Starting phenix.real_space_refine on Tue Nov 18 14:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfy_23309/11_2025/7lfy_23309_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfy_23309/11_2025/7lfy_23309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lfy_23309/11_2025/7lfy_23309_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfy_23309/11_2025/7lfy_23309_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lfy_23309/11_2025/7lfy_23309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfy_23309/11_2025/7lfy_23309.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 Na 3 4.78 5 C 9684 2.51 5 N 2396 2.21 5 O 2688 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: 14851 Number of models: 1 Model: "" Number of chains: 6 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {' NA': 3, 'PCG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.33, per 1000 atoms: 0.22 Number of scatterers: 14851 At special positions: 0 Unit cell: (96.993, 96.993, 114.402, 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) S 76 16.00 P 4 15.00 Na 3 11.00 O 2688 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: 1.22 Conformation dependent library (CDL) restraints added in 639.3 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: 0.50 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: 5.260A 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: 3.536A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.518A 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: 5.278A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.237A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 591 through 605 removed outlier: 3.641A 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: 3.587A 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: 3.770A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.735A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.610A 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: 5.276A pdb=" N ARG B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 removed outlier: 3.524A pdb=" N VAL B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.727A 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: 3.642A 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: 5.252A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.536A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.587A 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: 3.611A 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: 5.278A 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: 5.041A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.642A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.253A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.537A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.589A 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: 3.770A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.057A 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: 3.520A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.525A 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: 3.726A 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: 5.135A 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: 6.495A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.860A 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: 5.135A 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: 4.722A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.674A 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: 4.722A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.723A 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: 7.058A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.723A 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: 5.402A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.737A 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: 4.724A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.675A 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: 5.402A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.737A 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: 4.724A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.675A 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: 2.44 Time building geometry restraints manager: 1.56 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: 4290 1.34 - 1.45: 2431 1.45 - 1.57: 8339 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 2.77e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.73e+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 2.70e+01 bond pdb=" C1' PCG C 701 " pdb=" O4' PCG C 701 " ideal model delta sigma weight residual 1.409 1.478 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 20206 1.85 - 3.71: 282 3.71 - 5.56: 72 5.56 - 7.41: 24 7.41 - 9.27: 24 Bond angle restraints: 20608 Sorted by residual: angle pdb=" N ARG C 291 " pdb=" CA ARG C 291 " pdb=" C ARG C 291 " ideal model delta sigma weight residual 112.89 119.23 -6.34 1.24e+00 6.50e-01 2.62e+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 112.89 119.15 -6.26 1.24e+00 6.50e-01 2.55e+01 angle pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " pdb=" O3' PCG B 701 " ideal model delta sigma weight residual 100.83 110.10 -9.27 3.00e+00 1.11e-01 9.54e+00 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 8794 28.99 - 57.98: 286 57.98 - 86.97: 8 86.97 - 115.96: 4 115.96 - 144.95: 12 Dihedral angle restraints: 9104 sinusoidal: 3788 harmonic: 5316 Sorted by residual: dihedral pdb=" C3' PCG B 701 " pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O1A PCG B 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.64 -144.95 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG C 701 " pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O1A PCG C 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.66 -144.93 1 3.00e+01 1.11e-03 1.94e+01 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 -63.70 -144.89 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: 2277 0.131 - 0.263: 27 0.263 - 0.394: 4 0.394 - 0.525: 0 0.525 - 0.656: 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 A 701 " pdb=" O2A PCG A 701 " pdb=" O3' PCG A 701 " pdb=" O5' PCG A 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 1.07e+01 ... (remaining 2309 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 526 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+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 D 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+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 B 526 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+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: 2645 2.76 - 3.30: 15666 3.30 - 3.83: 26920 3.83 - 4.37: 32545 4.37 - 4.90: 53456 Nonbonded interactions: 131232 Sorted by model distance: nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.227 3.040 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.227 3.040 nonbonded pdb=" OE2 GLU C 365 " pdb="NA NA A 704 " model vdw 2.290 2.470 ... (remaining 131227 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.000 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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= 0.232 Angle : 0.697 9.268 20608 Z= 0.370 Chirality : 0.052 0.656 2312 Planarity : 0.003 0.028 2540 Dihedral : 14.963 144.954 5696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.25 % Allowed : 2.65 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1792 helix: -0.53 (0.14), residues: 1080 sheet: -1.26 (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 0.015 0.001 TYR C 349 PHE 0.014 0.002 PHE B 389 TRP 0.024 0.002 TRP D 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00482 (15196) covalent geometry : angle 0.69656 (20608) hydrogen bonds : bond 0.12175 ( 904) hydrogen bonds : angle 6.69127 ( 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 386 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 382 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7504 (m-30) cc_final: 0.6936 (m-30) REVERT: A 269 GLU cc_start: 0.8228 (pm20) cc_final: 0.7767 (pt0) REVERT: A 302 ASN cc_start: 0.8411 (t0) cc_final: 0.7873 (t0) REVERT: A 305 MET cc_start: 0.7662 (ttp) cc_final: 0.7418 (ttm) REVERT: A 399 MET cc_start: 0.6409 (mtt) cc_final: 0.6177 (mtt) REVERT: A 604 MET cc_start: 0.4282 (mmt) cc_final: 0.3997 (mpp) REVERT: B 204 ASP cc_start: 0.7497 (m-30) cc_final: 0.6922 (m-30) REVERT: B 269 GLU cc_start: 0.8257 (pm20) cc_final: 0.7761 (pt0) REVERT: B 305 MET cc_start: 0.7631 (ttp) cc_final: 0.7391 (ttm) REVERT: B 399 MET cc_start: 0.6383 (mtt) cc_final: 0.6179 (mtt) REVERT: B 604 MET cc_start: 0.4176 (mmt) cc_final: 0.3880 (mpp) REVERT: C 204 ASP cc_start: 0.7498 (m-30) cc_final: 0.6925 (m-30) REVERT: C 269 GLU cc_start: 0.8237 (pm20) cc_final: 0.7747 (pt0) REVERT: C 305 MET cc_start: 0.7641 (ttp) cc_final: 0.7371 (ttm) REVERT: C 399 MET cc_start: 0.6383 (mtt) cc_final: 0.6067 (mtt) REVERT: C 604 MET cc_start: 0.4174 (mmt) cc_final: 0.3894 (mpp) REVERT: D 204 ASP cc_start: 0.7502 (m-30) cc_final: 0.6933 (m-30) REVERT: D 269 GLU cc_start: 0.8245 (pm20) cc_final: 0.7773 (pt0) REVERT: D 302 ASN cc_start: 0.8386 (t0) cc_final: 0.7839 (t0) REVERT: D 305 MET cc_start: 0.7672 (ttp) cc_final: 0.7400 (ttm) REVERT: D 399 MET cc_start: 0.6408 (mtt) cc_final: 0.6095 (mtt) REVERT: D 604 MET cc_start: 0.4206 (mmt) cc_final: 0.3949 (mpp) outliers start: 4 outliers final: 0 residues processed: 386 average time/residue: 0.1495 time to fit residues: 81.3853 Evaluate side-chains 204 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 302 ASN A 402 ASN A 411 GLN A 468 ASN A 496 GLN B 238 ASN B 302 ASN B 402 ASN B 411 GLN B 468 ASN B 496 GLN C 238 ASN C 302 ASN C 402 ASN C 411 GLN C 468 ASN C 496 GLN D 238 ASN D 302 ASN D 402 ASN D 411 GLN D 468 ASN D 496 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114010 restraints weight = 21370.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113828 restraints weight = 20446.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114258 restraints weight = 16747.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114709 restraints weight = 14985.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115061 restraints weight = 12930.608| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15196 Z= 0.180 Angle : 0.594 8.103 20608 Z= 0.308 Chirality : 0.043 0.142 2312 Planarity : 0.004 0.043 2540 Dihedral : 13.008 154.137 2120 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.48 % Allowed : 10.74 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1792 helix: 0.73 (0.16), residues: 1060 sheet: -1.06 (0.70), residues: 56 loop : -0.36 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 291 TYR 0.019 0.001 TYR B 349 PHE 0.014 0.002 PHE D 574 TRP 0.021 0.002 TRP B 168 HIS 0.004 0.002 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00416 (15196) covalent geometry : angle 0.59429 (20608) hydrogen bonds : bond 0.04179 ( 904) hydrogen bonds : angle 4.92665 ( 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 262 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7813 (m-30) cc_final: 0.7294 (m-30) REVERT: A 269 GLU cc_start: 0.8208 (pm20) cc_final: 0.7801 (pt0) REVERT: A 302 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8156 (t0) REVERT: A 578 LYS cc_start: 0.4994 (tttm) cc_final: 0.4226 (tmmt) REVERT: A 604 MET cc_start: 0.4184 (mmt) cc_final: 0.3575 (mpp) REVERT: B 204 ASP cc_start: 0.7806 (m-30) cc_final: 0.7276 (m-30) REVERT: B 269 GLU cc_start: 0.8198 (pm20) cc_final: 0.7800 (pt0) REVERT: B 302 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8115 (t0) REVERT: B 604 MET cc_start: 0.4188 (mmt) cc_final: 0.3589 (mpp) REVERT: C 204 ASP cc_start: 0.7813 (m-30) cc_final: 0.7258 (m-30) REVERT: C 269 GLU cc_start: 0.8210 (pm20) cc_final: 0.7779 (pt0) REVERT: C 302 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8128 (t0) REVERT: C 578 LYS cc_start: 0.4974 (tttm) cc_final: 0.4045 (tmmt) REVERT: C 604 MET cc_start: 0.4178 (mmt) cc_final: 0.3584 (mpp) REVERT: D 204 ASP cc_start: 0.7815 (m-30) cc_final: 0.7290 (m-30) REVERT: D 269 GLU cc_start: 0.8206 (pm20) cc_final: 0.7791 (pt0) REVERT: D 302 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8167 (t0) REVERT: D 578 LYS cc_start: 0.5035 (tttm) cc_final: 0.4161 (tmmt) REVERT: D 604 MET cc_start: 0.4172 (mmt) cc_final: 0.3585 (mpp) outliers start: 24 outliers final: 17 residues processed: 239 average time/residue: 0.1106 time to fit residues: 41.1318 Evaluate side-chains 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 0.0020 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 314 ASN B 302 ASN B 314 ASN C 302 ASN C 314 ASN D 302 ASN D 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.145310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116787 restraints weight = 21274.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117146 restraints weight = 19490.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118224 restraints weight = 15239.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118486 restraints weight = 11806.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118534 restraints weight = 11295.850| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15196 Z= 0.118 Angle : 0.503 7.176 20608 Z= 0.264 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.732 150.038 2120 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 11.11 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1792 helix: 1.06 (0.16), residues: 1080 sheet: -0.46 (0.72), residues: 56 loop : -0.53 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 347 TYR 0.011 0.001 TYR C 196 PHE 0.010 0.001 PHE A 298 TRP 0.017 0.001 TRP C 168 HIS 0.004 0.002 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00258 (15196) covalent geometry : angle 0.50346 (20608) hydrogen bonds : bond 0.03718 ( 904) hydrogen bonds : angle 4.50179 ( 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 253 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.9129 (tp) cc_final: 0.8918 (tp) REVERT: A 204 ASP cc_start: 0.7780 (m-30) cc_final: 0.7276 (m-30) REVERT: A 229 LEU cc_start: 0.8368 (tp) cc_final: 0.8071 (tp) REVERT: A 269 GLU cc_start: 0.8154 (pm20) cc_final: 0.7683 (pt0) REVERT: A 302 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 604 MET cc_start: 0.4062 (mmt) cc_final: 0.3538 (mpp) REVERT: B 172 ILE cc_start: 0.9128 (tp) cc_final: 0.8913 (tp) REVERT: B 204 ASP cc_start: 0.7774 (m-30) cc_final: 0.7274 (m-30) REVERT: B 269 GLU cc_start: 0.8152 (pm20) cc_final: 0.7680 (pt0) REVERT: B 302 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8151 (t0) REVERT: B 604 MET cc_start: 0.4079 (mmt) cc_final: 0.3551 (mpp) REVERT: C 172 ILE cc_start: 0.9122 (tp) cc_final: 0.8915 (tp) REVERT: C 204 ASP cc_start: 0.7786 (m-30) cc_final: 0.7282 (m-30) REVERT: C 269 GLU cc_start: 0.8158 (pm20) cc_final: 0.7670 (pt0) REVERT: C 302 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8169 (t0) REVERT: C 604 MET cc_start: 0.4032 (mmt) cc_final: 0.3530 (mpp) REVERT: D 172 ILE cc_start: 0.9118 (tp) cc_final: 0.8914 (tp) REVERT: D 204 ASP cc_start: 0.7783 (m-30) cc_final: 0.7276 (m-30) REVERT: D 269 GLU cc_start: 0.8153 (pm20) cc_final: 0.7680 (pt0) REVERT: D 302 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8194 (t0) REVERT: D 578 LYS cc_start: 0.4878 (tttm) cc_final: 0.4471 (tmmt) REVERT: D 604 MET cc_start: 0.4022 (mmt) cc_final: 0.3537 (mpp) outliers start: 29 outliers final: 8 residues processed: 234 average time/residue: 0.1186 time to fit residues: 42.3513 Evaluate side-chains 207 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 465 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 238 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117039 restraints weight = 21172.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115624 restraints weight = 20898.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116001 restraints weight = 17594.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116492 restraints weight = 15718.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116712 restraints weight = 13712.435| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15196 Z= 0.128 Angle : 0.500 7.414 20608 Z= 0.261 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.757 151.255 2120 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.90 % Allowed : 12.04 % 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: 0.91 (0.20), residues: 1792 helix: 1.24 (0.16), residues: 1080 sheet: 0.02 (0.73), residues: 56 loop : -0.30 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.013 0.001 TYR B 196 PHE 0.010 0.001 PHE B 298 TRP 0.016 0.001 TRP B 168 HIS 0.004 0.002 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00287 (15196) covalent geometry : angle 0.50045 (20608) hydrogen bonds : bond 0.03585 ( 904) hydrogen bonds : angle 4.39364 ( 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 256 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7754 (m-30) cc_final: 0.7341 (m-30) REVERT: A 269 GLU cc_start: 0.8130 (pm20) cc_final: 0.7694 (pt0) REVERT: A 604 MET cc_start: 0.4186 (mmt) cc_final: 0.3641 (mpp) REVERT: B 172 ILE cc_start: 0.9155 (tp) cc_final: 0.8951 (tp) REVERT: B 204 ASP cc_start: 0.7753 (m-30) cc_final: 0.7396 (m-30) REVERT: B 269 GLU cc_start: 0.8120 (pm20) cc_final: 0.7677 (pt0) REVERT: B 604 MET cc_start: 0.4193 (mmt) cc_final: 0.3630 (mpp) REVERT: C 172 ILE cc_start: 0.9133 (tp) cc_final: 0.8928 (tp) REVERT: C 204 ASP cc_start: 0.7771 (m-30) cc_final: 0.7325 (m-30) REVERT: C 269 GLU cc_start: 0.8128 (pm20) cc_final: 0.7686 (pt0) REVERT: C 604 MET cc_start: 0.4161 (mmt) cc_final: 0.3626 (mpp) REVERT: D 172 ILE cc_start: 0.9153 (tp) cc_final: 0.8946 (tp) REVERT: D 204 ASP cc_start: 0.7764 (m-30) cc_final: 0.7353 (m-30) REVERT: D 269 GLU cc_start: 0.8134 (pm20) cc_final: 0.7701 (pt0) REVERT: D 578 LYS cc_start: 0.4928 (tttm) cc_final: 0.4465 (tmmt) REVERT: D 604 MET cc_start: 0.4137 (mmt) cc_final: 0.3619 (mpp) outliers start: 47 outliers final: 30 residues processed: 234 average time/residue: 0.1082 time to fit residues: 39.7087 Evaluate side-chains 220 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 582 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 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 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113061 restraints weight = 21224.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114255 restraints weight = 15666.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114600 restraints weight = 12610.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114776 restraints weight = 11918.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114822 restraints weight = 11621.362| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3916 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= 0.143 Angle : 0.518 7.360 20608 Z= 0.269 Chirality : 0.040 0.147 2312 Planarity : 0.003 0.031 2540 Dihedral : 12.814 151.797 2120 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.15 % Allowed : 13.33 % Favored : 83.52 % 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: 1.07 (0.20), residues: 1792 helix: 1.28 (0.16), residues: 1084 sheet: 0.77 (0.79), residues: 48 loop : -0.13 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 561 TYR 0.014 0.001 TYR C 196 PHE 0.009 0.001 PHE C 261 TRP 0.017 0.001 TRP B 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00330 (15196) covalent geometry : angle 0.51765 (20608) hydrogen bonds : bond 0.03604 ( 904) hydrogen bonds : angle 4.38074 ( 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 254 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7762 (m-30) cc_final: 0.7409 (m-30) REVERT: A 269 GLU cc_start: 0.8132 (pm20) cc_final: 0.7681 (pt0) REVERT: A 596 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6199 (mm-30) REVERT: A 604 MET cc_start: 0.4475 (mmt) cc_final: 0.3755 (mpp) REVERT: B 204 ASP cc_start: 0.7757 (m-30) cc_final: 0.7403 (m-30) REVERT: B 269 GLU cc_start: 0.8113 (pm20) cc_final: 0.7666 (pt0) REVERT: B 596 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6166 (mm-30) REVERT: B 604 MET cc_start: 0.4472 (mmt) cc_final: 0.3751 (mpp) REVERT: C 172 ILE cc_start: 0.9150 (tp) cc_final: 0.8914 (tp) REVERT: C 204 ASP cc_start: 0.7762 (m-30) cc_final: 0.7415 (m-30) REVERT: C 269 GLU cc_start: 0.8113 (pm20) cc_final: 0.7674 (pt0) REVERT: C 596 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6277 (mm-30) REVERT: C 604 MET cc_start: 0.4505 (mmt) cc_final: 0.3789 (mpp) REVERT: D 204 ASP cc_start: 0.7766 (m-30) cc_final: 0.7401 (m-30) REVERT: D 269 GLU cc_start: 0.8128 (pm20) cc_final: 0.7693 (pt0) REVERT: D 578 LYS cc_start: 0.5025 (tttm) cc_final: 0.4553 (tmmt) REVERT: D 596 GLU cc_start: 0.6501 (mm-30) cc_final: 0.6247 (mm-30) REVERT: D 604 MET cc_start: 0.4480 (mmt) cc_final: 0.3772 (mpp) outliers start: 51 outliers final: 32 residues processed: 229 average time/residue: 0.1120 time to fit residues: 39.9023 Evaluate side-chains 222 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111396 restraints weight = 21183.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112603 restraints weight = 15367.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113423 restraints weight = 12657.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113724 restraints weight = 11085.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114028 restraints weight = 10611.510| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15196 Z= 0.153 Angle : 0.529 7.769 20608 Z= 0.273 Chirality : 0.041 0.148 2312 Planarity : 0.003 0.034 2540 Dihedral : 12.812 151.233 2120 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.02 % Allowed : 15.43 % Favored : 81.54 % 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: 1.11 (0.20), residues: 1792 helix: 1.29 (0.15), residues: 1084 sheet: 0.64 (0.79), residues: 48 loop : -0.07 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 291 TYR 0.015 0.001 TYR C 196 PHE 0.009 0.001 PHE C 261 TRP 0.017 0.001 TRP C 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00351 (15196) covalent geometry : angle 0.52896 (20608) hydrogen bonds : bond 0.03628 ( 904) hydrogen bonds : angle 4.40745 ( 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 262 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7649 (m-30) cc_final: 0.7337 (m-30) REVERT: A 269 GLU cc_start: 0.8132 (pm20) cc_final: 0.7685 (pt0) REVERT: B 204 ASP cc_start: 0.7645 (m-30) cc_final: 0.7314 (m-30) REVERT: B 269 GLU cc_start: 0.8120 (pm20) cc_final: 0.7670 (pt0) REVERT: B 422 HIS cc_start: 0.6675 (m170) cc_final: 0.6440 (m-70) REVERT: C 204 ASP cc_start: 0.7651 (m-30) cc_final: 0.7310 (m-30) REVERT: C 269 GLU cc_start: 0.8122 (pm20) cc_final: 0.7691 (pt0) REVERT: D 204 ASP cc_start: 0.7650 (m-30) cc_final: 0.7335 (m-30) REVERT: D 246 PHE cc_start: 0.8658 (t80) cc_final: 0.8456 (t80) REVERT: D 269 GLU cc_start: 0.8111 (pm20) cc_final: 0.7691 (pt0) REVERT: D 490 GLU cc_start: 0.5770 (mp0) cc_final: 0.5538 (mp0) REVERT: D 578 LYS cc_start: 0.5144 (tttm) cc_final: 0.4735 (tmmt) REVERT: D 604 MET cc_start: 0.4708 (mmt) cc_final: 0.3944 (mpp) outliers start: 49 outliers final: 30 residues processed: 233 average time/residue: 0.1121 time to fit residues: 40.2481 Evaluate side-chains 231 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER 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 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 175 optimal weight: 30.0000 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 163 ASN D 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112251 restraints weight = 21014.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113526 restraints weight = 15880.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114583 restraints weight = 12810.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114933 restraints weight = 10499.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115197 restraints weight = 10507.518| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15196 Z= 0.135 Angle : 0.517 7.554 20608 Z= 0.268 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.027 2540 Dihedral : 12.791 151.151 2120 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.96 % Allowed : 16.60 % Favored : 80.43 % 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: 1.21 (0.20), residues: 1792 helix: 1.37 (0.15), residues: 1084 sheet: 0.65 (0.79), residues: 48 loop : -0.01 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 347 TYR 0.014 0.001 TYR B 196 PHE 0.010 0.001 PHE B 574 TRP 0.017 0.001 TRP B 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00307 (15196) covalent geometry : angle 0.51719 (20608) hydrogen bonds : bond 0.03532 ( 904) hydrogen bonds : angle 4.33730 ( 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 244 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.667 Fit side-chains REVERT: A 204 ASP cc_start: 0.7638 (m-30) cc_final: 0.7347 (m-30) REVERT: A 269 GLU cc_start: 0.8115 (pm20) cc_final: 0.7679 (pt0) REVERT: A 578 LYS cc_start: 0.4657 (tptm) cc_final: 0.4314 (ttpt) REVERT: B 204 ASP cc_start: 0.7647 (m-30) cc_final: 0.7351 (m-30) REVERT: B 269 GLU cc_start: 0.8099 (pm20) cc_final: 0.7676 (pt0) REVERT: B 422 HIS cc_start: 0.6670 (m170) cc_final: 0.6446 (m-70) REVERT: C 204 ASP cc_start: 0.7646 (m-30) cc_final: 0.7334 (m-30) REVERT: C 269 GLU cc_start: 0.8094 (pm20) cc_final: 0.7675 (pt0) REVERT: D 204 ASP cc_start: 0.7649 (m-30) cc_final: 0.7343 (m-30) REVERT: D 246 PHE cc_start: 0.8589 (t80) cc_final: 0.8368 (t80) REVERT: D 269 GLU cc_start: 0.8093 (pm20) cc_final: 0.7689 (pt0) outliers start: 48 outliers final: 38 residues processed: 221 average time/residue: 0.1114 time to fit residues: 38.1362 Evaluate side-chains 227 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 0.0040 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113729 restraints weight = 21232.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113841 restraints weight = 15034.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113627 restraints weight = 12400.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113648 restraints weight = 12778.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113687 restraints weight = 11995.289| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15196 Z= 0.153 Angle : 0.537 7.615 20608 Z= 0.282 Chirality : 0.041 0.146 2312 Planarity : 0.003 0.032 2540 Dihedral : 12.799 150.786 2120 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.78 % Allowed : 16.60 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1792 helix: 1.28 (0.15), residues: 1084 sheet: 0.64 (0.79), residues: 48 loop : 0.01 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.015 0.001 TYR B 196 PHE 0.021 0.001 PHE D 535 TRP 0.016 0.001 TRP C 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00349 (15196) covalent geometry : angle 0.53731 (20608) hydrogen bonds : bond 0.03658 ( 904) hydrogen bonds : angle 4.44423 ( 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 238 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7669 (m-30) cc_final: 0.7389 (m-30) REVERT: A 269 GLU cc_start: 0.8121 (pm20) cc_final: 0.7692 (pt0) REVERT: A 546 GLU cc_start: 0.7496 (pm20) cc_final: 0.7292 (pm20) REVERT: A 578 LYS cc_start: 0.4654 (tptm) cc_final: 0.4434 (ttpt) REVERT: B 204 ASP cc_start: 0.7666 (m-30) cc_final: 0.7383 (m-30) REVERT: B 269 GLU cc_start: 0.8119 (pm20) cc_final: 0.7692 (pt0) REVERT: B 422 HIS cc_start: 0.6609 (m170) cc_final: 0.6345 (m-70) REVERT: C 204 ASP cc_start: 0.7659 (m-30) cc_final: 0.7358 (m-30) REVERT: C 269 GLU cc_start: 0.8106 (pm20) cc_final: 0.7695 (pt0) REVERT: D 204 ASP cc_start: 0.7672 (m-30) cc_final: 0.7387 (m-30) REVERT: D 269 GLU cc_start: 0.8111 (pm20) cc_final: 0.7696 (pt0) outliers start: 45 outliers final: 37 residues processed: 221 average time/residue: 0.1232 time to fit residues: 40.9323 Evaluate side-chains 221 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 0.0570 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 55 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 302 ASN B 302 ASN C 238 ASN C 302 ASN D 163 ASN D 238 ASN D 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114158 restraints weight = 21326.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115753 restraints weight = 16017.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116515 restraints weight = 12714.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117070 restraints weight = 10787.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117207 restraints weight = 10763.535| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15196 Z= 0.115 Angle : 0.518 7.839 20608 Z= 0.269 Chirality : 0.040 0.149 2312 Planarity : 0.003 0.026 2540 Dihedral : 12.746 151.205 2120 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.22 % Allowed : 16.85 % Favored : 80.93 % 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: 1.22 (0.20), residues: 1792 helix: 1.36 (0.15), residues: 1084 sheet: 0.67 (0.80), residues: 48 loop : 0.02 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.014 0.001 TYR A 196 PHE 0.017 0.001 PHE D 535 TRP 0.017 0.001 TRP C 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00256 (15196) covalent geometry : angle 0.51770 (20608) hydrogen bonds : bond 0.03425 ( 904) hydrogen bonds : angle 4.36132 ( 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 232 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.593 Fit side-chains REVERT: A 204 ASP cc_start: 0.7645 (m-30) cc_final: 0.7367 (m-30) REVERT: A 269 GLU cc_start: 0.8078 (pm20) cc_final: 0.7650 (pt0) REVERT: A 546 GLU cc_start: 0.7449 (pm20) cc_final: 0.7197 (pm20) REVERT: A 578 LYS cc_start: 0.4656 (tptm) cc_final: 0.4359 (ttpt) REVERT: B 204 ASP cc_start: 0.7637 (m-30) cc_final: 0.7363 (m-30) REVERT: B 269 GLU cc_start: 0.8065 (pm20) cc_final: 0.7640 (pt0) REVERT: B 422 HIS cc_start: 0.6627 (m170) cc_final: 0.6240 (m-70) REVERT: C 204 ASP cc_start: 0.7623 (m-30) cc_final: 0.7320 (m-30) REVERT: C 269 GLU cc_start: 0.8068 (pm20) cc_final: 0.7647 (pt0) REVERT: C 578 LYS cc_start: 0.5810 (pttm) cc_final: 0.5570 (pttm) REVERT: D 204 ASP cc_start: 0.7641 (m-30) cc_final: 0.7364 (m-30) REVERT: D 269 GLU cc_start: 0.8063 (pm20) cc_final: 0.7658 (pt0) REVERT: D 546 GLU cc_start: 0.7507 (pm20) cc_final: 0.7224 (pm20) outliers start: 36 outliers final: 32 residues processed: 213 average time/residue: 0.1175 time to fit residues: 38.3848 Evaluate side-chains 213 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 302 ASN C 302 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113802 restraints weight = 21161.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115174 restraints weight = 16060.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115680 restraints weight = 13079.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116396 restraints weight = 11239.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116400 restraints weight = 11113.471| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15196 Z= 0.130 Angle : 0.527 7.845 20608 Z= 0.275 Chirality : 0.040 0.146 2312 Planarity : 0.003 0.026 2540 Dihedral : 12.755 150.962 2120 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.98 % Allowed : 16.73 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1792 helix: 1.34 (0.15), residues: 1084 sheet: 0.63 (0.79), residues: 48 loop : 0.03 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 277 TYR 0.015 0.001 TYR B 196 PHE 0.033 0.001 PHE D 246 TRP 0.016 0.001 TRP C 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00292 (15196) covalent geometry : angle 0.52664 (20608) hydrogen bonds : bond 0.03501 ( 904) hydrogen bonds : angle 4.39139 ( 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 225 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.589 Fit side-chains REVERT: A 204 ASP cc_start: 0.7661 (m-30) cc_final: 0.7412 (m-30) REVERT: A 240 TYR cc_start: 0.7615 (t80) cc_final: 0.7114 (t80) REVERT: A 269 GLU cc_start: 0.8085 (pm20) cc_final: 0.7651 (pt0) REVERT: A 546 GLU cc_start: 0.7453 (pm20) cc_final: 0.7194 (pm20) REVERT: A 578 LYS cc_start: 0.4700 (tptm) cc_final: 0.4395 (ttpt) REVERT: B 204 ASP cc_start: 0.7662 (m-30) cc_final: 0.7408 (m-30) REVERT: B 240 TYR cc_start: 0.7548 (t80) cc_final: 0.7022 (t80) REVERT: B 269 GLU cc_start: 0.8078 (pm20) cc_final: 0.7645 (pt0) REVERT: C 204 ASP cc_start: 0.7634 (m-30) cc_final: 0.7385 (m-30) REVERT: C 269 GLU cc_start: 0.8069 (pm20) cc_final: 0.7662 (pt0) REVERT: C 578 LYS cc_start: 0.5809 (pttm) cc_final: 0.5536 (pttm) REVERT: D 204 ASP cc_start: 0.7661 (m-30) cc_final: 0.7408 (m-30) REVERT: D 240 TYR cc_start: 0.7603 (t80) cc_final: 0.7050 (t80) REVERT: D 269 GLU cc_start: 0.8083 (pm20) cc_final: 0.7674 (pt0) REVERT: D 546 GLU cc_start: 0.7464 (pm20) cc_final: 0.7184 (pm20) REVERT: D 578 LYS cc_start: 0.4271 (tptp) cc_final: 0.3966 (ttpt) outliers start: 32 outliers final: 31 residues processed: 208 average time/residue: 0.0998 time to fit residues: 33.5521 Evaluate side-chains 213 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 302 ASN B 245 GLN B 302 ASN C 302 ASN D 226 GLN D 302 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112702 restraints weight = 21186.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113833 restraints weight = 16376.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114204 restraints weight = 12666.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114207 restraints weight = 12068.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114469 restraints weight = 12353.526| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15196 Z= 0.152 Angle : 0.548 7.978 20608 Z= 0.284 Chirality : 0.041 0.144 2312 Planarity : 0.003 0.031 2540 Dihedral : 12.782 150.651 2120 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.28 % Allowed : 16.79 % Favored : 80.93 % 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: 1.10 (0.20), residues: 1792 helix: 1.26 (0.15), residues: 1084 sheet: 0.60 (0.79), residues: 48 loop : -0.01 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.015 0.001 TYR C 196 PHE 0.047 0.002 PHE D 246 TRP 0.016 0.001 TRP B 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00349 (15196) covalent geometry : angle 0.54755 (20608) hydrogen bonds : bond 0.03585 ( 904) hydrogen bonds : angle 4.44246 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.37 seconds wall clock time: 40 minutes 40.38 seconds (2440.38 seconds total)