Starting phenix.real_space_refine on Wed Mar 4 15:59:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfy_23309/03_2026/7lfy_23309_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfy_23309/03_2026/7lfy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lfy_23309/03_2026/7lfy_23309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfy_23309/03_2026/7lfy_23309.map" model { file = "/net/cci-nas-00/data/ceres_data/7lfy_23309/03_2026/7lfy_23309_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfy_23309/03_2026/7lfy_23309_neut.cif" } 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14851 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} 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} Time building chain proxies: 3.27, 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: 1.26 Conformation dependent library (CDL) restraints added in 366.5 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: 0.42 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: 2.60 Time building geometry restraints manager: 1.57 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: 1.870 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.310 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- 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 : 0.560 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: 0.1373 time to fit residues: 74.9394 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 : 0.575 ------------------------------------------------------------------------------- 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 = 20447.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114261 restraints weight = 16747.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114723 restraints weight = 14974.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115090 restraints weight = 12903.358| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7814 (m-30) cc_final: 0.7293 (m-30) REVERT: A 269 GLU cc_start: 0.8207 (pm20) cc_final: 0.7800 (pt0) REVERT: A 302 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8156 (t0) REVERT: A 578 LYS cc_start: 0.4993 (tttm) cc_final: 0.4226 (tmmt) REVERT: A 604 MET cc_start: 0.4188 (mmt) cc_final: 0.3580 (mpp) REVERT: B 204 ASP cc_start: 0.7804 (m-30) cc_final: 0.7281 (m-30) REVERT: B 269 GLU cc_start: 0.8198 (pm20) cc_final: 0.7801 (pt0) REVERT: B 302 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8119 (t0) REVERT: B 604 MET cc_start: 0.4195 (mmt) cc_final: 0.3594 (mpp) REVERT: C 204 ASP cc_start: 0.7813 (m-30) cc_final: 0.7260 (m-30) REVERT: C 269 GLU cc_start: 0.8211 (pm20) cc_final: 0.7779 (pt0) REVERT: C 302 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 578 LYS cc_start: 0.4975 (tttm) cc_final: 0.4045 (tmmt) REVERT: C 604 MET cc_start: 0.4180 (mmt) cc_final: 0.3584 (mpp) REVERT: D 204 ASP cc_start: 0.7815 (m-30) cc_final: 0.7291 (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: 0.8168 (t0) REVERT: D 578 LYS cc_start: 0.5036 (tttm) cc_final: 0.4162 (tmmt) REVERT: D 604 MET cc_start: 0.4173 (mmt) cc_final: 0.3586 (mpp) outliers start: 24 outliers final: 17 residues processed: 239 average time/residue: 0.1025 time to fit residues: 38.0877 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 : 0.532 ------------------------------------------------------------------------------- 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: 0.0870 chunk 18 optimal weight: 2.9990 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: 0.8980 overall best weight: 0.5970 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.145783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115617 restraints weight = 21351.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117511 restraints weight = 14709.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118443 restraints weight = 11505.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118989 restraints weight = 9832.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119210 restraints weight = 9460.267| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3245 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= 0.118 Angle : 0.499 6.912 20608 Z= 0.262 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.730 150.099 2120 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 11.17 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1792 helix: 1.08 (0.16), residues: 1080 sheet: -0.44 (0.72), residues: 56 loop : -0.54 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 347 TYR 0.012 0.001 TYR C 196 PHE 0.009 0.001 PHE A 298 TRP 0.018 0.001 TRP C 168 HIS 0.004 0.002 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00255 (15196) covalent geometry : angle 0.49932 (20608) hydrogen bonds : bond 0.03691 ( 904) hydrogen bonds : angle 4.49474 ( 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 252 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.9125 (tp) cc_final: 0.8913 (tp) REVERT: A 204 ASP cc_start: 0.7745 (m-30) cc_final: 0.7248 (m-30) REVERT: A 229 LEU cc_start: 0.8388 (tp) cc_final: 0.8087 (tp) REVERT: A 269 GLU cc_start: 0.8138 (pm20) cc_final: 0.7660 (pt0) REVERT: A 302 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8188 (t0) REVERT: A 604 MET cc_start: 0.4486 (mmt) cc_final: 0.3866 (mpp) REVERT: B 172 ILE cc_start: 0.9121 (tp) cc_final: 0.8906 (tp) REVERT: B 204 ASP cc_start: 0.7742 (m-30) cc_final: 0.7241 (m-30) REVERT: B 269 GLU cc_start: 0.8125 (pm20) cc_final: 0.7645 (pt0) REVERT: B 302 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8208 (t0) REVERT: B 604 MET cc_start: 0.4503 (mmt) cc_final: 0.3877 (mpp) REVERT: C 172 ILE cc_start: 0.9119 (tp) cc_final: 0.8914 (tp) REVERT: C 204 ASP cc_start: 0.7749 (m-30) cc_final: 0.7248 (m-30) REVERT: C 269 GLU cc_start: 0.8142 (pm20) cc_final: 0.7642 (pt0) REVERT: C 302 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8183 (t0) REVERT: C 578 LYS cc_start: 0.5119 (tttm) cc_final: 0.4284 (tmmt) REVERT: C 604 MET cc_start: 0.4490 (mmt) cc_final: 0.3880 (mpp) REVERT: D 172 ILE cc_start: 0.9114 (tp) cc_final: 0.8896 (tp) REVERT: D 204 ASP cc_start: 0.7747 (m-30) cc_final: 0.7248 (m-30) REVERT: D 269 GLU cc_start: 0.8135 (pm20) cc_final: 0.7655 (pt0) REVERT: D 302 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8199 (t0) REVERT: D 578 LYS cc_start: 0.5042 (tttm) cc_final: 0.4519 (tmmt) REVERT: D 604 MET cc_start: 0.4472 (mmt) cc_final: 0.3880 (mpp) outliers start: 29 outliers final: 8 residues processed: 233 average time/residue: 0.1020 time to fit residues: 36.6521 Evaluate side-chains 215 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 8 optimal weight: 0.0470 chunk 90 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.145556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116641 restraints weight = 21122.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116335 restraints weight = 21502.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118635 restraints weight = 15961.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118573 restraints weight = 10955.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118698 restraints weight = 11042.064| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3572 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= 0.117 Angle : 0.493 7.465 20608 Z= 0.257 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.027 2540 Dihedral : 12.745 151.663 2120 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 11.98 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1792 helix: 1.30 (0.16), residues: 1080 sheet: 0.06 (0.73), residues: 56 loop : -0.33 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 218 TYR 0.013 0.001 TYR B 196 PHE 0.009 0.001 PHE B 298 TRP 0.015 0.001 TRP B 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00261 (15196) covalent geometry : angle 0.49253 (20608) hydrogen bonds : bond 0.03492 ( 904) hydrogen bonds : angle 4.35866 ( 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 249 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7739 (m-30) cc_final: 0.7322 (m-30) REVERT: A 269 GLU cc_start: 0.8139 (pm20) cc_final: 0.7702 (pt0) REVERT: A 604 MET cc_start: 0.4104 (mmt) cc_final: 0.3588 (mpp) REVERT: B 204 ASP cc_start: 0.7736 (m-30) cc_final: 0.7364 (m-30) REVERT: B 246 PHE cc_start: 0.8611 (t80) cc_final: 0.8364 (t80) REVERT: B 269 GLU cc_start: 0.8115 (pm20) cc_final: 0.7666 (pt0) REVERT: B 604 MET cc_start: 0.4082 (mmt) cc_final: 0.3556 (mpp) REVERT: C 204 ASP cc_start: 0.7751 (m-30) cc_final: 0.7286 (m-30) REVERT: C 269 GLU cc_start: 0.8113 (pm20) cc_final: 0.7666 (pt0) REVERT: C 604 MET cc_start: 0.4063 (mmt) cc_final: 0.3564 (mpp) REVERT: D 204 ASP cc_start: 0.7748 (m-30) cc_final: 0.7311 (m-30) REVERT: D 269 GLU cc_start: 0.8136 (pm20) cc_final: 0.7701 (pt0) REVERT: D 578 LYS cc_start: 0.4933 (tttm) cc_final: 0.4473 (tmmt) REVERT: D 604 MET cc_start: 0.4036 (mmt) cc_final: 0.3544 (mpp) outliers start: 38 outliers final: 22 residues processed: 232 average time/residue: 0.1088 time to fit residues: 38.8137 Evaluate side-chains 205 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR 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 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 593 THR Chi-restraints excluded: chain C residue 260 TYR 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 526 VAL Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 260 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 6.9990 chunk 163 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 238 ASN D 302 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120298 restraints weight = 21163.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118457 restraints weight = 19547.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118691 restraints weight = 19604.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118920 restraints weight = 18871.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119689 restraints weight = 15519.983| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15196 Z= 0.112 Angle : 0.498 7.500 20608 Z= 0.258 Chirality : 0.040 0.150 2312 Planarity : 0.003 0.027 2540 Dihedral : 12.735 152.524 2120 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.28 % Allowed : 14.69 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1792 helix: 1.42 (0.16), residues: 1080 sheet: 0.14 (0.73), residues: 56 loop : -0.20 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 561 TYR 0.013 0.001 TYR C 196 PHE 0.006 0.001 PHE A 298 TRP 0.015 0.001 TRP A 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00251 (15196) covalent geometry : angle 0.49765 (20608) hydrogen bonds : bond 0.03362 ( 904) hydrogen bonds : angle 4.28730 ( 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 226 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.481 Fit side-chains REVERT: A 204 ASP cc_start: 0.7784 (m-30) cc_final: 0.7411 (m-30) REVERT: A 246 PHE cc_start: 0.8601 (t80) cc_final: 0.8351 (t80) REVERT: A 269 GLU cc_start: 0.8105 (pm20) cc_final: 0.7675 (pt0) REVERT: A 578 LYS cc_start: 0.4584 (tttm) cc_final: 0.4296 (tptm) REVERT: A 604 MET cc_start: 0.4052 (mmt) cc_final: 0.3568 (mpp) REVERT: B 204 ASP cc_start: 0.7764 (m-30) cc_final: 0.7403 (m-30) REVERT: B 269 GLU cc_start: 0.8076 (pm20) cc_final: 0.7645 (pt0) REVERT: B 604 MET cc_start: 0.4026 (mmt) cc_final: 0.3550 (mpp) REVERT: C 204 ASP cc_start: 0.7787 (m-30) cc_final: 0.7406 (m-30) REVERT: C 269 GLU cc_start: 0.8090 (pm20) cc_final: 0.7650 (pt0) REVERT: C 604 MET cc_start: 0.4042 (mmt) cc_final: 0.3565 (mpp) REVERT: D 204 ASP cc_start: 0.7782 (m-30) cc_final: 0.7409 (m-30) REVERT: D 246 PHE cc_start: 0.8596 (t80) cc_final: 0.8356 (t80) REVERT: D 269 GLU cc_start: 0.8112 (pm20) cc_final: 0.7674 (pt0) REVERT: D 578 LYS cc_start: 0.5045 (tttm) cc_final: 0.4589 (tmmt) REVERT: D 596 GLU cc_start: 0.6243 (mm-30) cc_final: 0.5997 (mm-30) REVERT: D 604 MET cc_start: 0.4011 (mmt) cc_final: 0.3540 (mpp) outliers start: 37 outliers final: 24 residues processed: 214 average time/residue: 0.1067 time to fit residues: 35.3980 Evaluate side-chains 201 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 542 SER Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 260 TYR 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 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 260 TYR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 0.0000 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114713 restraints weight = 21085.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115975 restraints weight = 15715.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116959 restraints weight = 12456.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117148 restraints weight = 10814.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117508 restraints weight = 10615.004| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15196 Z= 0.125 Angle : 0.507 7.759 20608 Z= 0.262 Chirality : 0.040 0.149 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.738 151.580 2120 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.53 % Allowed : 15.86 % Favored : 81.60 % 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: 1.28 (0.20), residues: 1792 helix: 1.47 (0.15), residues: 1080 sheet: 0.96 (0.80), residues: 48 loop : -0.10 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.014 0.001 TYR B 196 PHE 0.007 0.001 PHE B 298 TRP 0.015 0.001 TRP C 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00284 (15196) covalent geometry : angle 0.50665 (20608) hydrogen bonds : bond 0.03420 ( 904) hydrogen bonds : angle 4.25115 ( 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 245 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.632 Fit side-chains REVERT: A 204 ASP cc_start: 0.7720 (m-30) cc_final: 0.7336 (m-30) REVERT: A 269 GLU cc_start: 0.8074 (pm20) cc_final: 0.7635 (pt0) REVERT: A 578 LYS cc_start: 0.4860 (tttm) cc_final: 0.4470 (pttm) REVERT: A 604 MET cc_start: 0.4486 (mmt) cc_final: 0.3853 (mpp) REVERT: B 204 ASP cc_start: 0.7711 (m-30) cc_final: 0.7336 (m-30) REVERT: B 269 GLU cc_start: 0.8062 (pm20) cc_final: 0.7624 (pt0) REVERT: B 578 LYS cc_start: 0.4528 (tptm) cc_final: 0.3943 (pttm) REVERT: B 604 MET cc_start: 0.4457 (mmt) cc_final: 0.3769 (mpp) REVERT: C 204 ASP cc_start: 0.7715 (m-30) cc_final: 0.7340 (m-30) REVERT: C 269 GLU cc_start: 0.8067 (pm20) cc_final: 0.7635 (pt0) REVERT: C 422 HIS cc_start: 0.6666 (m170) cc_final: 0.6425 (m-70) REVERT: C 604 MET cc_start: 0.4525 (mmt) cc_final: 0.3860 (mpp) REVERT: D 204 ASP cc_start: 0.7713 (m-30) cc_final: 0.7332 (m-30) REVERT: D 269 GLU cc_start: 0.8064 (pm20) cc_final: 0.7636 (pt0) REVERT: D 422 HIS cc_start: 0.6652 (m170) cc_final: 0.6413 (m-70) REVERT: D 578 LYS cc_start: 0.5166 (tttm) cc_final: 0.4636 (tmmt) REVERT: D 596 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6486 (mm-30) REVERT: D 604 MET cc_start: 0.4466 (mmt) cc_final: 0.3796 (mpp) outliers start: 41 outliers final: 32 residues processed: 224 average time/residue: 0.1054 time to fit residues: 37.3492 Evaluate side-chains 216 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ILE 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 526 VAL 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 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 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 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 237 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 245 GLN B 302 ASN C 245 GLN D 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114466 restraints weight = 21086.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113748 restraints weight = 16778.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113629 restraints weight = 13712.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113674 restraints weight = 12868.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113783 restraints weight = 12307.872| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15196 Z= 0.173 Angle : 0.553 7.569 20608 Z= 0.285 Chirality : 0.041 0.147 2312 Planarity : 0.004 0.043 2540 Dihedral : 12.835 151.302 2120 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.35 % Allowed : 16.85 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1792 helix: 1.28 (0.15), residues: 1084 sheet: 0.69 (0.77), residues: 48 loop : 0.00 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.016 0.001 TYR B 349 PHE 0.014 0.002 PHE B 246 TRP 0.016 0.001 TRP A 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00397 (15196) covalent geometry : angle 0.55315 (20608) hydrogen bonds : bond 0.03837 ( 904) hydrogen bonds : angle 4.42542 ( 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 236 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7675 (m-30) cc_final: 0.7376 (m-30) REVERT: A 269 GLU cc_start: 0.8135 (pm20) cc_final: 0.7698 (pt0) REVERT: A 422 HIS cc_start: 0.6606 (m170) cc_final: 0.6372 (m-70) REVERT: B 204 ASP cc_start: 0.7686 (m-30) cc_final: 0.7378 (m-30) REVERT: B 269 GLU cc_start: 0.8126 (pm20) cc_final: 0.7684 (pt0) REVERT: B 422 HIS cc_start: 0.6601 (m170) cc_final: 0.6401 (m-70) REVERT: C 204 ASP cc_start: 0.7682 (m-30) cc_final: 0.7369 (m-30) REVERT: C 269 GLU cc_start: 0.8111 (pm20) cc_final: 0.7685 (pt0) REVERT: C 422 HIS cc_start: 0.6636 (m170) cc_final: 0.6414 (m-70) REVERT: D 204 ASP cc_start: 0.7665 (m-30) cc_final: 0.7367 (m-30) REVERT: D 269 GLU cc_start: 0.8115 (pm20) cc_final: 0.7697 (pt0) REVERT: D 422 HIS cc_start: 0.6625 (m170) cc_final: 0.6409 (m-70) REVERT: D 578 LYS cc_start: 0.4985 (tttm) cc_final: 0.4593 (tmmt) outliers start: 38 outliers final: 30 residues processed: 216 average time/residue: 0.1071 time to fit residues: 35.7267 Evaluate side-chains 214 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.0010 chunk 35 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 174 optimal weight: 0.0870 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114507 restraints weight = 21108.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115985 restraints weight = 16217.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117064 restraints weight = 12849.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117590 restraints weight = 10766.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117787 restraints weight = 10466.496| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15196 Z= 0.110 Angle : 0.508 7.663 20608 Z= 0.262 Chirality : 0.040 0.149 2312 Planarity : 0.003 0.026 2540 Dihedral : 12.738 152.035 2120 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.28 % Allowed : 16.85 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.20), residues: 1792 helix: 1.42 (0.15), residues: 1084 sheet: 0.74 (0.77), residues: 48 loop : 0.06 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.014 0.001 TYR A 196 PHE 0.012 0.001 PHE D 246 TRP 0.017 0.001 TRP B 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00241 (15196) covalent geometry : angle 0.50839 (20608) hydrogen bonds : bond 0.03378 ( 904) hydrogen bonds : angle 4.28346 ( 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 225 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.564 Fit side-chains REVERT: A 204 ASP cc_start: 0.7632 (m-30) cc_final: 0.7323 (m-30) REVERT: A 269 GLU cc_start: 0.8052 (pm20) cc_final: 0.7615 (pt0) REVERT: A 422 HIS cc_start: 0.6610 (m170) cc_final: 0.6276 (m-70) REVERT: B 204 ASP cc_start: 0.7637 (m-30) cc_final: 0.7321 (m-30) REVERT: B 269 GLU cc_start: 0.8037 (pm20) cc_final: 0.7611 (pt0) REVERT: B 422 HIS cc_start: 0.6571 (m170) cc_final: 0.6253 (m-70) REVERT: C 204 ASP cc_start: 0.7627 (m-30) cc_final: 0.7304 (m-30) REVERT: C 240 TYR cc_start: 0.7845 (t80) cc_final: 0.7602 (t80) REVERT: C 269 GLU cc_start: 0.8043 (pm20) cc_final: 0.7622 (pt0) REVERT: C 546 GLU cc_start: 0.7431 (pm20) cc_final: 0.7158 (pm20) REVERT: C 578 LYS cc_start: 0.4518 (tptm) cc_final: 0.4225 (tttp) REVERT: D 204 ASP cc_start: 0.7642 (m-30) cc_final: 0.7319 (m-30) REVERT: D 269 GLU cc_start: 0.8048 (pm20) cc_final: 0.7625 (pt0) REVERT: D 578 LYS cc_start: 0.4979 (tttm) cc_final: 0.4536 (tmmt) outliers start: 37 outliers final: 32 residues processed: 210 average time/residue: 0.1060 time to fit residues: 35.0839 Evaluate side-chains 208 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 505 TYR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 0.0020 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112945 restraints weight = 21377.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114562 restraints weight = 16013.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115439 restraints weight = 12587.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115825 restraints weight = 10851.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116082 restraints weight = 10670.283| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4619 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= 0.131 Angle : 0.521 7.828 20608 Z= 0.268 Chirality : 0.040 0.147 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.747 150.985 2120 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 16.85 % Favored : 80.99 % 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: 1.27 (0.20), residues: 1792 helix: 1.40 (0.15), residues: 1084 sheet: 0.71 (0.76), residues: 48 loop : 0.04 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.015 0.001 TYR C 196 PHE 0.023 0.001 PHE D 535 TRP 0.015 0.001 TRP C 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00295 (15196) covalent geometry : angle 0.52107 (20608) hydrogen bonds : bond 0.03443 ( 904) hydrogen bonds : angle 4.33204 ( 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 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.600 Fit side-chains REVERT: A 204 ASP cc_start: 0.7644 (m-30) cc_final: 0.7369 (m-30) REVERT: A 269 GLU cc_start: 0.8081 (pm20) cc_final: 0.7654 (pt0) REVERT: A 578 LYS cc_start: 0.5930 (pttm) cc_final: 0.5634 (tttm) REVERT: B 204 ASP cc_start: 0.7634 (m-30) cc_final: 0.7359 (m-30) REVERT: B 269 GLU cc_start: 0.8071 (pm20) cc_final: 0.7645 (pt0) REVERT: B 422 HIS cc_start: 0.6603 (m170) cc_final: 0.6212 (m-70) REVERT: B 578 LYS cc_start: 0.5672 (pttm) cc_final: 0.5260 (pttm) REVERT: C 204 ASP cc_start: 0.7629 (m-30) cc_final: 0.7348 (m-30) REVERT: C 269 GLU cc_start: 0.8073 (pm20) cc_final: 0.7653 (pt0) REVERT: C 546 GLU cc_start: 0.7457 (pm20) cc_final: 0.7214 (pm20) REVERT: C 578 LYS cc_start: 0.4638 (tptm) cc_final: 0.4224 (tttp) REVERT: D 204 ASP cc_start: 0.7636 (m-30) cc_final: 0.7367 (m-30) REVERT: D 269 GLU cc_start: 0.8082 (pm20) cc_final: 0.7655 (pt0) REVERT: D 578 LYS cc_start: 0.5101 (tttm) cc_final: 0.4639 (tmmt) REVERT: D 596 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6685 (mp0) outliers start: 35 outliers final: 31 residues processed: 203 average time/residue: 0.0947 time to fit residues: 30.9176 Evaluate side-chains 206 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 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 505 TYR 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 465 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 42 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 166 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118961 restraints weight = 21097.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116895 restraints weight = 20743.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118013 restraints weight = 20083.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118386 restraints weight = 17351.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118403 restraints weight = 15249.407| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4723 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= 0.116 Angle : 0.512 7.952 20608 Z= 0.263 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.027 2540 Dihedral : 12.726 151.262 2120 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 17.41 % Favored : 80.56 % 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: 1.29 (0.20), residues: 1792 helix: 1.42 (0.15), residues: 1084 sheet: 0.76 (0.77), residues: 48 loop : 0.02 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.014 0.001 TYR C 196 PHE 0.018 0.001 PHE D 535 TRP 0.016 0.001 TRP B 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00259 (15196) covalent geometry : angle 0.51180 (20608) hydrogen bonds : bond 0.03319 ( 904) hydrogen bonds : angle 4.31169 ( 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 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.604 Fit side-chains REVERT: A 204 ASP cc_start: 0.7679 (m-30) cc_final: 0.7390 (m-30) REVERT: A 269 GLU cc_start: 0.8095 (pm20) cc_final: 0.7679 (pt0) REVERT: B 204 ASP cc_start: 0.7671 (m-30) cc_final: 0.7389 (m-30) REVERT: B 269 GLU cc_start: 0.8066 (pm20) cc_final: 0.7655 (pt0) REVERT: C 204 ASP cc_start: 0.7661 (m-30) cc_final: 0.7370 (m-30) REVERT: C 269 GLU cc_start: 0.8072 (pm20) cc_final: 0.7670 (pt0) REVERT: C 578 LYS cc_start: 0.4444 (tptm) cc_final: 0.4203 (tttp) REVERT: D 204 ASP cc_start: 0.7682 (m-30) cc_final: 0.7418 (m-30) REVERT: D 269 GLU cc_start: 0.8080 (pm20) cc_final: 0.7678 (pt0) REVERT: D 578 LYS cc_start: 0.4849 (tttm) cc_final: 0.4564 (tmmt) outliers start: 33 outliers final: 31 residues processed: 205 average time/residue: 0.0945 time to fit residues: 31.2286 Evaluate side-chains 206 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 505 TYR 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 465 ILE Chi-restraints excluded: chain B residue 505 TYR 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 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 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 542 SER 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: 0.8980 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 173 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113583 restraints weight = 21187.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115097 restraints weight = 15400.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115535 restraints weight = 12897.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116009 restraints weight = 11320.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116126 restraints weight = 11166.862| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4770 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= 0.137 Angle : 0.527 7.849 20608 Z= 0.272 Chirality : 0.040 0.146 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.746 150.825 2120 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.04 % Allowed : 17.41 % Favored : 80.56 % 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: 1.25 (0.20), residues: 1792 helix: 1.35 (0.15), residues: 1088 sheet: 0.73 (0.76), residues: 48 loop : 0.10 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.015 0.001 TYR B 543 PHE 0.027 0.001 PHE D 535 TRP 0.015 0.001 TRP D 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00314 (15196) covalent geometry : angle 0.52695 (20608) hydrogen bonds : bond 0.03446 ( 904) hydrogen bonds : angle 4.34959 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.76 seconds wall clock time: 37 minutes 34.54 seconds (2254.54 seconds total)