Starting phenix.real_space_refine on Fri Jul 3 15:03:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfy_23309/07_2026/7lfy_23309_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfy_23309/07_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_23309/07_2026/7lfy_23309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfy_23309/07_2026/7lfy_23309.map" model { file = "/net/cci-nas-00/data/ceres_data/7lfy_23309/07_2026/7lfy_23309_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfy_23309/07_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-6108/lib/python3.11/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, 23 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.56, per 1000 atoms: 0.24 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: 1.10 Conformation dependent library (CDL) restraints added in 593.8 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: 0.32 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: 2.64 Time building geometry restraints manager: 1.51 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 3.210 ... (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: 1.490 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.050 Find NCS groups from input model: 0.320 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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/Z covalent geometry : bond 0.00482 / 0.23 (15196) covalent geometry : angle 0.69656 / 0.37 (20608) hydrogen bonds : bond 0.12175 / 7.96 ( 904) hydrogen bonds : angle 6.69127 / 4.86 ( 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 : 0.567 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: 0.1368 time to fit residues: 74.7430 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 : 0.510 ------------------------------------------------------------------------------- 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: 6.9990 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... 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 = 0.3797 r_free = 0.3797 target = 0.144105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112504 restraints weight = 21349.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114243 restraints weight = 15754.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115072 restraints weight = 12289.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115527 restraints weight = 10594.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115809 restraints weight = 10411.599| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15196 Z= 0.183 Angle : 0.588 8.016 20608 Z= 0.306 Chirality : 0.043 0.142 2312 Planarity : 0.004 0.043 2540 Dihedral : 12.960 153.170 2120 Min Nonbonded Distance : 2.575 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: 0.72 (0.16), residues: 1060 sheet: -1.05 (0.71), residues: 56 loop : -0.34 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 347 TYR 0.018 0.001 TYR B 349 PHE 0.013 0.002 PHE D 574 TRP 0.021 0.002 TRP B 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (15196) covalent geometry : angle 0.58817 / 0.31 (20608) hydrogen bonds : bond 0.04190 / 2.71 ( 904) hydrogen bonds : angle 4.94650 / 3.57 ( 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 264 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7758 (m-30) cc_final: 0.7247 (m-30) REVERT: A 269 GLU cc_start: 0.8197 (pm20) cc_final: 0.7770 (pt0) REVERT: A 302 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8132 (t0) REVERT: A 578 LYS cc_start: 0.5086 (tttm) cc_final: 0.4108 (tmmt) REVERT: A 604 MET cc_start: 0.4569 (mmt) cc_final: 0.3873 (mpp) REVERT: B 204 ASP cc_start: 0.7757 (m-30) cc_final: 0.7218 (m-30) REVERT: B 269 GLU cc_start: 0.8184 (pm20) cc_final: 0.7770 (pt0) REVERT: B 302 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8103 (t0) REVERT: B 604 MET cc_start: 0.4570 (mmt) cc_final: 0.3878 (mpp) REVERT: C 204 ASP cc_start: 0.7768 (m-30) cc_final: 0.7211 (m-30) REVERT: C 269 GLU cc_start: 0.8196 (pm20) cc_final: 0.7743 (pt0) REVERT: C 302 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8119 (t0) REVERT: C 578 LYS cc_start: 0.5040 (tttm) cc_final: 0.4225 (tmmt) REVERT: C 604 MET cc_start: 0.4562 (mmt) cc_final: 0.3872 (mpp) REVERT: D 204 ASP cc_start: 0.7762 (m-30) cc_final: 0.7223 (m-30) REVERT: D 269 GLU cc_start: 0.8194 (pm20) cc_final: 0.7759 (pt0) REVERT: D 302 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8145 (t0) REVERT: D 578 LYS cc_start: 0.5068 (tttm) cc_final: 0.4799 (tttm) REVERT: D 604 MET cc_start: 0.4620 (mmt) cc_final: 0.3934 (mpp) outliers start: 24 outliers final: 17 residues processed: 241 average time/residue: 0.1010 time to fit residues: 38.0630 Evaluate side-chains 207 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 0.0170 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3817 r_free = 0.3817 target = 0.146132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117363 restraints weight = 21220.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117717 restraints weight = 17341.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118047 restraints weight = 13837.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118226 restraints weight = 12544.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118392 restraints weight = 12516.086| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15196 Z= 0.113 Angle : 0.497 7.284 20608 Z= 0.261 Chirality : 0.040 0.150 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.716 149.971 2120 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.54 % Allowed : 11.36 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1792 helix: 1.09 (0.16), residues: 1080 sheet: -0.43 (0.72), residues: 56 loop : -0.53 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 347 TYR 0.011 0.001 TYR C 196 PHE 0.011 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.004 0.002 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15196) covalent geometry : angle 0.49662 / 0.26 (20608) hydrogen bonds : bond 0.03650 / 2.37 ( 904) hydrogen bonds : angle 4.48783 / 3.21 ( 2652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7781 (m-30) cc_final: 0.7280 (m-30) REVERT: A 229 LEU cc_start: 0.8386 (tp) cc_final: 0.8089 (tp) REVERT: A 269 GLU cc_start: 0.8152 (pm20) cc_final: 0.7680 (pt0) REVERT: A 578 LYS cc_start: 0.5198 (tttm) cc_final: 0.4881 (tttm) REVERT: A 604 MET cc_start: 0.4334 (mmt) cc_final: 0.3751 (mpp) REVERT: B 172 ILE cc_start: 0.9126 (tp) cc_final: 0.8920 (tp) REVERT: B 204 ASP cc_start: 0.7780 (m-30) cc_final: 0.7276 (m-30) REVERT: B 269 GLU cc_start: 0.8146 (pm20) cc_final: 0.7673 (pt0) REVERT: B 302 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8239 (t0) REVERT: B 604 MET cc_start: 0.4326 (mmt) cc_final: 0.3751 (mpp) REVERT: C 172 ILE cc_start: 0.9117 (tp) cc_final: 0.8913 (tp) REVERT: C 204 ASP cc_start: 0.7786 (m-30) cc_final: 0.7280 (m-30) REVERT: C 269 GLU cc_start: 0.8154 (pm20) cc_final: 0.7667 (pt0) REVERT: C 302 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8252 (t0) REVERT: C 604 MET cc_start: 0.4316 (mmt) cc_final: 0.3747 (mpp) REVERT: D 204 ASP cc_start: 0.7779 (m-30) cc_final: 0.7281 (m-30) REVERT: D 269 GLU cc_start: 0.8160 (pm20) cc_final: 0.7696 (pt0) REVERT: D 578 LYS cc_start: 0.5018 (tttm) cc_final: 0.4485 (tmmt) REVERT: D 604 MET cc_start: 0.4292 (mmt) cc_final: 0.3742 (mpp) outliers start: 25 outliers final: 8 residues processed: 238 average time/residue: 0.1024 time to fit residues: 37.6067 Evaluate side-chains 201 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR 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 465 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 167 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN A 302 ASN B 238 ASN B 302 ASN C 238 ASN C 302 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 = 0.3778 r_free = 0.3778 target = 0.142877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116043 restraints weight = 21221.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114055 restraints weight = 20176.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114901 restraints weight = 19292.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115252 restraints weight = 17078.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115625 restraints weight = 14013.908| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15196 Z= 0.158 Angle : 0.527 7.368 20608 Z= 0.275 Chirality : 0.041 0.146 2312 Planarity : 0.004 0.035 2540 Dihedral : 12.802 150.726 2120 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.02 % Allowed : 11.85 % Favored : 85.12 % 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: 0.82 (0.20), residues: 1792 helix: 1.13 (0.16), residues: 1084 sheet: -0.09 (0.73), residues: 56 loop : -0.26 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.015 0.001 TYR B 349 PHE 0.010 0.001 PHE C 261 TRP 0.017 0.001 TRP A 168 HIS 0.004 0.002 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (15196) covalent geometry : angle 0.52656 / 0.28 (20608) hydrogen bonds : bond 0.03766 / 2.42 ( 904) hydrogen bonds : angle 4.49624 / 3.22 ( 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 253 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7763 (m-30) cc_final: 0.7374 (m-30) REVERT: A 269 GLU cc_start: 0.8153 (pm20) cc_final: 0.7701 (pt0) REVERT: A 604 MET cc_start: 0.4163 (mmt) cc_final: 0.3561 (mpp) REVERT: B 172 ILE cc_start: 0.9153 (tp) cc_final: 0.8944 (tp) REVERT: B 204 ASP cc_start: 0.7758 (m-30) cc_final: 0.7343 (m-30) REVERT: B 269 GLU cc_start: 0.8134 (pm20) cc_final: 0.7682 (pt0) REVERT: B 302 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8283 (t0) REVERT: B 604 MET cc_start: 0.4156 (mmt) cc_final: 0.3570 (mpp) REVERT: C 172 ILE cc_start: 0.9145 (tp) cc_final: 0.8923 (tp) REVERT: C 204 ASP cc_start: 0.7769 (m-30) cc_final: 0.7324 (m-30) REVERT: C 269 GLU cc_start: 0.8140 (pm20) cc_final: 0.7696 (pt0) REVERT: C 302 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8303 (t0) REVERT: C 604 MET cc_start: 0.4159 (mmt) cc_final: 0.3583 (mpp) REVERT: D 204 ASP cc_start: 0.7768 (m-30) cc_final: 0.7365 (m-30) REVERT: D 269 GLU cc_start: 0.8144 (pm20) cc_final: 0.7710 (pt0) REVERT: D 578 LYS cc_start: 0.4925 (tttm) cc_final: 0.4479 (tmmt) REVERT: D 604 MET cc_start: 0.4185 (mmt) cc_final: 0.3605 (mpp) outliers start: 49 outliers final: 30 residues processed: 229 average time/residue: 0.0900 time to fit residues: 33.0179 Evaluate side-chains 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 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 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 582 MET Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 ASN C 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113723 restraints weight = 21181.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114969 restraints weight = 15460.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115469 restraints weight = 11923.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115665 restraints weight = 10794.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115791 restraints weight = 10964.018| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15196 Z= 0.140 Angle : 0.521 7.529 20608 Z= 0.269 Chirality : 0.040 0.147 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.819 151.849 2120 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.84 % Allowed : 13.89 % Favored : 83.27 % 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: 1.05 (0.20), residues: 1792 helix: 1.25 (0.16), residues: 1084 sheet: 0.84 (0.80), residues: 48 loop : -0.13 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.014 0.001 TYR C 196 PHE 0.009 0.001 PHE B 298 TRP 0.016 0.001 TRP B 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (15196) covalent geometry : angle 0.52142 / 0.27 (20608) hydrogen bonds : bond 0.03645 / 2.35 ( 904) hydrogen bonds : angle 4.40630 / 3.14 ( 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 248 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7748 (m-30) cc_final: 0.7401 (m-30) REVERT: A 269 GLU cc_start: 0.8128 (pm20) cc_final: 0.7685 (pt0) REVERT: A 604 MET cc_start: 0.4394 (mmt) cc_final: 0.3700 (mpp) REVERT: B 204 ASP cc_start: 0.7726 (m-30) cc_final: 0.7405 (m-30) REVERT: B 269 GLU cc_start: 0.8105 (pm20) cc_final: 0.7668 (pt0) REVERT: B 604 MET cc_start: 0.4438 (mmt) cc_final: 0.3761 (mpp) REVERT: C 204 ASP cc_start: 0.7739 (m-30) cc_final: 0.7409 (m-30) REVERT: C 269 GLU cc_start: 0.8109 (pm20) cc_final: 0.7679 (pt0) REVERT: C 604 MET cc_start: 0.4419 (mmt) cc_final: 0.3701 (mpp) REVERT: D 204 ASP cc_start: 0.7747 (m-30) cc_final: 0.7391 (m-30) REVERT: D 269 GLU cc_start: 0.8123 (pm20) cc_final: 0.7694 (pt0) REVERT: D 604 MET cc_start: 0.4363 (mmt) cc_final: 0.3661 (mpp) outliers start: 46 outliers final: 35 residues processed: 221 average time/residue: 0.1035 time to fit residues: 36.2245 Evaluate side-chains 220 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 465 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 ASN C 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112884 restraints weight = 21171.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114378 restraints weight = 15858.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115369 restraints weight = 12366.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115678 restraints weight = 10543.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115957 restraints weight = 10216.267| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4084 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 : 0.510 7.498 20608 Z= 0.264 Chirality : 0.040 0.147 2312 Planarity : 0.003 0.027 2540 Dihedral : 12.801 151.787 2120 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.96 % Allowed : 14.63 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1792 helix: 1.31 (0.15), residues: 1084 sheet: 0.87 (0.81), residues: 48 loop : -0.06 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.014 0.001 TYR C 196 PHE 0.007 0.001 PHE B 298 TRP 0.016 0.001 TRP B 168 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15196) covalent geometry : angle 0.51037 / 0.26 (20608) hydrogen bonds : bond 0.03541 / 2.28 ( 904) hydrogen bonds : angle 4.32686 / 3.08 ( 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 247 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.580 Fit side-chains REVERT: A 204 ASP cc_start: 0.7715 (m-30) cc_final: 0.7376 (m-30) REVERT: A 269 GLU cc_start: 0.8112 (pm20) cc_final: 0.7671 (pt0) REVERT: A 578 LYS cc_start: 0.4881 (tttm) cc_final: 0.4645 (pttm) REVERT: A 604 MET cc_start: 0.4610 (mmt) cc_final: 0.3892 (mpp) REVERT: B 204 ASP cc_start: 0.7697 (m-30) cc_final: 0.7363 (m-30) REVERT: B 269 GLU cc_start: 0.8098 (pm20) cc_final: 0.7659 (pt0) REVERT: B 604 MET cc_start: 0.4581 (mmt) cc_final: 0.3853 (mpp) REVERT: C 204 ASP cc_start: 0.7701 (m-30) cc_final: 0.7357 (m-30) REVERT: C 269 GLU cc_start: 0.8095 (pm20) cc_final: 0.7676 (pt0) REVERT: C 604 MET cc_start: 0.4587 (mmt) cc_final: 0.3866 (mpp) REVERT: D 204 ASP cc_start: 0.7705 (m-30) cc_final: 0.7359 (m-30) REVERT: D 269 GLU cc_start: 0.8106 (pm20) cc_final: 0.7687 (pt0) REVERT: D 604 MET cc_start: 0.4579 (mmt) cc_final: 0.3866 (mpp) outliers start: 48 outliers final: 35 residues processed: 218 average time/residue: 0.0993 time to fit residues: 34.2572 Evaluate side-chains 231 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 526 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN B 245 GLN B 302 ASN C 302 ASN D 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112447 restraints weight = 20980.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113781 restraints weight = 15418.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114421 restraints weight = 12498.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115196 restraints weight = 10885.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115493 restraints weight = 9758.498| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4335 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= 0.140 Angle : 0.517 7.574 20608 Z= 0.267 Chirality : 0.040 0.148 2312 Planarity : 0.003 0.030 2540 Dihedral : 12.787 151.248 2120 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.65 % Allowed : 15.93 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1792 helix: 1.37 (0.15), residues: 1084 sheet: 0.84 (0.78), residues: 48 loop : 0.05 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.015 0.001 TYR D 196 PHE 0.015 0.001 PHE B 246 TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15196) covalent geometry : angle 0.51727 / 0.27 (20608) hydrogen bonds : bond 0.03529 / 2.28 ( 904) hydrogen bonds : angle 4.35194 / 3.09 ( 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 249 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.583 Fit side-chains REVERT: A 204 ASP cc_start: 0.7654 (m-30) cc_final: 0.7347 (m-30) REVERT: A 269 GLU cc_start: 0.8104 (pm20) cc_final: 0.7677 (pt0) REVERT: A 422 HIS cc_start: 0.6651 (m170) cc_final: 0.6412 (m-70) REVERT: A 578 LYS cc_start: 0.4990 (tttm) cc_final: 0.4780 (pttm) REVERT: A 604 MET cc_start: 0.4696 (mmt) cc_final: 0.3893 (mpp) REVERT: B 204 ASP cc_start: 0.7651 (m-30) cc_final: 0.7325 (m-30) REVERT: B 269 GLU cc_start: 0.8086 (pm20) cc_final: 0.7665 (pt0) REVERT: B 422 HIS cc_start: 0.6641 (m170) cc_final: 0.6390 (m-70) REVERT: C 204 ASP cc_start: 0.7657 (m-30) cc_final: 0.7325 (m-30) REVERT: C 269 GLU cc_start: 0.8087 (pm20) cc_final: 0.7676 (pt0) REVERT: C 422 HIS cc_start: 0.6678 (m170) cc_final: 0.6427 (m-70) REVERT: C 604 MET cc_start: 0.4701 (mmt) cc_final: 0.3908 (mpp) REVERT: D 204 ASP cc_start: 0.7647 (m-30) cc_final: 0.7337 (m-30) REVERT: D 269 GLU cc_start: 0.8083 (pm20) cc_final: 0.7677 (pt0) REVERT: D 578 LYS cc_start: 0.5896 (pttm) cc_final: 0.5693 (tttm) REVERT: D 604 MET cc_start: 0.4690 (mmt) cc_final: 0.3906 (mpp) outliers start: 43 outliers final: 31 residues processed: 231 average time/residue: 0.1042 time to fit residues: 37.1638 Evaluate side-chains 227 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 582 MET 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 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 505 TYR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 134 optimal weight: 9.9990 chunk 56 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 ASN C 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116181 restraints weight = 21146.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117539 restraints weight = 15714.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118494 restraints weight = 12523.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118979 restraints weight = 10557.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119089 restraints weight = 10196.884| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4509 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= 0.106 Angle : 0.497 7.739 20608 Z= 0.258 Chirality : 0.040 0.151 2312 Planarity : 0.003 0.026 2540 Dihedral : 12.715 151.716 2120 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.22 % Allowed : 16.54 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1792 helix: 1.47 (0.16), residues: 1084 sheet: 0.89 (0.76), residues: 48 loop : 0.11 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 277 TYR 0.013 0.001 TYR A 196 PHE 0.017 0.001 PHE C 246 TRP 0.017 0.001 TRP B 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15196) covalent geometry : angle 0.49708 / 0.26 (20608) hydrogen bonds : bond 0.03279 / 2.15 ( 904) hydrogen bonds : angle 4.26246 / 3.02 ( 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 228 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.440 Fit side-chains REVERT: A 204 ASP cc_start: 0.7654 (m-30) cc_final: 0.7356 (m-30) REVERT: A 269 GLU cc_start: 0.8062 (pm20) cc_final: 0.7660 (pt0) REVERT: A 302 ASN cc_start: 0.9129 (t0) cc_final: 0.8923 (t0) REVERT: A 422 HIS cc_start: 0.6629 (m170) cc_final: 0.6310 (m-70) REVERT: A 578 LYS cc_start: 0.4698 (tttm) cc_final: 0.4439 (pttm) REVERT: A 604 MET cc_start: 0.4674 (mmt) cc_final: 0.3871 (mpp) REVERT: B 204 ASP cc_start: 0.7647 (m-30) cc_final: 0.7352 (m-30) REVERT: B 269 GLU cc_start: 0.8045 (pm20) cc_final: 0.7646 (pt0) REVERT: B 422 HIS cc_start: 0.6622 (m170) cc_final: 0.6314 (m-70) REVERT: B 604 MET cc_start: 0.4646 (mmt) cc_final: 0.3846 (mpp) REVERT: C 204 ASP cc_start: 0.7641 (m-30) cc_final: 0.7334 (m-30) REVERT: C 269 GLU cc_start: 0.8053 (pm20) cc_final: 0.7658 (pt0) REVERT: C 422 HIS cc_start: 0.6616 (m170) cc_final: 0.6267 (m-70) REVERT: C 578 LYS cc_start: 0.5709 (pttm) cc_final: 0.5503 (tttm) REVERT: C 604 MET cc_start: 0.4652 (mmt) cc_final: 0.3844 (mpp) REVERT: D 204 ASP cc_start: 0.7647 (m-30) cc_final: 0.7361 (m-30) REVERT: D 269 GLU cc_start: 0.8060 (pm20) cc_final: 0.7659 (pt0) REVERT: D 604 MET cc_start: 0.4664 (mmt) cc_final: 0.3876 (mpp) outliers start: 36 outliers final: 29 residues processed: 211 average time/residue: 0.1024 time to fit residues: 33.5913 Evaluate side-chains 204 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 505 TYR Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 505 TYR 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: 7.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 302 ASN D 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107402 restraints weight = 21459.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108715 restraints weight = 16664.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109569 restraints weight = 13525.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109601 restraints weight = 11438.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109872 restraints weight = 11853.879| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15196 Z= 0.248 Angle : 0.617 7.735 20608 Z= 0.322 Chirality : 0.044 0.139 2312 Planarity : 0.004 0.057 2540 Dihedral : 12.890 149.677 2120 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.10 % Allowed : 16.67 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1792 helix: 1.03 (0.15), residues: 1088 sheet: 0.44 (0.74), residues: 48 loop : -0.07 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 218 TYR 0.020 0.002 TYR B 349 PHE 0.015 0.002 PHE B 298 TRP 0.015 0.002 TRP A 442 HIS 0.004 0.002 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (15196) covalent geometry : angle 0.61729 / 0.32 (20608) hydrogen bonds : bond 0.04189 / 2.69 ( 904) hydrogen bonds : angle 4.65960 / 3.32 ( 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 229 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7683 (m-30) cc_final: 0.7431 (m-30) REVERT: A 216 PHE cc_start: 0.7940 (t80) cc_final: 0.7704 (t80) REVERT: A 269 GLU cc_start: 0.8135 (pm20) cc_final: 0.7697 (pt0) REVERT: B 204 ASP cc_start: 0.7685 (m-30) cc_final: 0.7432 (m-30) REVERT: B 216 PHE cc_start: 0.7961 (t80) cc_final: 0.7734 (t80) REVERT: B 269 GLU cc_start: 0.8134 (pm20) cc_final: 0.7700 (pt0) REVERT: C 204 ASP cc_start: 0.7693 (m-30) cc_final: 0.7430 (m-30) REVERT: C 216 PHE cc_start: 0.7939 (t80) cc_final: 0.7705 (t80) REVERT: C 269 GLU cc_start: 0.8123 (pm20) cc_final: 0.7696 (pt0) REVERT: D 204 ASP cc_start: 0.7696 (m-30) cc_final: 0.7458 (m-30) REVERT: D 216 PHE cc_start: 0.7950 (t80) cc_final: 0.7702 (t80) REVERT: D 269 GLU cc_start: 0.8129 (pm20) cc_final: 0.7706 (pt0) REVERT: D 578 LYS cc_start: 0.5345 (tttm) cc_final: 0.4963 (tmmt) outliers start: 34 outliers final: 26 residues processed: 213 average time/residue: 0.0939 time to fit residues: 32.1839 Evaluate side-chains 217 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 378 VAL 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 526 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 42 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 ASN C 302 ASN D 226 GLN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113726 restraints weight = 21078.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115036 restraints weight = 15674.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115884 restraints weight = 12587.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116264 restraints weight = 10878.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116342 restraints weight = 10476.328| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.122 Angle : 0.537 7.807 20608 Z= 0.278 Chirality : 0.041 0.147 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.794 151.271 2120 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.42 % Allowed : 17.28 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1792 helix: 1.20 (0.15), residues: 1084 sheet: 0.83 (0.80), residues: 48 loop : -0.04 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 299 TYR 0.015 0.001 TYR D 306 PHE 0.013 0.001 PHE B 574 TRP 0.018 0.001 TRP D 168 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15196) covalent geometry : angle 0.53717 / 0.28 (20608) hydrogen bonds : bond 0.03509 / 2.29 ( 904) hydrogen bonds : angle 4.50656 / 3.20 ( 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 226 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.786 Fit side-chains REVERT: A 204 ASP cc_start: 0.7612 (m-30) cc_final: 0.7375 (m-30) REVERT: A 269 GLU cc_start: 0.8071 (pm20) cc_final: 0.7624 (pt0) REVERT: A 302 ASN cc_start: 0.9165 (t0) cc_final: 0.8876 (t0) REVERT: B 204 ASP cc_start: 0.7623 (m-30) cc_final: 0.7360 (m-30) REVERT: B 269 GLU cc_start: 0.8061 (pm20) cc_final: 0.7619 (pt0) REVERT: C 204 ASP cc_start: 0.7623 (m-30) cc_final: 0.7352 (m-30) REVERT: C 269 GLU cc_start: 0.8058 (pm20) cc_final: 0.7635 (pt0) REVERT: D 204 ASP cc_start: 0.7653 (m-30) cc_final: 0.7376 (m-30) REVERT: D 269 GLU cc_start: 0.8071 (pm20) cc_final: 0.7633 (pt0) REVERT: D 578 LYS cc_start: 0.5284 (tttm) cc_final: 0.4833 (tmmt) outliers start: 23 outliers final: 21 residues processed: 216 average time/residue: 0.0969 time to fit residues: 33.3438 Evaluate side-chains 202 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 526 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain D residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 ASN C 302 ASN D 238 ASN D 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113232 restraints weight = 21193.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114468 restraints weight = 15630.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115180 restraints weight = 12998.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115474 restraints weight = 11151.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115610 restraints weight = 11046.934| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4812 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= 0.135 Angle : 0.540 7.832 20608 Z= 0.281 Chirality : 0.041 0.145 2312 Planarity : 0.003 0.035 2540 Dihedral : 12.789 150.738 2120 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.60 % Allowed : 17.72 % Favored : 80.68 % 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: 1.09 (0.20), residues: 1792 helix: 1.24 (0.15), residues: 1084 sheet: 0.64 (0.79), residues: 48 loop : 0.00 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.015 0.001 TYR C 196 PHE 0.012 0.001 PHE D 574 TRP 0.017 0.001 TRP D 168 HIS 0.004 0.002 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15196) covalent geometry : angle 0.54032 / 0.28 (20608) hydrogen bonds : bond 0.03530 / 2.28 ( 904) hydrogen bonds : angle 4.48548 / 3.19 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2126.29 seconds wall clock time: 37 minutes 56.75 seconds (2276.75 seconds total)