cc_final: 0.5828 (mtpp) REVERT: D 543 TYR cc_start: 0.7200 (p90) cc_final: 0.6807 (p90) REVERT: D 594 MET cc_start: 0.5256 (ppp) cc_final: 0.4218 (tpt) outliers start: 26 outliers final: 13 residues processed: 242 average time/residue: 0.1153 time to fit residues: 43.2016 Evaluate side-chains 239 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116931 restraints weight = 18390.244| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.64 r_work: 0.3195 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15196 Z= 0.116 Angle : 0.477 6.571 20608 Z= 0.249 Chirality : 0.040 0.149 2312 Planarity : 0.003 0.032 2540 Dihedral : 12.424 149.888 2120 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.79 % Allowed : 17.41 % Favored : 80.80 % 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 are not related in a simple way. whole: 1.23 (0.20), residues: 1792 helix: 1.48 (0.16), residues: 1084 sheet: -0.18 (0.61), residues: 56 loop : -0.13 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 407 TYR 0.016 0.001 TYR D 456 PHE 0.010 0.001 PHE C 298 TRP 0.017 0.001 TRP D 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00266 (15196) covalent geometry : angle 0.47707 (20608) hydrogen bonds : bond 0.03501 ( 904) hydrogen bonds : angle 4.35291 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.39 seconds wall clock time: 69 minutes 3.31 seconds (4143.31 seconds total)