Starting phenix.real_space_refine on Mon Jul 6 21:52:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfa_29983/07_2026/8gfa_29983_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfa_29983/07_2026/8gfa_29983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gfa_29983/07_2026/8gfa_29983_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfa_29983/07_2026/8gfa_29983_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gfa_29983/07_2026/8gfa_29983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfa_29983/07_2026/8gfa_29983.map" } resolution = 2.29 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= 0.017 sd= 0.093 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: 8 Type Number sf(0) Gaussians P 32 5.49 5 S 120 5.16 5 Cl 4 4.86 5 Na 2 4.78 5 C 12888 2.51 5 N 2812 2.21 5 O 3441 1.98 5 H 17380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 36679 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "B" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "C" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 8657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8657 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 486 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'DU0': 1, 'POV': 9, 'ZEI': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 538 Unusual residues: {'DU0': 1, 'POV': 10, 'ZEI': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 434 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'DU0': 1, 'POV': 8, 'ZEI': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 486 Unusual residues: {'DU0': 1, 'POV': 9, 'ZEI': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 5.83, per 1000 atoms: 0.16 Number of scatterers: 36679 At special positions: 0 Unit cell: (118.035, 118.68, 110.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 4 17.00 S 120 16.00 P 32 15.00 Na 2 11.00 O 3441 8.00 N 2812 7.00 C 12888 6.00 H 17380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 391 " distance=2.03 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: 3.42 Conformation dependent library (CDL) restraints added in 751.3 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 65.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.597A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.798A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.651A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.637A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 4.322A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.571A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'A' and resid 575 through 599 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.569A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 715 removed outlier: 3.563A pdb=" N ALA A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.596A pdb=" N LEU B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.798A pdb=" N LEU B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 314 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.651A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 430 through 455 removed outlier: 3.636A pdb=" N ILE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 removed outlier: 4.323A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.571A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 559 through 575 Processing helix chain 'B' and resid 575 through 599 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.570A pdb=" N LYS B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 715 removed outlier: 3.564A pdb=" N ALA B 691 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 214 through 224 removed outlier: 3.596A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.797A pdb=" N LEU C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.652A pdb=" N GLN C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 430 through 455 removed outlier: 3.637A pdb=" N ILE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 477 " --> pdb=" O PHE C 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 510 removed outlier: 4.322A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.571A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 Processing helix chain 'C' and resid 559 through 575 Processing helix chain 'C' and resid 575 through 599 Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.570A pdb=" N LYS C 640 " --> pdb=" O LEU C 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 644 No H-bonds generated for 'chain 'C' and resid 642 through 644' Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 715 removed outlier: 3.563A pdb=" N ALA C 691 " --> pdb=" O VAL C 687 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.596A pdb=" N LEU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 271 removed outlier: 3.798A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 321 removed outlier: 3.707A pdb=" N PHE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 346 through 355 removed outlier: 3.652A pdb=" N GLN D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.049A pdb=" N LEU D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 430 Processing helix chain 'D' and resid 430 through 455 removed outlier: 3.637A pdb=" N ILE D 434 " --> pdb=" O PHE D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 499 removed outlier: 3.707A pdb=" N TYR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 477 " --> pdb=" O PHE D 473 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 510 removed outlier: 4.322A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.570A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 559 through 575 Processing helix chain 'D' and resid 575 through 599 Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.570A pdb=" N LYS D 640 " --> pdb=" O LEU D 636 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 644 No H-bonds generated for 'chain 'D' and resid 642 through 644' Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 715 removed outlier: 3.564A pdb=" N ALA D 691 " --> pdb=" O VAL D 687 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 375 removed outlier: 7.202A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA A 374 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 375 removed outlier: 7.202A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA B 374 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 370 through 375 removed outlier: 7.203A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 370 through 375 removed outlier: 7.202A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA D 374 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2892 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: 7.85 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 17352 1.01 - 1.22: 98 1.22 - 1.43: 7831 1.43 - 1.63: 11483 1.63 - 1.84: 208 Bond restraints: 36972 Sorted by residual: bond pdb=" CG LEU A 638 " pdb=" CD2 LEU A 638 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.85e+01 bond pdb=" CG LEU B 638 " pdb=" CD2 LEU B 638 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.84e+01 bond pdb=" CG LEU D 638 " pdb=" CD2 LEU D 638 " ideal model delta sigma weight residual 1.521 1.379 0.142 3.30e-02 9.18e+02 1.84e+01 bond pdb=" CG LEU C 638 " pdb=" CD2 LEU C 638 " ideal model delta sigma weight residual 1.521 1.380 0.141 3.30e-02 9.18e+02 1.84e+01 bond pdb="C315 POV D1207 " pdb="C316 POV D1207 " ideal model delta sigma weight residual 1.522 1.437 0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 36967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.24: 65295 5.24 - 10.49: 197 10.49 - 15.73: 8 15.73 - 20.98: 0 20.98 - 26.22: 12 Bond angle restraints: 65512 Sorted by residual: angle pdb=" CG1 VAL A 295 " pdb=" CB VAL A 295 " pdb=" HB VAL A 295 " ideal model delta sigma weight residual 108.00 81.78 26.22 3.00e+00 1.11e-01 7.64e+01 angle pdb=" CG1 VAL D 295 " pdb=" CB VAL D 295 " pdb=" HB VAL D 295 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL B 295 " pdb=" CB VAL B 295 " pdb=" HB VAL B 295 " ideal model delta sigma weight residual 108.00 81.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb=" CG1 VAL C 295 " pdb=" CB VAL C 295 " pdb=" HB VAL C 295 " ideal model delta sigma weight residual 108.00 81.83 26.17 3.00e+00 1.11e-01 7.61e+01 angle pdb=" CG2 VAL B 295 " pdb=" CB VAL B 295 " pdb=" HB VAL B 295 " ideal model delta sigma weight residual 108.00 83.22 24.78 3.00e+00 1.11e-01 6.82e+01 ... (remaining 65507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 17572 35.57 - 71.14: 612 71.14 - 106.71: 64 106.71 - 142.27: 28 142.27 - 177.84: 16 Dihedral angle restraints: 18292 sinusoidal: 10520 harmonic: 7772 Sorted by residual: dihedral pdb=" CA ASN C 260 " pdb=" C ASN C 260 " pdb=" N GLN C 261 " pdb=" CA GLN C 261 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ASN A 260 " pdb=" C ASN A 260 " pdb=" N GLN A 261 " pdb=" CA GLN A 261 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ASN B 260 " pdb=" C ASN B 260 " pdb=" N GLN B 261 " pdb=" CA GLN B 261 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 18289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 2756 0.337 - 0.675: 0 0.675 - 1.012: 0 1.012 - 1.349: 0 1.349 - 1.687: 4 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CB VAL C 295 " pdb=" CA VAL C 295 " pdb=" CG1 VAL C 295 " pdb=" CG2 VAL C 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.94 -1.69 2.00e-01 2.50e+01 7.11e+01 chirality pdb=" CB VAL A 295 " pdb=" CA VAL A 295 " pdb=" CG1 VAL A 295 " pdb=" CG2 VAL A 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.94 -1.68 2.00e-01 2.50e+01 7.09e+01 chirality pdb=" CB VAL D 295 " pdb=" CA VAL D 295 " pdb=" CG1 VAL D 295 " pdb=" CG2 VAL D 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.95 -1.68 2.00e-01 2.50e+01 7.06e+01 ... (remaining 2757 not shown) Planarity restraints: 5128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 298 " -0.185 2.00e-02 2.50e+03 1.99e-01 5.94e+02 pdb=" CG ASN A 298 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 298 " 0.155 2.00e-02 2.50e+03 pdb=" ND2 ASN A 298 " 0.011 2.00e-02 2.50e+03 pdb="HD21 ASN A 298 " 0.290 2.00e-02 2.50e+03 pdb="HD22 ASN A 298 " -0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 298 " 0.185 2.00e-02 2.50e+03 1.99e-01 5.92e+02 pdb=" CG ASN B 298 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN B 298 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN B 298 " -0.011 2.00e-02 2.50e+03 pdb="HD21 ASN B 298 " -0.289 2.00e-02 2.50e+03 pdb="HD22 ASN B 298 " 0.306 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 298 " 0.184 2.00e-02 2.50e+03 1.98e-01 5.88e+02 pdb=" CG ASN D 298 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN D 298 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN D 298 " -0.012 2.00e-02 2.50e+03 pdb="HD21 ASN D 298 " -0.288 2.00e-02 2.50e+03 pdb="HD22 ASN D 298 " 0.305 2.00e-02 2.50e+03 ... (remaining 5125 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3874 2.24 - 2.83: 79411 2.83 - 3.42: 97245 3.42 - 4.01: 138959 4.01 - 4.60: 214984 Nonbonded interactions: 534473 Sorted by model distance: nonbonded pdb=" O HIS C 365 " pdb="HH22 ARG C 740 " model vdw 1.647 2.450 nonbonded pdb=" O HIS B 365 " pdb="HH22 ARG B 740 " model vdw 1.647 2.450 nonbonded pdb=" O HIS D 365 " pdb="HH22 ARG D 740 " model vdw 1.647 2.450 nonbonded pdb=" O HIS A 365 " pdb="HH22 ARG A 740 " model vdw 1.648 2.450 nonbonded pdb=" O ARG D 356 " pdb=" H ARG D 368 " model vdw 1.648 2.450 ... (remaining 534468 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 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) selection = (chain 'B' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) selection = (chain 'C' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) selection = (chain 'D' and (resid 199 through 1201 or (resid 1205 through 1207 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1208 through 1209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.240 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.980 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.018 0.142 19596 Z= 0.731 Angle : 1.234 14.613 26204 Z= 0.585 Chirality : 0.097 1.687 2760 Planarity : 0.006 0.045 3064 Dihedral : 20.024 177.844 8192 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -3.88 (0.15), residues: 2108 helix: -2.54 (0.11), residues: 1260 sheet: -1.97 (0.48), residues: 56 loop : -2.39 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.004 ARG D 499 TYR 0.026 0.004 TYR B 584 PHE 0.053 0.005 PHE A 449 TRP 0.033 0.004 TRP D 698 HIS 0.012 0.003 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.01776 / 0.73 (19592) covalent geometry : angle 1.23323 / 0.59 (26196) SS BOND : bond 0.00053 / 0.03 ( 4) SS BOND : angle 2.26198 / 1.39 ( 8) hydrogen bonds : bond 0.25803 / 17.36 ( 996) hydrogen bonds : angle 8.81716 / 6.41 ( 2892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 SER cc_start: 0.7731 (m) cc_final: 0.7356 (p) REVERT: A 335 MET cc_start: 0.7448 (mmm) cc_final: 0.6852 (mmt) REVERT: B 308 SER cc_start: 0.7742 (m) cc_final: 0.7340 (p) REVERT: B 507 PHE cc_start: 0.7752 (m-80) cc_final: 0.7477 (m-10) REVERT: C 363 CYS cc_start: 0.6231 (m) cc_final: 0.5978 (m) REVERT: C 379 HIS cc_start: 0.7354 (p90) cc_final: 0.7141 (p-80) REVERT: D 363 CYS cc_start: 0.6292 (m) cc_final: 0.6079 (m) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 1.3712 time to fit residues: 572.4453 Evaluate side-chains 220 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 GLN A 298 ASN A 629 ASN B 274 GLN B 298 ASN B 420 ASN B 629 ASN C 274 GLN C 298 ASN C 394 ASN C 629 ASN C 692 GLN D 274 GLN D 298 ASN D 394 ASN D 629 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.191284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136137 restraints weight = 60386.900| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.73 r_work: 0.3520 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19596 Z= 0.140 Angle : 0.613 11.344 26204 Z= 0.316 Chirality : 0.067 1.479 2760 Planarity : 0.005 0.050 3064 Dihedral : 21.762 169.498 4144 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.23 % Favored : 96.58 % Rotamer: Outliers : 1.28 % Allowed : 11.67 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.41 (0.17), residues: 2108 helix: -0.26 (0.13), residues: 1280 sheet: -2.09 (0.42), residues: 76 loop : -1.86 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.018 0.002 TYR B 632 PHE 0.013 0.002 PHE A 721 TRP 0.021 0.002 TRP A 698 HIS 0.002 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19592) covalent geometry : angle 0.61324 / 0.32 (26196) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.92859 / 0.60 ( 8) hydrogen bonds : bond 0.04894 / 3.37 ( 996) hydrogen bonds : angle 4.87198 / 3.59 ( 2892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 290 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASN cc_start: 0.6983 (t0) cc_final: 0.6313 (t0) REVERT: A 312 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7083 (mm-30) REVERT: A 379 HIS cc_start: 0.7297 (p-80) cc_final: 0.6878 (p-80) REVERT: A 398 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7567 (tt0) REVERT: A 502 SER cc_start: 0.7403 (t) cc_final: 0.7028 (p) REVERT: A 692 GLN cc_start: 0.7528 (mm110) cc_final: 0.7194 (tp40) REVERT: A 728 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: A 747 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6354 (tm-30) REVERT: B 311 ASN cc_start: 0.6941 (t0) cc_final: 0.6536 (t0) REVERT: B 312 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 315 MET cc_start: 0.6911 (mtt) cc_final: 0.6223 (mtt) REVERT: B 379 HIS cc_start: 0.6888 (p90) cc_final: 0.6543 (p-80) REVERT: B 398 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7433 (tt0) REVERT: B 502 SER cc_start: 0.7294 (t) cc_final: 0.6947 (p) REVERT: B 507 PHE cc_start: 0.8072 (m-80) cc_final: 0.7688 (m-80) REVERT: B 688 ASN cc_start: 0.8352 (t160) cc_final: 0.8148 (m110) REVERT: B 747 GLU cc_start: 0.6467 (tm-30) cc_final: 0.6214 (tm-30) REVERT: C 375 TYR cc_start: 0.7944 (t80) cc_final: 0.7589 (t80) REVERT: C 379 HIS cc_start: 0.6920 (p90) cc_final: 0.6634 (p-80) REVERT: C 398 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7433 (tt0) REVERT: C 500 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7241 (mmm160) REVERT: C 502 SER cc_start: 0.7296 (t) cc_final: 0.6966 (p) REVERT: C 507 PHE cc_start: 0.8099 (m-80) cc_final: 0.7643 (m-80) REVERT: C 688 ASN cc_start: 0.8345 (t160) cc_final: 0.8136 (m110) REVERT: C 692 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7265 (mm110) REVERT: C 747 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6416 (tm-30) REVERT: D 311 ASN cc_start: 0.6878 (t0) cc_final: 0.6425 (t0) REVERT: D 312 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7276 (mm-30) REVERT: D 315 MET cc_start: 0.6873 (mtt) cc_final: 0.5993 (mtt) REVERT: D 379 HIS cc_start: 0.6925 (p90) cc_final: 0.6584 (p-80) REVERT: D 398 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7437 (tt0) REVERT: D 433 ARG cc_start: 0.7615 (mmm160) cc_final: 0.7186 (tpt170) REVERT: D 502 SER cc_start: 0.7299 (t) cc_final: 0.6960 (p) REVERT: D 503 MET cc_start: 0.7031 (mmt) cc_final: 0.6829 (mmp) REVERT: D 507 PHE cc_start: 0.8136 (m-80) cc_final: 0.7666 (m-80) REVERT: D 688 ASN cc_start: 0.8355 (t160) cc_final: 0.8146 (m110) REVERT: D 692 GLN cc_start: 0.7342 (mm110) cc_final: 0.7034 (tp40) REVERT: D 747 GLU cc_start: 0.6482 (tm-30) cc_final: 0.6226 (tm-30) outliers start: 24 outliers final: 9 residues processed: 310 average time/residue: 1.0911 time to fit residues: 395.0703 Evaluate side-chains 254 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 728 GLN C 311 ASN C 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.184365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126332 restraints weight = 60006.056| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.84 r_work: 0.3374 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19596 Z= 0.218 Angle : 0.637 11.371 26204 Z= 0.328 Chirality : 0.070 1.554 2760 Planarity : 0.004 0.056 3064 Dihedral : 20.855 175.715 4144 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.13 % Favored : 96.68 % Rotamer: Outliers : 1.87 % Allowed : 13.70 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2108 helix: 0.50 (0.14), residues: 1276 sheet: -2.36 (0.47), residues: 76 loop : -1.69 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 499 TYR 0.022 0.002 TYR D 632 PHE 0.019 0.002 PHE D 650 TRP 0.016 0.002 TRP A 698 HIS 0.003 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (19592) covalent geometry : angle 0.63658 / 0.33 (26196) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.67727 / 0.44 ( 8) hydrogen bonds : bond 0.05018 / 3.43 ( 996) hydrogen bonds : angle 4.65583 / 3.43 ( 2892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASN cc_start: 0.6982 (t0) cc_final: 0.6459 (t0) REVERT: A 312 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 479 ILE cc_start: 0.8594 (mp) cc_final: 0.8306 (mt) REVERT: A 483 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 500 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7301 (mmm160) REVERT: A 692 GLN cc_start: 0.7742 (mm110) cc_final: 0.7179 (tp-100) REVERT: A 728 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: B 309 MET cc_start: 0.8120 (tpp) cc_final: 0.7908 (tpp) REVERT: B 311 ASN cc_start: 0.7012 (t0) cc_final: 0.6407 (t0) REVERT: B 312 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 500 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7282 (mmm160) REVERT: B 636 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8295 (tm) REVERT: B 692 GLN cc_start: 0.7737 (mm110) cc_final: 0.7138 (tp-100) REVERT: B 717 MET cc_start: 0.5110 (ttt) cc_final: 0.4569 (mtt) REVERT: C 309 MET cc_start: 0.8141 (tpp) cc_final: 0.7919 (tpp) REVERT: C 311 ASN cc_start: 0.7129 (t0) cc_final: 0.6551 (t0) REVERT: C 398 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7723 (tt0) REVERT: C 499 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7528 (mtt180) REVERT: C 636 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8314 (tm) REVERT: C 692 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7217 (tp-100) REVERT: D 309 MET cc_start: 0.8113 (tpp) cc_final: 0.7863 (tpp) REVERT: D 311 ASN cc_start: 0.6980 (t0) cc_final: 0.6477 (t0) REVERT: D 312 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7373 (mm-30) REVERT: D 398 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7746 (tt0) REVERT: D 433 ARG cc_start: 0.7695 (mmm160) cc_final: 0.7298 (tpt170) REVERT: D 499 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7521 (mtt180) REVERT: D 500 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7359 (mmm160) REVERT: D 636 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8286 (tm) REVERT: D 692 GLN cc_start: 0.7662 (mm110) cc_final: 0.7109 (tp-100) REVERT: D 717 MET cc_start: 0.5084 (ttt) cc_final: 0.4532 (mtt) REVERT: D 737 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6632 (m-30) outliers start: 35 outliers final: 6 residues processed: 277 average time/residue: 1.1100 time to fit residues: 355.7797 Evaluate side-chains 235 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 107 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN B 394 ASN B 728 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.183331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125669 restraints weight = 60235.621| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.84 r_work: 0.3362 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19596 Z= 0.206 Angle : 0.604 11.322 26204 Z= 0.311 Chirality : 0.070 1.551 2760 Planarity : 0.004 0.055 3064 Dihedral : 19.884 175.482 4144 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.42 % Favored : 96.39 % Rotamer: Outliers : 2.57 % Allowed : 14.29 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.22 (0.18), residues: 2108 helix: 0.83 (0.14), residues: 1288 sheet: -2.42 (0.47), residues: 76 loop : -1.59 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 499 TYR 0.020 0.002 TYR D 632 PHE 0.018 0.002 PHE A 721 TRP 0.016 0.002 TRP C 698 HIS 0.002 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (19592) covalent geometry : angle 0.60373 / 0.31 (26196) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.95759 / 0.61 ( 8) hydrogen bonds : bond 0.04654 / 3.19 ( 996) hydrogen bonds : angle 4.44969 / 3.28 ( 2892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6806 (t80) REVERT: A 311 ASN cc_start: 0.7068 (t0) cc_final: 0.6494 (t0) REVERT: A 312 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 483 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 500 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7335 (mmm160) REVERT: A 561 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: A 636 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8243 (tm) REVERT: B 309 MET cc_start: 0.8095 (tpp) cc_final: 0.7817 (tpp) REVERT: B 311 ASN cc_start: 0.7050 (t0) cc_final: 0.6461 (t0) REVERT: B 312 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 500 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7333 (mmm160) REVERT: B 561 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 636 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8246 (tm) REVERT: B 692 GLN cc_start: 0.7699 (mm110) cc_final: 0.7384 (tp40) REVERT: C 309 MET cc_start: 0.8130 (tpp) cc_final: 0.7655 (tpp) REVERT: C 311 ASN cc_start: 0.7146 (t0) cc_final: 0.6627 (t0) REVERT: C 500 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7338 (mmm160) REVERT: C 561 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: C 636 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8240 (tm) REVERT: C 717 MET cc_start: 0.5095 (ttt) cc_final: 0.4512 (mtt) REVERT: D 309 MET cc_start: 0.8122 (tpp) cc_final: 0.7876 (tpp) REVERT: D 311 ASN cc_start: 0.7032 (t0) cc_final: 0.6481 (t0) REVERT: D 312 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7475 (mm-30) REVERT: D 315 MET cc_start: 0.7004 (mtt) cc_final: 0.5998 (mtt) REVERT: D 433 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7296 (tpt170) REVERT: D 500 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7259 (mmm160) REVERT: D 561 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: D 636 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8252 (tm) outliers start: 48 outliers final: 19 residues processed: 277 average time/residue: 1.3030 time to fit residues: 411.8178 Evaluate side-chains 248 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 728 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.182908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125412 restraints weight = 60481.541| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.85 r_work: 0.3362 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19596 Z= 0.183 Angle : 0.577 11.351 26204 Z= 0.298 Chirality : 0.069 1.549 2760 Planarity : 0.004 0.053 3064 Dihedral : 18.680 169.492 4144 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.37 % Favored : 96.44 % Rotamer: Outliers : 2.41 % Allowed : 15.47 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.04 (0.18), residues: 2108 helix: 1.04 (0.14), residues: 1292 sheet: -2.53 (0.43), residues: 84 loop : -1.46 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.020 0.002 TYR B 375 PHE 0.017 0.002 PHE B 721 TRP 0.019 0.002 TRP D 273 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (19592) covalent geometry : angle 0.57667 / 0.30 (26196) SS BOND : bond 0.00087 / 0.04 ( 4) SS BOND : angle 0.63942 / 0.41 ( 8) hydrogen bonds : bond 0.04478 / 3.07 ( 996) hydrogen bonds : angle 4.31954 / 3.17 ( 2892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 TYR cc_start: 0.7848 (t80) cc_final: 0.7644 (t80) REVERT: A 305 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6871 (t80) REVERT: A 309 MET cc_start: 0.8068 (tpp) cc_final: 0.7794 (tpp) REVERT: A 311 ASN cc_start: 0.7132 (t0) cc_final: 0.6532 (t0) REVERT: A 312 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 483 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 500 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7445 (mmm160) REVERT: A 636 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8233 (tm) REVERT: A 692 GLN cc_start: 0.7767 (mm110) cc_final: 0.7451 (tp40) REVERT: B 309 MET cc_start: 0.8092 (tpp) cc_final: 0.7608 (tpp) REVERT: B 311 ASN cc_start: 0.7067 (t0) cc_final: 0.6540 (t0) REVERT: B 312 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 379 HIS cc_start: 0.7093 (p90) cc_final: 0.6892 (p-80) REVERT: B 433 ARG cc_start: 0.7921 (tpt170) cc_final: 0.7516 (tpt170) REVERT: B 500 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7437 (mmm160) REVERT: B 636 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8249 (tm) REVERT: B 692 GLN cc_start: 0.7723 (mm110) cc_final: 0.7403 (tp40) REVERT: C 309 MET cc_start: 0.8110 (tpp) cc_final: 0.7811 (tpp) REVERT: C 311 ASN cc_start: 0.7173 (t0) cc_final: 0.6633 (t0) REVERT: C 500 ARG cc_start: 0.7753 (mmm160) cc_final: 0.7256 (mmm160) REVERT: C 636 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8243 (tm) REVERT: C 692 GLN cc_start: 0.8005 (tp40) cc_final: 0.7135 (tp-100) REVERT: D 309 MET cc_start: 0.8109 (tpp) cc_final: 0.7690 (tpp) REVERT: D 311 ASN cc_start: 0.7113 (t0) cc_final: 0.6538 (t0) REVERT: D 312 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7475 (mm-30) REVERT: D 379 HIS cc_start: 0.7376 (p-80) cc_final: 0.7076 (p-80) REVERT: D 433 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7315 (tpt170) REVERT: D 500 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7249 (mmm160) REVERT: D 636 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8250 (tm) REVERT: D 737 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6521 (m-30) outliers start: 45 outliers final: 16 residues processed: 268 average time/residue: 1.1695 time to fit residues: 361.9242 Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 261 GLN B 728 GLN C 261 GLN C 438 ASN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.181880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124764 restraints weight = 60599.980| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.84 r_work: 0.3351 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19596 Z= 0.201 Angle : 0.594 11.073 26204 Z= 0.306 Chirality : 0.066 1.451 2760 Planarity : 0.004 0.053 3064 Dihedral : 18.684 160.972 4144 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.97 % Rotamer: Outliers : 2.25 % Allowed : 16.43 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.10 (0.18), residues: 2108 helix: 1.07 (0.14), residues: 1280 sheet: -2.46 (0.45), residues: 84 loop : -1.38 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 429 TYR 0.017 0.002 TYR D 632 PHE 0.019 0.002 PHE C 721 TRP 0.014 0.002 TRP D 698 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (19592) covalent geometry : angle 0.59406 / 0.31 (26196) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 0.67868 / 0.43 ( 8) hydrogen bonds : bond 0.04553 / 3.11 ( 996) hydrogen bonds : angle 4.33521 / 3.17 ( 2892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 TYR cc_start: 0.7853 (t80) cc_final: 0.7645 (t80) REVERT: A 305 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6807 (t80) REVERT: A 311 ASN cc_start: 0.7228 (t0) cc_final: 0.6826 (t0) REVERT: A 312 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 315 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6358 (mtt) REVERT: A 433 ARG cc_start: 0.7921 (tpt170) cc_final: 0.7521 (tpt170) REVERT: A 479 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8285 (mt) REVERT: A 483 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 500 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7370 (mmm160) REVERT: A 636 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8226 (tm) REVERT: A 689 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8105 (mptp) REVERT: A 717 MET cc_start: 0.5323 (ttt) cc_final: 0.4745 (mtt) REVERT: A 728 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: B 305 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6619 (t80) REVERT: B 309 MET cc_start: 0.8083 (tpp) cc_final: 0.7608 (tpp) REVERT: B 311 ASN cc_start: 0.7216 (t0) cc_final: 0.6586 (t0) REVERT: B 312 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 433 ARG cc_start: 0.7917 (tpt170) cc_final: 0.7510 (tpt170) REVERT: B 500 ARG cc_start: 0.7814 (mmm160) cc_final: 0.7452 (mmm160) REVERT: B 636 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8241 (tm) REVERT: C 305 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6615 (t80) REVERT: C 309 MET cc_start: 0.8085 (tpp) cc_final: 0.7785 (tpp) REVERT: C 311 ASN cc_start: 0.7292 (t0) cc_final: 0.6711 (t0) REVERT: C 364 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7083 (ttp-110) REVERT: C 433 ARG cc_start: 0.7911 (tpt170) cc_final: 0.7514 (tpt170) REVERT: C 500 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7280 (mmm160) REVERT: C 636 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8257 (tm) REVERT: C 692 GLN cc_start: 0.8032 (tp40) cc_final: 0.7171 (tp-100) REVERT: D 305 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6550 (t80) REVERT: D 309 MET cc_start: 0.8089 (tpp) cc_final: 0.7532 (tpp) REVERT: D 311 ASN cc_start: 0.7207 (t0) cc_final: 0.6804 (t0) REVERT: D 379 HIS cc_start: 0.7319 (p-80) cc_final: 0.7014 (p-80) REVERT: D 433 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7301 (tpt170) REVERT: D 500 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7298 (mmm160) REVERT: D 636 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8250 (tm) REVERT: D 737 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6573 (m-30) outliers start: 42 outliers final: 17 residues processed: 252 average time/residue: 1.1800 time to fit residues: 341.7826 Evaluate side-chains 256 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 202 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 261 GLN B 438 ASN B 728 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.182250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124787 restraints weight = 60643.842| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.85 r_work: 0.3355 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19596 Z= 0.189 Angle : 0.581 11.015 26204 Z= 0.299 Chirality : 0.067 1.477 2760 Planarity : 0.004 0.053 3064 Dihedral : 18.082 145.867 4144 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 2.14 % Allowed : 16.86 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.20 (0.18), residues: 2108 helix: 1.15 (0.14), residues: 1280 sheet: -2.42 (0.47), residues: 84 loop : -1.33 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.016 0.002 TYR D 632 PHE 0.018 0.002 PHE C 721 TRP 0.017 0.002 TRP D 273 HIS 0.001 0.000 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (19592) covalent geometry : angle 0.58106 / 0.30 (26196) SS BOND : bond 0.00065 / 0.03 ( 4) SS BOND : angle 0.65142 / 0.42 ( 8) hydrogen bonds : bond 0.04457 / 3.05 ( 996) hydrogen bonds : angle 4.27219 / 3.13 ( 2892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 309 MET cc_start: 0.8091 (tpp) cc_final: 0.7648 (tpp) REVERT: A 311 ASN cc_start: 0.7327 (t0) cc_final: 0.6655 (t0) REVERT: A 312 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 433 ARG cc_start: 0.7927 (tpt170) cc_final: 0.7528 (tpt170) REVERT: A 483 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 500 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7439 (mmm160) REVERT: A 506 LEU cc_start: 0.7859 (mm) cc_final: 0.7484 (mt) REVERT: A 636 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8233 (tm) REVERT: A 692 GLN cc_start: 0.7764 (mm110) cc_final: 0.7454 (tp40) REVERT: A 728 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: B 305 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 309 MET cc_start: 0.8112 (tpp) cc_final: 0.7667 (tpp) REVERT: B 311 ASN cc_start: 0.7326 (t0) cc_final: 0.6671 (t0) REVERT: B 312 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 433 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7481 (tpt170) REVERT: B 500 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7431 (mmm160) REVERT: B 506 LEU cc_start: 0.7789 (mm) cc_final: 0.7510 (mt) REVERT: B 636 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8255 (tm) REVERT: B 692 GLN cc_start: 0.7754 (mm110) cc_final: 0.7449 (tp40) REVERT: B 717 MET cc_start: 0.5455 (tmt) cc_final: 0.5238 (tmt) REVERT: C 305 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6595 (t80) REVERT: C 309 MET cc_start: 0.8120 (tpp) cc_final: 0.7853 (tpp) REVERT: C 311 ASN cc_start: 0.7341 (t0) cc_final: 0.6741 (t0) REVERT: C 364 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7115 (ttp-110) REVERT: C 433 ARG cc_start: 0.7912 (tpt170) cc_final: 0.7519 (tpt170) REVERT: C 500 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7274 (mmm160) REVERT: C 506 LEU cc_start: 0.7840 (mm) cc_final: 0.7543 (mt) REVERT: C 636 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8246 (tm) REVERT: C 737 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: D 305 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6578 (t80) REVERT: D 309 MET cc_start: 0.8129 (tpp) cc_final: 0.7599 (tpp) REVERT: D 364 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7049 (ttp-170) REVERT: D 433 ARG cc_start: 0.7702 (mmm160) cc_final: 0.7298 (tpt170) REVERT: D 500 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7268 (mmm160) REVERT: D 506 LEU cc_start: 0.7833 (mm) cc_final: 0.7515 (mt) REVERT: D 636 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8264 (tm) REVERT: D 737 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6615 (m-30) outliers start: 40 outliers final: 17 residues processed: 263 average time/residue: 1.1308 time to fit residues: 342.3877 Evaluate side-chains 257 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 261 GLN B 728 GLN C 261 GLN C 692 GLN D 261 GLN D 438 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.181404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124313 restraints weight = 60609.147| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.83 r_work: 0.3348 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 19596 Z= 0.209 Angle : 0.599 11.057 26204 Z= 0.309 Chirality : 0.067 1.476 2760 Planarity : 0.004 0.051 3064 Dihedral : 17.946 116.122 4144 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.09 % Allowed : 16.49 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.14 (0.18), residues: 2108 helix: 1.08 (0.14), residues: 1280 sheet: -2.36 (0.47), residues: 84 loop : -1.31 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 213 TYR 0.017 0.002 TYR D 632 PHE 0.020 0.002 PHE A 721 TRP 0.018 0.002 TRP D 273 HIS 0.001 0.000 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (19592) covalent geometry : angle 0.59919 / 0.31 (26196) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 0.65748 / 0.42 ( 8) hydrogen bonds : bond 0.04574 / 3.12 ( 996) hydrogen bonds : angle 4.34247 / 3.18 ( 2892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6784 (t80) REVERT: A 309 MET cc_start: 0.8098 (tpp) cc_final: 0.7845 (tpp) REVERT: A 311 ASN cc_start: 0.7399 (t0) cc_final: 0.6721 (t0) REVERT: A 433 ARG cc_start: 0.7904 (tpt170) cc_final: 0.7501 (tpt170) REVERT: A 479 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8290 (mt) REVERT: A 483 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 500 ARG cc_start: 0.7790 (mmm160) cc_final: 0.7441 (mmm160) REVERT: A 636 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8230 (tm) REVERT: B 305 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6654 (t80) REVERT: B 309 MET cc_start: 0.8101 (tpp) cc_final: 0.7868 (tpp) REVERT: B 311 ASN cc_start: 0.7425 (t0) cc_final: 0.6729 (t0) REVERT: B 312 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 433 ARG cc_start: 0.7887 (tpt170) cc_final: 0.7466 (tpt170) REVERT: B 500 ARG cc_start: 0.7778 (mmm160) cc_final: 0.7429 (mmm160) REVERT: B 636 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8255 (tm) REVERT: C 305 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6631 (t80) REVERT: C 309 MET cc_start: 0.8119 (tpp) cc_final: 0.7870 (tpp) REVERT: C 311 ASN cc_start: 0.7453 (t0) cc_final: 0.6836 (t0) REVERT: C 364 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7119 (ttp-110) REVERT: C 433 ARG cc_start: 0.7915 (tpt170) cc_final: 0.7510 (tpt170) REVERT: C 500 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7385 (mmm160) REVERT: C 636 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8254 (tm) REVERT: C 692 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7576 (mm110) REVERT: C 737 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: D 305 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6557 (t80) REVERT: D 309 MET cc_start: 0.8102 (tpp) cc_final: 0.7649 (tpp) REVERT: D 311 ASN cc_start: 0.7402 (t0) cc_final: 0.6951 (t0) REVERT: D 364 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7093 (ttp-110) REVERT: D 433 ARG cc_start: 0.7693 (mmm160) cc_final: 0.7291 (tpt170) REVERT: D 500 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7386 (mmm160) REVERT: D 507 PHE cc_start: 0.7908 (m-80) cc_final: 0.7589 (m-80) REVERT: D 636 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8268 (tm) REVERT: D 725 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7236 (pttm) REVERT: D 737 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6649 (m-30) outliers start: 39 outliers final: 17 residues processed: 261 average time/residue: 1.0461 time to fit residues: 315.9120 Evaluate side-chains 259 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Chi-restraints excluded: chain D residue 737 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 171 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 261 GLN B 728 GLN C 261 GLN C 749 ASN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126473 restraints weight = 60934.664| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.83 r_work: 0.3377 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19596 Z= 0.138 Angle : 0.547 10.910 26204 Z= 0.282 Chirality : 0.065 1.464 2760 Planarity : 0.004 0.049 3064 Dihedral : 16.877 95.781 4144 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.77 % Allowed : 17.08 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.50 (0.18), residues: 2108 helix: 1.38 (0.14), residues: 1292 sheet: -2.24 (0.50), residues: 76 loop : -1.25 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.013 0.001 TYR D 632 PHE 0.015 0.001 PHE A 721 TRP 0.023 0.002 TRP D 273 HIS 0.001 0.000 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (19592) covalent geometry : angle 0.54660 / 0.28 (26196) SS BOND : bond 0.00075 / 0.04 ( 4) SS BOND : angle 0.68366 / 0.44 ( 8) hydrogen bonds : bond 0.04136 / 2.83 ( 996) hydrogen bonds : angle 4.15725 / 3.05 ( 2892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.6985 (m-30) cc_final: 0.6323 (m-30) REVERT: A 305 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6813 (t80) REVERT: A 309 MET cc_start: 0.8105 (tpp) cc_final: 0.7864 (tpp) REVERT: A 311 ASN cc_start: 0.7290 (t0) cc_final: 0.6751 (t0) REVERT: A 433 ARG cc_start: 0.7843 (tpt170) cc_final: 0.7449 (tpt170) REVERT: A 500 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7380 (mmm160) REVERT: A 692 GLN cc_start: 0.7685 (mm110) cc_final: 0.7401 (tp40) REVERT: A 753 TRP cc_start: 0.6294 (m100) cc_final: 0.6036 (m100) REVERT: B 235 ASP cc_start: 0.6977 (m-30) cc_final: 0.6321 (m-30) REVERT: B 305 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6528 (t80) REVERT: B 309 MET cc_start: 0.8111 (tpp) cc_final: 0.7878 (tpp) REVERT: B 433 ARG cc_start: 0.7855 (tpt170) cc_final: 0.7439 (tpt170) REVERT: B 500 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7398 (mmm160) REVERT: B 506 LEU cc_start: 0.7776 (mm) cc_final: 0.7444 (mt) REVERT: B 692 GLN cc_start: 0.7684 (mm110) cc_final: 0.7400 (tp40) REVERT: B 717 MET cc_start: 0.5339 (tmt) cc_final: 0.5099 (tmt) REVERT: C 235 ASP cc_start: 0.7012 (m-30) cc_final: 0.6364 (m-30) REVERT: C 305 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6444 (t80) REVERT: C 309 MET cc_start: 0.8124 (tpp) cc_final: 0.7888 (tpp) REVERT: C 311 ASN cc_start: 0.7367 (t0) cc_final: 0.6770 (t0) REVERT: C 364 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.7009 (ttp-170) REVERT: C 433 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7475 (tpt170) REVERT: C 500 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7383 (mmm160) REVERT: C 506 LEU cc_start: 0.7971 (mm) cc_final: 0.7753 (mm) REVERT: C 692 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7306 (tp-100) REVERT: C 737 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: D 235 ASP cc_start: 0.6988 (m-30) cc_final: 0.6339 (m-30) REVERT: D 305 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6403 (t80) REVERT: D 309 MET cc_start: 0.8109 (tpp) cc_final: 0.7864 (tpp) REVERT: D 311 ASN cc_start: 0.7387 (t0) cc_final: 0.6904 (t0) REVERT: D 364 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6994 (ttp-170) REVERT: D 433 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7288 (tpt170) REVERT: D 500 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7362 (mmm160) REVERT: D 692 GLN cc_start: 0.7679 (mm110) cc_final: 0.7411 (tp40) REVERT: D 725 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7196 (pttm) outliers start: 33 outliers final: 13 residues processed: 258 average time/residue: 1.1972 time to fit residues: 356.2617 Evaluate side-chains 245 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.181764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124951 restraints weight = 61014.282| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.83 r_work: 0.3353 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19596 Z= 0.181 Angle : 0.579 11.014 26204 Z= 0.299 Chirality : 0.067 1.477 2760 Planarity : 0.004 0.051 3064 Dihedral : 17.177 89.811 4144 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.45 % Allowed : 18.15 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.43 (0.18), residues: 2108 helix: 1.29 (0.14), residues: 1292 sheet: -2.16 (0.47), residues: 84 loop : -1.20 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.016 0.002 TYR D 632 PHE 0.017 0.002 PHE A 721 TRP 0.025 0.002 TRP C 273 HIS 0.001 0.000 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (19592) covalent geometry : angle 0.57923 / 0.30 (26196) SS BOND : bond 0.00033 / 0.02 ( 4) SS BOND : angle 0.68039 / 0.44 ( 8) hydrogen bonds : bond 0.04402 / 3.01 ( 996) hydrogen bonds : angle 4.24101 / 3.11 ( 2892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7010 (m-30) cc_final: 0.6386 (m-30) REVERT: A 305 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6739 (t80) REVERT: A 309 MET cc_start: 0.8124 (tpp) cc_final: 0.7894 (tpp) REVERT: A 311 ASN cc_start: 0.7383 (t0) cc_final: 0.6803 (t0) REVERT: A 433 ARG cc_start: 0.7860 (tpt170) cc_final: 0.7466 (tpt170) REVERT: A 500 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7405 (mmm160) REVERT: A 506 LEU cc_start: 0.7772 (mm) cc_final: 0.7480 (mt) REVERT: A 692 GLN cc_start: 0.7735 (mm110) cc_final: 0.7442 (tp40) REVERT: A 753 TRP cc_start: 0.6309 (m100) cc_final: 0.5982 (m100) REVERT: B 235 ASP cc_start: 0.6962 (m-30) cc_final: 0.6324 (m-30) REVERT: B 305 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6580 (t80) REVERT: B 309 MET cc_start: 0.8097 (tpp) cc_final: 0.7880 (tpp) REVERT: B 311 ASN cc_start: 0.7383 (t0) cc_final: 0.6838 (t0) REVERT: B 433 ARG cc_start: 0.7873 (tpt170) cc_final: 0.7460 (tpt170) REVERT: B 500 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7402 (mmm160) REVERT: B 506 LEU cc_start: 0.7807 (mm) cc_final: 0.7463 (mt) REVERT: B 692 GLN cc_start: 0.7740 (mm110) cc_final: 0.7439 (tp40) REVERT: B 753 TRP cc_start: 0.6185 (m100) cc_final: 0.5838 (m100) REVERT: C 235 ASP cc_start: 0.6995 (m-30) cc_final: 0.6353 (m-30) REVERT: C 305 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6468 (t80) REVERT: C 309 MET cc_start: 0.8093 (tpp) cc_final: 0.7875 (tpp) REVERT: C 311 ASN cc_start: 0.7430 (t0) cc_final: 0.6812 (t0) REVERT: C 364 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7107 (ttp-170) REVERT: C 433 ARG cc_start: 0.7863 (tpt170) cc_final: 0.7463 (tpt170) REVERT: C 500 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7384 (mmm160) REVERT: C 692 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7271 (tp-100) REVERT: C 737 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: D 235 ASP cc_start: 0.6975 (m-30) cc_final: 0.6333 (m-30) REVERT: D 305 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6434 (t80) REVERT: D 309 MET cc_start: 0.8093 (tpp) cc_final: 0.7857 (tpp) REVERT: D 311 ASN cc_start: 0.7465 (t0) cc_final: 0.6964 (t0) REVERT: D 364 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7100 (ttp-110) REVERT: D 433 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7283 (tpt170) REVERT: D 500 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7369 (mmm160) REVERT: D 506 LEU cc_start: 0.7802 (mm) cc_final: 0.7497 (mt) REVERT: D 692 GLN cc_start: 0.7709 (mm110) cc_final: 0.7439 (tp40) REVERT: D 725 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7194 (pttm) REVERT: D 753 TRP cc_start: 0.6253 (m100) cc_final: 0.5866 (m100) outliers start: 27 outliers final: 12 residues processed: 243 average time/residue: 1.2287 time to fit residues: 343.5701 Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN A 749 ASN B 261 GLN C 261 GLN D 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.182362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126075 restraints weight = 60611.522| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.81 r_work: 0.3369 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19596 Z= 0.152 Angle : 0.556 10.961 26204 Z= 0.287 Chirality : 0.066 1.470 2760 Planarity : 0.004 0.050 3064 Dihedral : 16.594 87.701 4144 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.34 % Allowed : 18.52 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: 0.56 (0.18), residues: 2108 helix: 1.40 (0.14), residues: 1292 sheet: -2.05 (0.48), residues: 84 loop : -1.16 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.014 0.001 TYR D 632 PHE 0.015 0.002 PHE A 721 TRP 0.028 0.002 TRP B 273 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (19592) covalent geometry : angle 0.55547 / 0.29 (26196) SS BOND : bond 0.00064 / 0.03 ( 4) SS BOND : angle 0.63996 / 0.41 ( 8) hydrogen bonds : bond 0.04223 / 2.88 ( 996) hydrogen bonds : angle 4.17202 / 3.06 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17260.83 seconds wall clock time: 292 minutes 10.52 seconds (17530.52 seconds total)