Starting phenix.real_space_refine on Tue Nov 18 14:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfw_23307/11_2025/7lfw_23307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfw_23307/11_2025/7lfw_23307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lfw_23307/11_2025/7lfw_23307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfw_23307/11_2025/7lfw_23307.map" model { file = "/net/cci-nas-00/data/ceres_data/7lfw_23307/11_2025/7lfw_23307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfw_23307/11_2025/7lfw_23307.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 3.53, per 1000 atoms: 0.24 Number of scatterers: 14846 At special positions: 0 Unit cell: (96.485, 96.485, 114.104, 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: 1.38 Conformation dependent library (CDL) restraints added in 614.2 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: 0.45 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: 3.827A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.535A 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: 3.525A 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: 4.236A 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: 3.641A 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: 3.525A 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: 4.462A 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: 3.535A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.588A 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: 3.770A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.734A 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: 3.525A 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: 4.235A 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: 3.641A 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: 4.908A 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: 3.525A 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: 4.236A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.463A 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: 7.057A 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: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A 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: 6.494A 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: 7.057A 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: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A 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: 7.058A 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: 7.860A 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: 6.494A 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: 7.058A 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: 7.860A 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: 7.057A 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: 4.723A 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: 6.494A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 7.057A 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: 4.723A 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: 7.058A 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: 7.860A 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: 7.058A 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: 7.860A 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: 1.83 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: 4358 1.34 - 1.45: 2369 1.45 - 1.57: 8333 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 1.477 0.105 2.00e-02 2.50e+03 2.76e+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 2.72e+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 2.72e+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 2.69e+01 bond pdb=" C1' PCG B 701 " pdb=" O4' PCG B 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 - 1.86: 20211 1.86 - 3.71: 277 3.71 - 5.57: 72 5.57 - 7.43: 24 7.43 - 9.28: 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 112.89 119.24 -6.35 1.24e+00 6.50e-01 2.62e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.21 -6.32 1.24e+00 6.50e-01 2.60e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.16 -6.27 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 100.83 110.11 -9.28 3.00e+00 1.11e-01 9.57e+00 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 8794 28.99 - 57.99: 286 57.99 - 86.98: 8 86.98 - 115.97: 4 115.97 - 144.96: 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 -63.63 -144.96 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 -63.65 -144.94 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG D 701 " pdb=" O3' PCG D 701 " pdb=" PA PCG D 701 " pdb=" O1A PCG D 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.68 -144.91 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 - 0.263: 28 0.263 - 0.394: 4 0.394 - 0.525: 0 0.525 - 0.657: 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 -3.36 -0.66 2.00e-01 2.50e+01 1.08e+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 1.54e-02 2.37e+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 2.36e+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 B 526 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C VAL B 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2644 2.76 - 3.30: 15656 3.30 - 3.83: 26907 3.83 - 4.37: 32515 4.37 - 4.90: 53421 Nonbonded interactions: 131143 Sorted by model distance: 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 2.226 3.040 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.319 3.040 ... (remaining 131138 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.290 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:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.105 15196 Z= 0.230 Angle : 0.696 9.283 20608 Z= 0.370 Chirality : 0.052 0.657 2312 Planarity : 0.003 0.028 2540 Dihedral : 14.963 144.963 5696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.25 % Allowed : 2.72 % Favored : 97.04 % 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: -1.26 (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 0.014 0.001 TYR C 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 0.00481 (15196) covalent geometry : angle 0.69617 (20608) hydrogen bonds : bond 0.12174 ( 904) hydrogen bonds : angle 6.69145 ( 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 267 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.647 Fit side-chains REVERT: A 266 ASN cc_start: 0.7431 (t0) cc_final: 0.7210 (t0) REVERT: A 428 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7404 (mptp) REVERT: A 450 GLU cc_start: 0.6476 (pt0) cc_final: 0.6115 (pp20) REVERT: A 496 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7093 (mt0) REVERT: A 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6228 (mptp) REVERT: B 266 ASN cc_start: 0.7432 (t0) cc_final: 0.7217 (t0) REVERT: B 428 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7399 (mptp) REVERT: B 450 GLU cc_start: 0.6477 (pt0) cc_final: 0.6119 (pp20) REVERT: B 496 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7107 (mt0) REVERT: B 605 LYS cc_start: 0.6441 (ptmt) cc_final: 0.6225 (mptp) REVERT: C 266 ASN cc_start: 0.7427 (t0) cc_final: 0.7206 (t0) REVERT: C 428 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7416 (mptp) REVERT: C 450 GLU cc_start: 0.6478 (pt0) cc_final: 0.6129 (pp20) REVERT: C 496 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7142 (mt0) REVERT: C 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6226 (mptp) REVERT: D 266 ASN cc_start: 0.7421 (t0) cc_final: 0.7182 (t0) REVERT: D 428 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7399 (mptp) REVERT: D 450 GLU cc_start: 0.6475 (pt0) cc_final: 0.6117 (pp20) REVERT: D 496 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7089 (mt0) REVERT: D 605 LYS cc_start: 0.6449 (ptmt) cc_final: 0.6219 (mptp) outliers start: 4 outliers final: 4 residues processed: 267 average time/residue: 0.7754 time to fit residues: 223.8266 Evaluate side-chains 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain D residue 291 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 395 ASN A 402 ASN A 468 ASN A 534 GLN B 238 ASN B 302 ASN B 395 ASN B 402 ASN B 468 ASN B 534 GLN C 238 ASN C 395 ASN C 402 ASN C 468 ASN C 534 GLN D 238 ASN D 395 ASN D 402 ASN D 468 ASN D 534 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120307 restraints weight = 17662.248| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.71 r_work: 0.3129 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1729 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= 0.128 Angle : 0.533 7.466 20608 Z= 0.278 Chirality : 0.041 0.152 2312 Planarity : 0.004 0.034 2540 Dihedral : 12.893 154.318 2136 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.68 % Allowed : 9.81 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.21), residues: 1792 helix: 0.93 (0.16), residues: 1064 sheet: -0.69 (0.69), residues: 56 loop : -0.47 (0.28), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 347 TYR 0.013 0.001 TYR B 349 PHE 0.013 0.001 PHE D 389 TRP 0.018 0.001 TRP C 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00282 (15196) covalent geometry : angle 0.53293 (20608) hydrogen bonds : bond 0.03951 ( 904) hydrogen bonds : angle 4.88159 ( 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 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.553 Fit side-chains REVERT: A 266 ASN cc_start: 0.7805 (t0) cc_final: 0.7542 (t0) REVERT: A 341 GLU cc_start: 0.7875 (tp30) cc_final: 0.7658 (tp30) REVERT: A 428 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7570 (mptt) REVERT: A 450 GLU cc_start: 0.6604 (pt0) cc_final: 0.6263 (pp20) REVERT: A 496 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7302 (mt0) REVERT: A 605 LYS cc_start: 0.6541 (ptmt) cc_final: 0.6242 (mptp) REVERT: B 266 ASN cc_start: 0.7803 (t0) cc_final: 0.7535 (t0) REVERT: B 428 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7590 (mptt) REVERT: B 450 GLU cc_start: 0.6603 (pt0) cc_final: 0.6292 (pp20) REVERT: B 496 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7316 (mt0) REVERT: B 605 LYS cc_start: 0.6534 (ptmt) cc_final: 0.6228 (mptp) REVERT: C 266 ASN cc_start: 0.7761 (t0) cc_final: 0.7519 (t0) REVERT: C 428 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7612 (mptt) REVERT: C 450 GLU cc_start: 0.6598 (pt0) cc_final: 0.6272 (pp20) REVERT: C 452 GLU cc_start: 0.7970 (tp30) cc_final: 0.7749 (tp30) REVERT: C 496 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7299 (mt0) REVERT: C 605 LYS cc_start: 0.6523 (ptmt) cc_final: 0.6222 (mptp) REVERT: D 266 ASN cc_start: 0.7763 (t0) cc_final: 0.7519 (t0) REVERT: D 428 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7588 (mptt) REVERT: D 450 GLU cc_start: 0.6572 (pt0) cc_final: 0.6252 (pp20) REVERT: D 452 GLU cc_start: 0.7976 (tp30) cc_final: 0.7749 (tp30) REVERT: D 496 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7325 (mt0) REVERT: D 605 LYS cc_start: 0.6516 (ptmt) cc_final: 0.6230 (mptp) outliers start: 11 outliers final: 4 residues processed: 209 average time/residue: 0.6696 time to fit residues: 152.9591 Evaluate side-chains 196 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119491 restraints weight = 17847.898| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.76 r_work: 0.3099 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15196 Z= 0.147 Angle : 0.525 8.018 20608 Z= 0.273 Chirality : 0.041 0.143 2312 Planarity : 0.004 0.027 2540 Dihedral : 12.792 151.353 2120 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.80 % Allowed : 11.79 % Favored : 87.41 % 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: 0.79 (0.21), residues: 1792 helix: 1.14 (0.16), residues: 1068 sheet: -0.07 (0.70), residues: 56 loop : -0.31 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.016 0.001 TYR D 349 PHE 0.013 0.002 PHE B 389 TRP 0.019 0.002 TRP C 168 HIS 0.001 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00336 (15196) covalent geometry : angle 0.52489 (20608) hydrogen bonds : bond 0.03891 ( 904) hydrogen bonds : angle 4.71048 ( 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 198 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.608 Fit side-chains REVERT: A 266 ASN cc_start: 0.7817 (t0) cc_final: 0.7579 (t0) REVERT: A 341 GLU cc_start: 0.7870 (tp30) cc_final: 0.7652 (tp30) REVERT: A 428 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7561 (mptt) REVERT: A 450 GLU cc_start: 0.6639 (pt0) cc_final: 0.6314 (pp20) REVERT: A 496 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7256 (mt0) REVERT: A 605 LYS cc_start: 0.6579 (ptmt) cc_final: 0.6241 (mptp) REVERT: B 266 ASN cc_start: 0.7805 (t0) cc_final: 0.7568 (t0) REVERT: B 407 ARG cc_start: 0.7746 (tpt170) cc_final: 0.7420 (tpm-80) REVERT: B 428 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7591 (mptt) REVERT: B 450 GLU cc_start: 0.6603 (pt0) cc_final: 0.6306 (pp20) REVERT: B 496 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7266 (mt0) REVERT: B 605 LYS cc_start: 0.6603 (ptmt) cc_final: 0.6248 (mptp) REVERT: C 266 ASN cc_start: 0.7802 (t0) cc_final: 0.7564 (t0) REVERT: C 407 ARG cc_start: 0.7759 (tpt170) cc_final: 0.7430 (tpm-80) REVERT: C 428 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7584 (mptt) REVERT: C 450 GLU cc_start: 0.6626 (pt0) cc_final: 0.6305 (pp20) REVERT: C 496 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7267 (mt0) REVERT: C 605 LYS cc_start: 0.6580 (ptmt) cc_final: 0.6230 (mptp) REVERT: D 266 ASN cc_start: 0.7812 (t0) cc_final: 0.7556 (t0) REVERT: D 407 ARG cc_start: 0.7735 (tpt170) cc_final: 0.7416 (tpm-80) REVERT: D 428 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7564 (mptt) REVERT: D 450 GLU cc_start: 0.6592 (pt0) cc_final: 0.6293 (pp20) REVERT: D 496 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7257 (mt0) REVERT: D 605 LYS cc_start: 0.6582 (ptmt) cc_final: 0.6240 (mptp) outliers start: 13 outliers final: 4 residues processed: 193 average time/residue: 0.6745 time to fit residues: 142.6068 Evaluate side-chains 173 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 155 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119745 restraints weight = 17908.584| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.78 r_work: 0.3128 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15196 Z= 0.131 Angle : 0.506 8.258 20608 Z= 0.263 Chirality : 0.040 0.143 2312 Planarity : 0.003 0.027 2540 Dihedral : 12.719 150.169 2120 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.36 % Allowed : 12.16 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1792 helix: 1.27 (0.16), residues: 1068 sheet: 0.19 (0.70), residues: 56 loop : -0.18 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 462 TYR 0.014 0.001 TYR A 349 PHE 0.012 0.001 PHE A 535 TRP 0.019 0.002 TRP C 168 HIS 0.001 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00297 (15196) covalent geometry : angle 0.50597 (20608) hydrogen bonds : bond 0.03701 ( 904) hydrogen bonds : angle 4.58986 ( 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 193 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.621 Fit side-chains REVERT: A 228 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 266 ASN cc_start: 0.7989 (t0) cc_final: 0.7716 (t0) REVERT: A 341 GLU cc_start: 0.8126 (tp30) cc_final: 0.7880 (tp30) REVERT: A 428 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7506 (mptt) REVERT: A 450 GLU cc_start: 0.6735 (pt0) cc_final: 0.6317 (pp20) REVERT: A 496 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7359 (mt0) REVERT: A 605 LYS cc_start: 0.6713 (ptmt) cc_final: 0.6342 (mptp) REVERT: B 228 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 266 ASN cc_start: 0.8036 (t0) cc_final: 0.7763 (t0) REVERT: B 428 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7542 (mptt) REVERT: B 450 GLU cc_start: 0.6747 (pt0) cc_final: 0.6305 (pp20) REVERT: B 496 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7358 (mt0) REVERT: B 605 LYS cc_start: 0.6766 (ptmt) cc_final: 0.6364 (mptp) REVERT: C 228 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8227 (mm) REVERT: C 232 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7054 (mm-30) REVERT: C 266 ASN cc_start: 0.8009 (t0) cc_final: 0.7741 (t0) REVERT: C 428 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7536 (mptt) REVERT: C 450 GLU cc_start: 0.6754 (pt0) cc_final: 0.6296 (pp20) REVERT: C 496 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7348 (mt0) REVERT: C 605 LYS cc_start: 0.6715 (ptmt) cc_final: 0.6341 (mptp) REVERT: D 228 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8253 (mm) REVERT: D 266 ASN cc_start: 0.8002 (t0) cc_final: 0.7729 (t0) REVERT: D 428 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7503 (mptt) REVERT: D 450 GLU cc_start: 0.6731 (pt0) cc_final: 0.6294 (pp20) REVERT: D 496 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7370 (mt0) REVERT: D 605 LYS cc_start: 0.6757 (ptmt) cc_final: 0.6344 (mptp) outliers start: 22 outliers final: 11 residues processed: 182 average time/residue: 0.7038 time to fit residues: 139.3953 Evaluate side-chains 181 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120552 restraints weight = 17850.950| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.65 r_work: 0.3144 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15196 Z= 0.150 Angle : 0.516 7.383 20608 Z= 0.269 Chirality : 0.040 0.141 2312 Planarity : 0.004 0.027 2540 Dihedral : 12.698 148.689 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.48 % Allowed : 12.59 % Favored : 85.93 % 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: 1.02 (0.20), residues: 1792 helix: 1.25 (0.16), residues: 1068 sheet: 0.22 (0.66), residues: 56 loop : -0.08 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 462 TYR 0.017 0.001 TYR A 349 PHE 0.013 0.001 PHE C 389 TRP 0.020 0.001 TRP D 168 HIS 0.002 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00345 (15196) covalent geometry : angle 0.51579 (20608) hydrogen bonds : bond 0.03788 ( 904) hydrogen bonds : angle 4.60017 ( 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 198 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.705 Fit side-chains REVERT: A 228 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 232 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7064 (mm-30) REVERT: A 266 ASN cc_start: 0.7918 (t0) cc_final: 0.7652 (t0) REVERT: A 341 GLU cc_start: 0.8051 (tp30) cc_final: 0.7821 (tp30) REVERT: A 428 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7482 (mptt) REVERT: A 450 GLU cc_start: 0.6719 (pt0) cc_final: 0.6316 (pp20) REVERT: A 496 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7296 (mt0) REVERT: A 605 LYS cc_start: 0.6769 (ptmt) cc_final: 0.6361 (mptp) REVERT: B 228 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8191 (mm) REVERT: B 232 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7059 (mm-30) REVERT: B 266 ASN cc_start: 0.7937 (t0) cc_final: 0.7666 (t0) REVERT: B 428 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7521 (mptt) REVERT: B 450 GLU cc_start: 0.6689 (pt0) cc_final: 0.6289 (pp20) REVERT: B 496 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7323 (mt0) REVERT: B 605 LYS cc_start: 0.6810 (ptmt) cc_final: 0.6389 (mptp) REVERT: C 228 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8166 (mm) REVERT: C 232 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7081 (mm-30) REVERT: C 266 ASN cc_start: 0.7920 (t0) cc_final: 0.7655 (t0) REVERT: C 428 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7515 (mptt) REVERT: C 450 GLU cc_start: 0.6684 (pt0) cc_final: 0.6274 (pp20) REVERT: C 496 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7300 (mt0) REVERT: C 605 LYS cc_start: 0.6781 (ptmt) cc_final: 0.6363 (mptp) REVERT: D 228 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8216 (mm) REVERT: D 232 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 266 ASN cc_start: 0.7914 (t0) cc_final: 0.7645 (t0) REVERT: D 428 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7490 (mptt) REVERT: D 450 GLU cc_start: 0.6640 (pt0) cc_final: 0.6257 (pp20) REVERT: D 496 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7317 (mt0) REVERT: D 605 LYS cc_start: 0.6776 (ptmt) cc_final: 0.6362 (mptp) outliers start: 24 outliers final: 11 residues processed: 187 average time/residue: 0.7058 time to fit residues: 143.8250 Evaluate side-chains 181 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN B 444 ASN C 395 ASN C 419 GLN C 444 ASN D 395 ASN D 419 GLN D 444 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118962 restraints weight = 17760.616| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.76 r_work: 0.3102 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15196 Z= 0.194 Angle : 0.559 9.222 20608 Z= 0.287 Chirality : 0.042 0.139 2312 Planarity : 0.004 0.031 2540 Dihedral : 12.740 145.336 2120 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.73 % Allowed : 13.21 % Favored : 85.06 % 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: 0.93 (0.20), residues: 1792 helix: 1.15 (0.16), residues: 1068 sheet: 0.71 (0.68), residues: 48 loop : -0.12 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 347 TYR 0.019 0.002 TYR D 349 PHE 0.015 0.002 PHE C 389 TRP 0.021 0.002 TRP D 168 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00449 (15196) covalent geometry : angle 0.55857 (20608) hydrogen bonds : bond 0.04000 ( 904) hydrogen bonds : angle 4.72915 ( 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 198 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.609 Fit side-chains REVERT: A 232 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 266 ASN cc_start: 0.8033 (t0) cc_final: 0.7795 (t0) REVERT: A 341 GLU cc_start: 0.8148 (tp30) cc_final: 0.7887 (tp30) REVERT: A 389 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: A 428 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7505 (mptt) REVERT: A 450 GLU cc_start: 0.6778 (pt0) cc_final: 0.6361 (pp20) REVERT: A 475 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7432 (ptpt) REVERT: A 496 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7388 (mt0) REVERT: A 605 LYS cc_start: 0.6977 (ptmt) cc_final: 0.6494 (mptp) REVERT: B 232 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 266 ASN cc_start: 0.8050 (t0) cc_final: 0.7809 (t0) REVERT: B 389 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: B 428 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7527 (mptt) REVERT: B 450 GLU cc_start: 0.6782 (pt0) cc_final: 0.6422 (pp20) REVERT: B 496 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7337 (mt0) REVERT: B 605 LYS cc_start: 0.6997 (ptmt) cc_final: 0.6517 (mptp) REVERT: C 228 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 232 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7110 (mm-30) REVERT: C 266 ASN cc_start: 0.8058 (t0) cc_final: 0.7811 (t0) REVERT: C 389 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: C 428 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7502 (mptt) REVERT: C 450 GLU cc_start: 0.6762 (pt0) cc_final: 0.6373 (pp20) REVERT: C 475 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7439 (ptpt) REVERT: C 496 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7386 (mt0) REVERT: C 605 LYS cc_start: 0.6861 (ptmt) cc_final: 0.6389 (mptp) REVERT: D 232 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7113 (mm-30) REVERT: D 266 ASN cc_start: 0.8021 (t0) cc_final: 0.7781 (t0) REVERT: D 389 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: D 428 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7490 (mptt) REVERT: D 450 GLU cc_start: 0.6740 (pt0) cc_final: 0.6357 (pp20) REVERT: D 475 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7435 (ptpt) REVERT: D 496 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7394 (mt0) REVERT: D 605 LYS cc_start: 0.6996 (ptmt) cc_final: 0.6514 (mptp) outliers start: 28 outliers final: 15 residues processed: 186 average time/residue: 0.7141 time to fit residues: 144.1842 Evaluate side-chains 186 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 178 optimal weight: 0.0020 chunk 97 optimal weight: 7.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124369 restraints weight = 17743.604| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.74 r_work: 0.3186 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15196 Z= 0.105 Angle : 0.496 8.899 20608 Z= 0.253 Chirality : 0.039 0.145 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.610 146.927 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.74 % Allowed : 14.69 % 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: 1.31 (0.20), residues: 1792 helix: 1.48 (0.16), residues: 1064 sheet: 0.66 (0.66), residues: 48 loop : 0.01 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 218 TYR 0.013 0.001 TYR C 199 PHE 0.010 0.001 PHE D 535 TRP 0.020 0.001 TRP D 168 HIS 0.001 0.000 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00226 (15196) covalent geometry : angle 0.49563 (20608) hydrogen bonds : bond 0.03481 ( 904) hydrogen bonds : angle 4.43806 ( 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 175 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.607 Fit side-chains REVERT: A 232 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6977 (mm-30) REVERT: A 266 ASN cc_start: 0.7891 (t0) cc_final: 0.7610 (t0) REVERT: A 341 GLU cc_start: 0.8073 (tp30) cc_final: 0.7856 (tp30) REVERT: A 428 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7516 (mptt) REVERT: A 450 GLU cc_start: 0.6599 (pt0) cc_final: 0.6262 (pp20) REVERT: A 496 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7337 (mt0) REVERT: A 540 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: A 605 LYS cc_start: 0.6738 (ptmt) cc_final: 0.6391 (mptp) REVERT: B 232 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7009 (mm-30) REVERT: B 266 ASN cc_start: 0.7898 (t0) cc_final: 0.7620 (t0) REVERT: B 428 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7538 (mptt) REVERT: B 450 GLU cc_start: 0.6634 (pt0) cc_final: 0.6284 (pp20) REVERT: B 496 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7337 (mt0) REVERT: B 540 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: B 605 LYS cc_start: 0.6760 (ptmt) cc_final: 0.6405 (mptp) REVERT: C 228 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 232 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6993 (mm-30) REVERT: C 266 ASN cc_start: 0.7907 (t0) cc_final: 0.7627 (t0) REVERT: C 428 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7546 (mptt) REVERT: C 450 GLU cc_start: 0.6660 (pt0) cc_final: 0.6274 (pp20) REVERT: C 496 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7324 (mt0) REVERT: C 540 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: C 605 LYS cc_start: 0.6741 (ptmt) cc_final: 0.6388 (mptp) REVERT: D 232 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6959 (mm-30) REVERT: D 266 ASN cc_start: 0.7868 (t0) cc_final: 0.7593 (t0) REVERT: D 428 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7499 (mptt) REVERT: D 450 GLU cc_start: 0.6656 (pt0) cc_final: 0.6283 (pp20) REVERT: D 496 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7331 (mt0) REVERT: D 540 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: D 605 LYS cc_start: 0.6737 (ptmt) cc_final: 0.6396 (mptp) outliers start: 12 outliers final: 7 residues processed: 164 average time/residue: 0.7408 time to fit residues: 131.9314 Evaluate side-chains 164 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 157 optimal weight: 0.5980 chunk 145 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 146 optimal weight: 0.0370 chunk 178 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN A 422 HIS B 395 ASN B 419 GLN B 422 HIS C 395 ASN C 419 GLN C 422 HIS D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122280 restraints weight = 17874.641| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.73 r_work: 0.3153 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2672 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= 0.118 Angle : 0.506 8.380 20608 Z= 0.257 Chirality : 0.039 0.142 2312 Planarity : 0.004 0.035 2540 Dihedral : 12.598 146.113 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.11 % Allowed : 14.94 % Favored : 83.95 % 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: 1.37 (0.20), residues: 1792 helix: 1.55 (0.16), residues: 1064 sheet: 0.52 (0.66), residues: 48 loop : 0.01 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 347 TYR 0.012 0.001 TYR A 349 PHE 0.013 0.001 PHE A 535 TRP 0.018 0.001 TRP C 168 HIS 0.001 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00266 (15196) covalent geometry : angle 0.50650 (20608) hydrogen bonds : bond 0.03512 ( 904) hydrogen bonds : angle 4.43609 ( 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 186 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.643 Fit side-chains REVERT: A 232 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7049 (mm-30) REVERT: A 266 ASN cc_start: 0.7995 (t0) cc_final: 0.7717 (t0) REVERT: A 428 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7501 (mptt) REVERT: A 450 GLU cc_start: 0.6652 (pt0) cc_final: 0.6299 (pp20) REVERT: A 496 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7403 (mt0) REVERT: A 605 LYS cc_start: 0.6774 (ptmt) cc_final: 0.6381 (mptp) REVERT: B 232 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7058 (mm-30) REVERT: B 266 ASN cc_start: 0.7965 (t0) cc_final: 0.7690 (t0) REVERT: B 428 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7531 (mptt) REVERT: B 450 GLU cc_start: 0.6649 (pt0) cc_final: 0.6297 (pp20) REVERT: B 496 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7399 (mt0) REVERT: B 605 LYS cc_start: 0.6804 (ptmt) cc_final: 0.6405 (mptp) REVERT: C 232 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7049 (mm-30) REVERT: C 266 ASN cc_start: 0.7984 (t0) cc_final: 0.7704 (t0) REVERT: C 450 GLU cc_start: 0.6723 (pt0) cc_final: 0.6320 (pp20) REVERT: C 496 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7369 (mt0) REVERT: C 605 LYS cc_start: 0.6751 (ptmt) cc_final: 0.6376 (mptp) REVERT: D 232 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7032 (mm-30) REVERT: D 266 ASN cc_start: 0.7952 (t0) cc_final: 0.7672 (t0) REVERT: D 428 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7495 (mptt) REVERT: D 450 GLU cc_start: 0.6659 (pt0) cc_final: 0.6274 (pp20) REVERT: D 496 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7418 (mt0) REVERT: D 605 LYS cc_start: 0.6780 (ptmt) cc_final: 0.6394 (mptp) outliers start: 18 outliers final: 16 residues processed: 174 average time/residue: 0.7084 time to fit residues: 134.3128 Evaluate side-chains 176 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 402 ASN A 419 GLN A 422 HIS B 395 ASN B 419 GLN B 422 HIS C 395 ASN C 419 GLN C 422 HIS D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124204 restraints weight = 17926.639| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.96 r_work: 0.3146 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15196 Z= 0.123 Angle : 0.502 8.072 20608 Z= 0.258 Chirality : 0.040 0.142 2312 Planarity : 0.004 0.028 2540 Dihedral : 12.595 146.189 2120 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.11 % Allowed : 16.05 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.42 (0.20), residues: 1792 helix: 1.57 (0.16), residues: 1064 sheet: 0.56 (0.67), residues: 48 loop : 0.07 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.012 0.001 TYR A 349 PHE 0.011 0.001 PHE D 535 TRP 0.019 0.001 TRP C 168 HIS 0.001 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00278 (15196) covalent geometry : angle 0.50190 (20608) hydrogen bonds : bond 0.03533 ( 904) hydrogen bonds : angle 4.43424 ( 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 179 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.655 Fit side-chains REVERT: A 232 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 266 ASN cc_start: 0.7686 (t0) cc_final: 0.7451 (t0) REVERT: A 450 GLU cc_start: 0.6579 (pt0) cc_final: 0.6262 (pp20) REVERT: A 496 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7291 (mt0) REVERT: A 605 LYS cc_start: 0.6681 (ptmt) cc_final: 0.6334 (mptp) REVERT: B 232 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 266 ASN cc_start: 0.7683 (t0) cc_final: 0.7445 (t0) REVERT: B 450 GLU cc_start: 0.6576 (pt0) cc_final: 0.6256 (pp20) REVERT: B 496 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7287 (mt0) REVERT: B 605 LYS cc_start: 0.6690 (ptmt) cc_final: 0.6349 (mptp) REVERT: C 232 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 266 ASN cc_start: 0.7691 (t0) cc_final: 0.7450 (t0) REVERT: C 450 GLU cc_start: 0.6583 (pt0) cc_final: 0.6266 (pp20) REVERT: C 496 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7309 (mt0) REVERT: C 605 LYS cc_start: 0.6690 (ptmt) cc_final: 0.6355 (mptp) REVERT: D 232 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6979 (mm-30) REVERT: D 266 ASN cc_start: 0.7668 (t0) cc_final: 0.7428 (t0) REVERT: D 450 GLU cc_start: 0.6538 (pt0) cc_final: 0.6248 (pp20) REVERT: D 496 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7265 (mt0) REVERT: D 605 LYS cc_start: 0.6679 (ptmt) cc_final: 0.6335 (mptp) outliers start: 18 outliers final: 12 residues processed: 166 average time/residue: 0.7130 time to fit residues: 128.9856 Evaluate side-chains 163 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN A 422 HIS B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120086 restraints weight = 17880.206| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.71 r_work: 0.3114 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15196 Z= 0.147 Angle : 0.529 8.473 20608 Z= 0.272 Chirality : 0.040 0.140 2312 Planarity : 0.004 0.032 2540 Dihedral : 12.628 145.564 2120 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.05 % Allowed : 16.11 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1792 helix: 1.36 (0.15), residues: 1088 sheet: 0.51 (0.66), residues: 48 loop : 0.02 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.015 0.001 TYR D 349 PHE 0.013 0.001 PHE C 535 TRP 0.019 0.001 TRP C 168 HIS 0.002 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00338 (15196) covalent geometry : angle 0.52941 (20608) hydrogen bonds : bond 0.03671 ( 904) hydrogen bonds : angle 4.51529 ( 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 169 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.596 Fit side-chains REVERT: A 226 GLN cc_start: 0.8113 (mp10) cc_final: 0.7755 (mm110) REVERT: A 232 GLU cc_start: 0.7234 (mm-30) cc_final: 0.7004 (mm-30) REVERT: A 266 ASN cc_start: 0.7682 (t0) cc_final: 0.7477 (t0) REVERT: A 450 GLU cc_start: 0.6614 (pt0) cc_final: 0.6276 (pp20) REVERT: A 496 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7291 (mt0) REVERT: A 605 LYS cc_start: 0.6650 (ptmt) cc_final: 0.6310 (mptp) REVERT: B 232 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 266 ASN cc_start: 0.7680 (t0) cc_final: 0.7474 (t0) REVERT: B 450 GLU cc_start: 0.6639 (pt0) cc_final: 0.6319 (pp20) REVERT: B 496 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7293 (mt0) REVERT: B 605 LYS cc_start: 0.6697 (ptmt) cc_final: 0.6354 (mptp) REVERT: C 232 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7044 (mm-30) REVERT: C 266 ASN cc_start: 0.7694 (t0) cc_final: 0.7491 (t0) REVERT: C 450 GLU cc_start: 0.6630 (pt0) cc_final: 0.6300 (pp20) REVERT: C 496 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7308 (mt0) REVERT: C 605 LYS cc_start: 0.6694 (ptmt) cc_final: 0.6343 (mptp) REVERT: D 232 GLU cc_start: 0.7240 (mm-30) cc_final: 0.7011 (mm-30) REVERT: D 266 ASN cc_start: 0.7660 (t0) cc_final: 0.7458 (t0) REVERT: D 450 GLU cc_start: 0.6596 (pt0) cc_final: 0.6270 (pp20) REVERT: D 496 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7277 (mt0) REVERT: D 605 LYS cc_start: 0.6688 (ptmt) cc_final: 0.6347 (mptp) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.6962 time to fit residues: 121.6620 Evaluate side-chains 162 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120280 restraints weight = 17928.398| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.66 r_work: 0.3145 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15196 Z= 0.148 Angle : 0.531 8.025 20608 Z= 0.272 Chirality : 0.040 0.140 2312 Planarity : 0.004 0.027 2540 Dihedral : 12.634 145.486 2120 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.93 % Allowed : 16.05 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1792 helix: 1.35 (0.15), residues: 1088 sheet: 0.48 (0.66), residues: 48 loop : -0.01 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.015 0.001 TYR A 349 PHE 0.012 0.001 PHE B 535 TRP 0.019 0.001 TRP D 168 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00340 (15196) covalent geometry : angle 0.53057 (20608) hydrogen bonds : bond 0.03682 ( 904) hydrogen bonds : angle 4.53144 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4894.89 seconds wall clock time: 84 minutes 29.45 seconds (5069.45 seconds total)