Starting phenix.real_space_refine on Sat Mar 7 07:22:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfa_29983/03_2026/8gfa_29983_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfa_29983/03_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_29983/03_2026/8gfa_29983_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfa_29983/03_2026/8gfa_29983_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gfa_29983/03_2026/8gfa_29983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfa_29983/03_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-5986/lib/python3.9/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, 487 Unusual residues: {' NA': 1, 'DU0': 1, 'POV': 9, '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: "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, 435 Unusual residues: {' NA': 1, 'DU0': 1, 'POV': 8, '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: "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: 6.26, per 1000 atoms: 0.17 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: 2.67 Conformation dependent library (CDL) restraints added in 849.7 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: 0.70 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: 9.28 Time building geometry restraints manager: 3.60 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: 2.750 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: 0.160 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.390 Find NCS groups from input model: 0.840 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: 0.010 Load rotamer database and sin/cos tables:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 covalent geometry : bond 0.01776 (19592) covalent geometry : angle 1.23323 (26196) SS BOND : bond 0.00053 ( 4) SS BOND : angle 2.26198 ( 8) hydrogen bonds : bond 0.25803 ( 996) hydrogen bonds : angle 8.81716 ( 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 : 0.889 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: 1.4038 time to fit residues: 579.0048 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 : 0.917 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4330 r_free = 0.4330 target = 0.191397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135958 restraints weight = 60296.865| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.85 r_work: 0.3506 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2979 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= 0.135 Angle : 0.609 11.288 26204 Z= 0.313 Chirality : 0.067 1.475 2760 Planarity : 0.005 0.050 3064 Dihedral : 21.696 169.381 4144 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 1.28 % Allowed : 11.62 % Favored : 87.10 % 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: -1.38 (0.17), residues: 2108 helix: -0.24 (0.13), residues: 1280 sheet: -2.09 (0.42), residues: 76 loop : -1.84 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.017 0.002 TYR B 632 PHE 0.013 0.002 PHE A 721 TRP 0.021 0.002 TRP A 698 HIS 0.003 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00287 (19592) covalent geometry : angle 0.60877 (26196) SS BOND : bond 0.00091 ( 4) SS BOND : angle 0.94853 ( 8) hydrogen bonds : bond 0.04823 ( 996) hydrogen bonds : angle 4.83572 ( 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 317 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 0.814 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 311 ASN cc_start: 0.6922 (t0) cc_final: 0.6263 (t0) REVERT: A 312 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 379 HIS cc_start: 0.7316 (p-80) cc_final: 0.6910 (p-80) REVERT: A 398 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7613 (tt0) REVERT: A 502 SER cc_start: 0.7384 (t) cc_final: 0.7022 (p) REVERT: A 692 GLN cc_start: 0.7554 (mm110) cc_final: 0.7211 (tp40) REVERT: A 728 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6854 (tt0) REVERT: A 747 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6383 (tm-30) REVERT: B 311 ASN cc_start: 0.6901 (t0) cc_final: 0.6529 (t0) REVERT: B 312 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7204 (mm-30) REVERT: B 315 MET cc_start: 0.6867 (mtt) cc_final: 0.6242 (mtt) REVERT: B 379 HIS cc_start: 0.6898 (p90) cc_final: 0.6564 (p-80) REVERT: B 398 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7478 (tt0) REVERT: B 502 SER cc_start: 0.7271 (t) cc_final: 0.6937 (p) REVERT: B 507 PHE cc_start: 0.8079 (m-80) cc_final: 0.7697 (m-80) REVERT: B 692 GLN cc_start: 0.7474 (mm110) cc_final: 0.7112 (tp40) REVERT: B 747 GLU cc_start: 0.6482 (tm-30) cc_final: 0.6249 (tm-30) REVERT: C 375 TYR cc_start: 0.7957 (t80) cc_final: 0.7600 (t80) REVERT: C 379 HIS cc_start: 0.6937 (p90) cc_final: 0.6658 (p-80) REVERT: C 398 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7451 (tt0) REVERT: C 500 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7242 (mmm160) REVERT: C 502 SER cc_start: 0.7286 (t) cc_final: 0.6968 (p) REVERT: C 507 PHE cc_start: 0.8106 (m-80) cc_final: 0.7668 (m-80) REVERT: C 688 ASN cc_start: 0.8388 (t160) cc_final: 0.8166 (m110) REVERT: C 692 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7285 (mm110) REVERT: C 747 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6424 (tm-30) REVERT: D 311 ASN cc_start: 0.6839 (t0) cc_final: 0.6324 (t0) REVERT: D 312 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7246 (mm-30) REVERT: D 315 MET cc_start: 0.6851 (mtt) cc_final: 0.5865 (mtt) REVERT: D 379 HIS cc_start: 0.6941 (p90) cc_final: 0.6609 (p-80) REVERT: D 398 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7454 (tt0) REVERT: D 433 ARG cc_start: 0.7642 (mmm160) cc_final: 0.7213 (tpt170) REVERT: D 502 SER cc_start: 0.7294 (t) cc_final: 0.6970 (p) REVERT: D 507 PHE cc_start: 0.8146 (m-80) cc_final: 0.7675 (m-80) REVERT: D 688 ASN cc_start: 0.8364 (t160) cc_final: 0.8161 (m110) REVERT: D 692 GLN cc_start: 0.7390 (mm110) cc_final: 0.6852 (tp-100) REVERT: D 747 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6257 (tm-30) outliers start: 24 outliers final: 9 residues processed: 313 average time/residue: 1.0280 time to fit residues: 370.6922 Evaluate side-chains 255 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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: 0.9980 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 ASN C 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.184829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126807 restraints weight = 60037.430| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.84 r_work: 0.3380 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19596 Z= 0.202 Angle : 0.629 11.294 26204 Z= 0.324 Chirality : 0.070 1.548 2760 Planarity : 0.004 0.055 3064 Dihedral : 20.672 173.867 4144 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.13 % Favored : 96.68 % Rotamer: Outliers : 1.82 % Allowed : 13.60 % Favored : 84.58 % 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: -0.57 (0.18), residues: 2108 helix: 0.53 (0.14), residues: 1276 sheet: -2.35 (0.48), residues: 76 loop : -1.69 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 499 TYR 0.019 0.002 TYR D 632 PHE 0.019 0.002 PHE A 650 TRP 0.015 0.002 TRP A 698 HIS 0.003 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00448 (19592) covalent geometry : angle 0.62879 (26196) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.67098 ( 8) hydrogen bonds : bond 0.04951 ( 996) hydrogen bonds : angle 4.61210 ( 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 284 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASN cc_start: 0.6942 (t0) cc_final: 0.6412 (t0) REVERT: A 312 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 479 ILE cc_start: 0.8591 (mp) cc_final: 0.8301 (mt) REVERT: A 483 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 500 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7314 (mmm160) REVERT: A 692 GLN cc_start: 0.7719 (mm110) cc_final: 0.7155 (tp-100) REVERT: A 728 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: B 309 MET cc_start: 0.8132 (tpp) cc_final: 0.7878 (tpp) REVERT: B 311 ASN cc_start: 0.6979 (t0) cc_final: 0.6626 (t0) REVERT: B 312 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 315 MET cc_start: 0.7027 (mtt) cc_final: 0.6280 (mtt) REVERT: B 500 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7300 (mmm160) REVERT: B 636 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8299 (tm) REVERT: B 692 GLN cc_start: 0.7676 (mm110) cc_final: 0.7181 (tp-100) REVERT: C 309 MET cc_start: 0.8141 (tpp) cc_final: 0.7897 (tpp) REVERT: C 311 ASN cc_start: 0.7036 (t0) cc_final: 0.6448 (t0) REVERT: C 398 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7705 (tt0) REVERT: C 483 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8206 (mp) REVERT: C 499 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7475 (mtt180) REVERT: C 500 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7377 (mmm160) REVERT: C 636 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8298 (tm) REVERT: C 692 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7174 (tp-100) REVERT: D 309 MET cc_start: 0.8105 (tpp) cc_final: 0.7833 (tpp) REVERT: D 311 ASN cc_start: 0.6934 (t0) cc_final: 0.6412 (t0) REVERT: D 312 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7397 (mm-30) REVERT: D 398 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7718 (tt0) REVERT: D 433 ARG cc_start: 0.7691 (mmm160) cc_final: 0.7285 (tpt170) REVERT: D 499 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7478 (mtt180) REVERT: D 500 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7364 (mmm160) REVERT: D 636 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (tm) REVERT: D 692 GLN cc_start: 0.7661 (mm110) cc_final: 0.7092 (tp-100) outliers start: 34 outliers final: 10 residues processed: 276 average time/residue: 1.1493 time to fit residues: 361.4843 Evaluate side-chains 235 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 305 PHE 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 483 LEU 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 305 PHE 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 689 LYS 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: 4.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4254 r_free = 0.4254 target = 0.183744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125986 restraints weight = 60178.559| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.85 r_work: 0.3363 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19596 Z= 0.198 Angle : 0.596 11.378 26204 Z= 0.308 Chirality : 0.070 1.558 2760 Planarity : 0.004 0.055 3064 Dihedral : 19.735 175.849 4144 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.61 % Favored : 96.20 % Rotamer: Outliers : 2.52 % Allowed : 14.61 % Favored : 82.87 % 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: -0.18 (0.18), residues: 2108 helix: 0.86 (0.14), residues: 1292 sheet: -2.37 (0.47), residues: 76 loop : -1.58 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 499 TYR 0.020 0.002 TYR D 632 PHE 0.018 0.002 PHE C 721 TRP 0.016 0.002 TRP C 698 HIS 0.002 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00428 (19592) covalent geometry : angle 0.59610 (26196) SS BOND : bond 0.00088 ( 4) SS BOND : angle 1.00041 ( 8) hydrogen bonds : bond 0.04588 ( 996) hydrogen bonds : angle 4.37963 ( 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 293 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.920 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: 0.7275 (OUTLIER) cc_final: 0.6754 (t80) REVERT: A 311 ASN cc_start: 0.7051 (t0) cc_final: 0.6484 (t0) REVERT: A 312 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 483 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 500 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7321 (mmm160) REVERT: A 636 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8217 (tm) REVERT: A 717 MET cc_start: 0.5239 (ttt) cc_final: 0.4721 (mtt) REVERT: B 305 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6775 (t80) REVERT: B 311 ASN cc_start: 0.7008 (t0) cc_final: 0.6437 (t0) REVERT: B 312 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 500 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7325 (mmm160) REVERT: B 561 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: B 636 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8228 (tm) REVERT: B 717 MET cc_start: 0.5143 (ttt) cc_final: 0.4583 (mtt) REVERT: C 305 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6812 (t80) REVERT: C 309 MET cc_start: 0.8090 (tpp) cc_final: 0.7785 (tpp) REVERT: C 311 ASN cc_start: 0.7095 (t0) cc_final: 0.6556 (t0) REVERT: C 398 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7850 (tt0) REVERT: C 483 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 500 ARG cc_start: 0.7736 (mmm160) cc_final: 0.7312 (mmm160) REVERT: C 561 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: C 636 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8223 (tm) REVERT: D 305 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6799 (t80) REVERT: D 311 ASN cc_start: 0.6993 (t0) cc_final: 0.6445 (t0) REVERT: D 312 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7489 (mm-30) REVERT: D 315 MET cc_start: 0.7011 (mtt) cc_final: 0.6045 (mtt) REVERT: D 433 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7307 (tpt170) REVERT: D 500 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7241 (mmm160) REVERT: D 561 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: D 636 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8255 (tm) outliers start: 47 outliers final: 21 residues processed: 281 average time/residue: 1.2383 time to fit residues: 393.1650 Evaluate side-chains 255 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 320 LEU 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 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 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 483 LEU 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 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 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: 5.9990 chunk 63 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 728 GLN D 688 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.182705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125012 restraints weight = 60396.903| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.88 r_work: 0.3354 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19596 Z= 0.190 Angle : 0.583 11.326 26204 Z= 0.302 Chirality : 0.069 1.550 2760 Planarity : 0.004 0.053 3064 Dihedral : 18.761 167.024 4144 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.65 % Favored : 96.16 % Rotamer: Outliers : 2.36 % Allowed : 15.26 % Favored : 82.39 % 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: 0.02 (0.18), residues: 2108 helix: 1.03 (0.14), residues: 1292 sheet: -2.54 (0.43), residues: 84 loop : -1.49 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.017 0.002 TYR D 632 PHE 0.018 0.002 PHE D 721 TRP 0.016 0.002 TRP D 273 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00413 (19592) covalent geometry : angle 0.58295 (26196) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.65394 ( 8) hydrogen bonds : bond 0.04532 ( 996) hydrogen bonds : angle 4.32175 ( 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 276 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.869 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 247 TYR cc_start: 0.7869 (t80) cc_final: 0.7668 (t80) REVERT: A 305 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6838 (t80) REVERT: A 311 ASN cc_start: 0.7162 (t0) cc_final: 0.6557 (t0) REVERT: A 312 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 483 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 500 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7445 (mmm160) REVERT: A 636 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8244 (tm) REVERT: B 305 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6889 (t80) REVERT: B 311 ASN cc_start: 0.7101 (t0) cc_final: 0.6532 (t0) REVERT: B 312 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 379 HIS cc_start: 0.7381 (p-80) cc_final: 0.7085 (p-80) REVERT: B 433 ARG cc_start: 0.7913 (tpt170) cc_final: 0.7508 (tpt170) REVERT: B 500 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7454 (mmm160) REVERT: B 636 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8254 (tm) REVERT: C 305 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6888 (t80) REVERT: C 309 MET cc_start: 0.8094 (tpp) cc_final: 0.7773 (tpp) REVERT: C 311 ASN cc_start: 0.7177 (t0) cc_final: 0.6602 (t0) REVERT: C 433 ARG cc_start: 0.7909 (tpt170) cc_final: 0.7508 (tpt170) REVERT: C 483 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 500 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7267 (mmm160) REVERT: C 636 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8250 (tm) REVERT: C 692 GLN cc_start: 0.8009 (tp40) cc_final: 0.7133 (tp-100) REVERT: C 717 MET cc_start: 0.5314 (tmt) cc_final: 0.5066 (tmt) REVERT: D 305 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6845 (t80) REVERT: D 309 MET cc_start: 0.8098 (tpp) cc_final: 0.7677 (tpp) REVERT: D 311 ASN cc_start: 0.7108 (t0) cc_final: 0.6529 (t0) REVERT: D 312 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7511 (mm-30) REVERT: D 379 HIS cc_start: 0.7291 (p-80) cc_final: 0.6983 (p-80) REVERT: D 433 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7302 (tpt170) REVERT: D 500 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7262 (mmm160) REVERT: D 636 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8258 (tm) outliers start: 44 outliers final: 19 residues processed: 261 average time/residue: 1.1239 time to fit residues: 335.2012 Evaluate side-chains 250 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 B residue 305 PHE 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 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 315 MET 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 483 LEU 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 502 SER Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 LYS 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: 1.9990 chunk 96 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.182733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125621 restraints weight = 60584.708| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.86 r_work: 0.3358 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19596 Z= 0.171 Angle : 0.570 11.346 26204 Z= 0.293 Chirality : 0.068 1.534 2760 Planarity : 0.004 0.052 3064 Dihedral : 18.168 157.015 4144 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.56 % Favored : 96.25 % Rotamer: Outliers : 2.25 % Allowed : 16.86 % Favored : 80.89 % 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: 0.23 (0.18), residues: 2108 helix: 1.20 (0.14), residues: 1292 sheet: -2.45 (0.45), residues: 84 loop : -1.41 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 212 TYR 0.019 0.002 TYR B 375 PHE 0.017 0.002 PHE B 721 TRP 0.020 0.002 TRP D 273 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00369 (19592) covalent geometry : angle 0.56964 (26196) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.69986 ( 8) hydrogen bonds : bond 0.04367 ( 996) hydrogen bonds : angle 4.23249 ( 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 : 0.960 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 305 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 311 ASN cc_start: 0.7210 (t0) cc_final: 0.6610 (t0) REVERT: A 312 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 433 ARG cc_start: 0.7923 (tpt170) cc_final: 0.7527 (tpt170) REVERT: A 483 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 500 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7442 (mmm160) REVERT: A 506 LEU cc_start: 0.7910 (mm) cc_final: 0.7581 (mt) REVERT: A 692 GLN cc_start: 0.7759 (mm110) cc_final: 0.7441 (tp40) REVERT: A 728 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: B 305 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6856 (t80) REVERT: B 311 ASN cc_start: 0.7137 (t0) cc_final: 0.6556 (t0) REVERT: B 312 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 315 MET cc_start: 0.7054 (mtt) cc_final: 0.6073 (mtt) REVERT: B 379 HIS cc_start: 0.7425 (p-80) cc_final: 0.7125 (p-80) REVERT: B 433 ARG cc_start: 0.7927 (tpt170) cc_final: 0.7523 (tpt170) REVERT: B 500 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7439 (mmm160) REVERT: B 636 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8243 (tm) REVERT: C 305 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6784 (t80) REVERT: C 309 MET cc_start: 0.8085 (tpp) cc_final: 0.7777 (tpp) REVERT: C 433 ARG cc_start: 0.7920 (tpt170) cc_final: 0.7514 (tpt170) REVERT: C 483 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 500 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7272 (mmm160) REVERT: C 636 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8238 (tm) REVERT: C 692 GLN cc_start: 0.8027 (tp40) cc_final: 0.7151 (tp-100) REVERT: D 305 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6762 (t80) REVERT: D 309 MET cc_start: 0.8065 (tpp) cc_final: 0.7481 (tpp) REVERT: D 311 ASN cc_start: 0.7137 (t0) cc_final: 0.6566 (t0) REVERT: D 312 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 433 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7328 (tpt170) REVERT: D 500 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7261 (mmm160) REVERT: D 636 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8246 (tm) outliers start: 42 outliers final: 19 residues processed: 256 average time/residue: 1.1761 time to fit residues: 342.3315 Evaluate side-chains 251 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 651 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 320 LEU 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 479 ILE Chi-restraints excluded: chain C residue 483 LEU 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 689 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 202 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 438 ASN B 728 GLN C 261 GLN C 438 ASN D 261 GLN D 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.182247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124713 restraints weight = 60437.735| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.87 r_work: 0.3347 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19596 Z= 0.191 Angle : 0.579 11.207 26204 Z= 0.299 Chirality : 0.066 1.477 2760 Planarity : 0.004 0.055 3064 Dihedral : 18.065 140.855 4144 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.70 % Favored : 96.11 % Rotamer: Outliers : 2.14 % Allowed : 16.43 % 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: 0.19 (0.18), residues: 2108 helix: 1.15 (0.14), residues: 1280 sheet: -2.47 (0.45), residues: 84 loop : -1.34 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.017 0.002 TYR D 632 PHE 0.019 0.002 PHE A 721 TRP 0.016 0.002 TRP B 273 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00415 (19592) covalent geometry : angle 0.57880 (26196) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.62847 ( 8) hydrogen bonds : bond 0.04476 ( 996) hydrogen bonds : angle 4.27974 ( 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 276 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.820 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 305 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 311 ASN cc_start: 0.7316 (t0) cc_final: 0.6660 (t0) REVERT: A 312 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 433 ARG cc_start: 0.7926 (tpt170) cc_final: 0.7532 (tpt170) REVERT: A 483 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 500 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7437 (mmm160) REVERT: A 692 GLN cc_start: 0.7748 (mm110) cc_final: 0.7436 (tp40) REVERT: B 305 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6880 (t80) REVERT: B 311 ASN cc_start: 0.7264 (t0) cc_final: 0.6618 (t0) REVERT: B 312 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7456 (mm-30) REVERT: B 433 ARG cc_start: 0.7888 (tpt170) cc_final: 0.7479 (tpt170) REVERT: B 636 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8240 (tm) REVERT: C 305 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6761 (t80) REVERT: C 309 MET cc_start: 0.8119 (tpp) cc_final: 0.7839 (tpp) REVERT: C 311 ASN cc_start: 0.7362 (t0) cc_final: 0.6773 (t0) REVERT: C 364 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7294 (ttp-170) REVERT: C 433 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7464 (tpt170) REVERT: C 479 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8244 (mt) REVERT: C 483 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8249 (mp) REVERT: C 500 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7284 (mmm160) REVERT: C 636 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8249 (tm) REVERT: C 692 GLN cc_start: 0.8042 (tp40) cc_final: 0.7175 (tp-100) REVERT: C 717 MET cc_start: 0.5324 (tmt) cc_final: 0.5096 (tmt) REVERT: D 305 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6781 (t80) REVERT: D 311 ASN cc_start: 0.7266 (t0) cc_final: 0.6838 (t0) REVERT: D 364 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7097 (ttp-110) REVERT: D 433 ARG cc_start: 0.7702 (mmm160) cc_final: 0.7287 (tpt170) REVERT: D 500 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7270 (mmm160) REVERT: D 636 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8248 (tm) outliers start: 40 outliers final: 16 residues processed: 259 average time/residue: 1.1686 time to fit residues: 344.5666 Evaluate side-chains 257 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 320 LEU 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 483 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN D 438 ASN D 688 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126293 restraints weight = 60437.683| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.86 r_work: 0.3371 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5062 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= 0.142 Angle : 0.544 10.943 26204 Z= 0.281 Chirality : 0.066 1.468 2760 Planarity : 0.004 0.049 3064 Dihedral : 17.002 115.487 4144 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.32 % Favored : 96.49 % Rotamer: Outliers : 1.87 % Allowed : 17.02 % Favored : 81.10 % 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: 0.47 (0.18), residues: 2108 helix: 1.39 (0.14), residues: 1292 sheet: -2.40 (0.48), residues: 76 loop : -1.32 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.014 0.001 TYR D 632 PHE 0.015 0.001 PHE A 721 TRP 0.016 0.002 TRP D 273 HIS 0.001 0.000 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00305 (19592) covalent geometry : angle 0.54426 (26196) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.67408 ( 8) hydrogen bonds : bond 0.04130 ( 996) hydrogen bonds : angle 4.15230 ( 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 284 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.948 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 235 ASP cc_start: 0.7007 (m-30) cc_final: 0.6351 (m-30) REVERT: A 305 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6801 (t80) REVERT: A 309 MET cc_start: 0.8069 (tpp) cc_final: 0.7865 (tpp) REVERT: A 311 ASN cc_start: 0.7249 (t0) cc_final: 0.6614 (t0) REVERT: A 433 ARG cc_start: 0.7913 (tpt170) cc_final: 0.7524 (tpt170) REVERT: A 483 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8189 (mp) REVERT: A 500 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7369 (mmm160) REVERT: A 506 LEU cc_start: 0.7840 (mm) cc_final: 0.7522 (mt) REVERT: A 692 GLN cc_start: 0.7705 (mm110) cc_final: 0.7393 (tp40) REVERT: B 235 ASP cc_start: 0.6964 (m-30) cc_final: 0.6293 (m-30) REVERT: B 305 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6840 (t80) REVERT: B 311 ASN cc_start: 0.7199 (t0) cc_final: 0.6580 (t0) REVERT: B 315 MET cc_start: 0.7068 (mtt) cc_final: 0.6172 (mtt) REVERT: B 433 ARG cc_start: 0.7873 (tpt170) cc_final: 0.7470 (tpt170) REVERT: B 500 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7392 (mmm160) REVERT: B 506 LEU cc_start: 0.7897 (mm) cc_final: 0.7577 (mt) REVERT: B 692 GLN cc_start: 0.7727 (mm110) cc_final: 0.7428 (tp40) REVERT: C 235 ASP cc_start: 0.6993 (m-30) cc_final: 0.6337 (m-30) REVERT: C 305 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6740 (t80) REVERT: C 309 MET cc_start: 0.8097 (tpp) cc_final: 0.7848 (tpp) REVERT: C 433 ARG cc_start: 0.7892 (tpt170) cc_final: 0.7484 (tpt170) REVERT: C 483 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8220 (mp) REVERT: C 500 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7236 (mmm160) REVERT: C 506 LEU cc_start: 0.7879 (mm) cc_final: 0.7508 (mt) REVERT: C 737 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: D 235 ASP cc_start: 0.6993 (m-30) cc_final: 0.6334 (m-30) REVERT: D 305 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6662 (t80) REVERT: D 309 MET cc_start: 0.8106 (tpp) cc_final: 0.7815 (tpp) REVERT: D 311 ASN cc_start: 0.7227 (t0) cc_final: 0.6602 (t0) REVERT: D 312 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7630 (mm-30) REVERT: D 364 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7012 (ttp-170) REVERT: D 433 ARG cc_start: 0.7717 (mmm160) cc_final: 0.7315 (tpt170) REVERT: D 500 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7221 (mmm160) REVERT: D 506 LEU cc_start: 0.7911 (mm) cc_final: 0.7634 (mt) REVERT: D 692 GLN cc_start: 0.7723 (mm110) cc_final: 0.7417 (tp40) outliers start: 35 outliers final: 12 residues processed: 270 average time/residue: 1.1284 time to fit residues: 348.6697 Evaluate side-chains 252 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 483 LEU 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 651 THR 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: 5.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.181766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124569 restraints weight = 60709.225| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.87 r_work: 0.3344 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5117 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= 0.188 Angle : 0.582 11.049 26204 Z= 0.300 Chirality : 0.067 1.481 2760 Planarity : 0.004 0.050 3064 Dihedral : 17.351 94.411 4144 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 1.71 % Allowed : 17.34 % Favored : 80.94 % 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: 0.32 (0.18), residues: 2108 helix: 1.25 (0.14), residues: 1280 sheet: -2.38 (0.48), residues: 76 loop : -1.31 (0.22), residues: 752 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 0.015 0.002 TRP D 273 HIS 0.001 0.000 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00410 (19592) covalent geometry : angle 0.58216 (26196) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.66366 ( 8) hydrogen bonds : bond 0.04431 ( 996) hydrogen bonds : angle 4.24819 ( 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 262 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.871 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: A 305 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6773 (t80) REVERT: A 311 ASN cc_start: 0.7318 (t0) cc_final: 0.6772 (t0) REVERT: A 433 ARG cc_start: 0.7880 (tpt170) cc_final: 0.7486 (tpt170) REVERT: A 479 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 483 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 500 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7429 (mmm160) REVERT: A 692 GLN cc_start: 0.7736 (mm110) cc_final: 0.7429 (tp40) REVERT: B 305 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 311 ASN cc_start: 0.7287 (t0) cc_final: 0.6686 (t0) REVERT: B 433 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7468 (tpt170) REVERT: B 500 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7420 (mmm160) REVERT: B 692 GLN cc_start: 0.7753 (mm110) cc_final: 0.7459 (tp40) REVERT: B 717 MET cc_start: 0.5380 (tmt) cc_final: 0.5172 (tmt) REVERT: C 305 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6729 (t80) REVERT: C 309 MET cc_start: 0.8106 (tpp) cc_final: 0.7877 (tpp) REVERT: C 311 ASN cc_start: 0.7408 (t0) cc_final: 0.6810 (t0) REVERT: C 433 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7470 (tpt170) REVERT: C 479 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8237 (mt) REVERT: C 483 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 500 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7402 (mmm160) REVERT: C 692 GLN cc_start: 0.8047 (tp40) cc_final: 0.7177 (tp-100) REVERT: C 737 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6714 (m-30) REVERT: D 235 ASP cc_start: 0.6988 (m-30) cc_final: 0.6347 (m-30) REVERT: D 305 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6671 (t80) REVERT: D 309 MET cc_start: 0.8133 (tpp) cc_final: 0.7610 (tpp) REVERT: D 311 ASN cc_start: 0.7422 (t0) cc_final: 0.6925 (t0) REVERT: D 315 MET cc_start: 0.7124 (mtt) cc_final: 0.6591 (mtt) REVERT: D 364 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7095 (ttp-170) REVERT: D 433 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7294 (tpt170) REVERT: D 500 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7257 (mmm160) REVERT: D 692 GLN cc_start: 0.7736 (mm110) cc_final: 0.7435 (tp40) outliers start: 32 outliers final: 12 residues processed: 250 average time/residue: 1.1593 time to fit residues: 329.6368 Evaluate side-chains 250 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 651 THR Chi-restraints excluded: chain B residue 305 PHE 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 651 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 483 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 728 GLN C 261 GLN D 261 GLN D 688 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.182606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126106 restraints weight = 60872.614| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.86 r_work: 0.3365 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5211 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= 0.144 Angle : 0.546 10.940 26204 Z= 0.282 Chirality : 0.066 1.467 2760 Planarity : 0.004 0.048 3064 Dihedral : 16.697 87.365 4144 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 17.45 % Favored : 80.84 % 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: 0.54 (0.18), residues: 2108 helix: 1.42 (0.14), residues: 1292 sheet: -2.23 (0.49), residues: 76 loop : -1.26 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.014 0.001 TYR D 632 PHE 0.015 0.002 PHE A 721 TRP 0.019 0.002 TRP D 273 HIS 0.001 0.000 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00310 (19592) covalent geometry : angle 0.54577 (26196) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.65702 ( 8) hydrogen bonds : bond 0.04160 ( 996) hydrogen bonds : angle 4.14946 ( 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 262 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.968 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: 0.7002 (m-30) cc_final: 0.6340 (m-30) REVERT: A 305 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6729 (t80) REVERT: A 311 ASN cc_start: 0.7351 (t0) cc_final: 0.6798 (t0) REVERT: A 433 ARG cc_start: 0.7844 (tpt170) cc_final: 0.7454 (tpt170) REVERT: A 483 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 500 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7398 (mmm160) REVERT: A 692 GLN cc_start: 0.7679 (mm110) cc_final: 0.7375 (tp40) REVERT: B 235 ASP cc_start: 0.6933 (m-30) cc_final: 0.6274 (m-30) REVERT: B 305 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6740 (t80) REVERT: B 311 ASN cc_start: 0.7216 (t0) cc_final: 0.6614 (t0) REVERT: B 433 ARG cc_start: 0.7869 (tpt170) cc_final: 0.7454 (tpt170) REVERT: B 506 LEU cc_start: 0.7768 (mm) cc_final: 0.7450 (mt) REVERT: B 692 GLN cc_start: 0.7680 (mm110) cc_final: 0.7162 (tp-100) REVERT: B 753 TRP cc_start: 0.6197 (m100) cc_final: 0.5813 (m100) REVERT: C 235 ASP cc_start: 0.6965 (m-30) cc_final: 0.6316 (m-30) REVERT: C 305 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6712 (t80) REVERT: C 309 MET cc_start: 0.8103 (tpp) cc_final: 0.7867 (tpp) REVERT: C 433 ARG cc_start: 0.7865 (tpt170) cc_final: 0.7450 (tpt170) REVERT: C 483 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8201 (mp) REVERT: C 500 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7385 (mmm160) REVERT: C 506 LEU cc_start: 0.7824 (mm) cc_final: 0.7518 (mt) REVERT: C 737 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: C 753 TRP cc_start: 0.6179 (m100) cc_final: 0.5810 (m100) REVERT: D 235 ASP cc_start: 0.6971 (m-30) cc_final: 0.6320 (m-30) REVERT: D 305 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6674 (t80) REVERT: D 309 MET cc_start: 0.8125 (tpp) cc_final: 0.7870 (tpp) REVERT: D 311 ASN cc_start: 0.7414 (t0) cc_final: 0.6728 (t0) REVERT: D 315 MET cc_start: 0.7136 (mtt) cc_final: 0.6299 (mtt) REVERT: D 364 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7028 (ttp-170) REVERT: D 433 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7300 (tpt170) REVERT: D 466 MET cc_start: 0.6989 (mmt) cc_final: 0.6780 (mmt) REVERT: D 500 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7360 (mmm160) REVERT: D 506 LEU cc_start: 0.7834 (mm) cc_final: 0.7527 (mt) REVERT: D 692 GLN cc_start: 0.7695 (mm110) cc_final: 0.7398 (tp40) outliers start: 32 outliers final: 13 residues processed: 251 average time/residue: 1.1502 time to fit residues: 329.3354 Evaluate side-chains 246 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 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 479 ILE Chi-restraints excluded: chain C residue 483 LEU 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 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: 9.9990 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN C 261 GLN C 749 ASN D 261 GLN D 688 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123800 restraints weight = 60667.473| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.86 r_work: 0.3333 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 19596 Z= 0.225 Angle : 0.615 11.049 26204 Z= 0.316 Chirality : 0.068 1.480 2760 Planarity : 0.004 0.053 3064 Dihedral : 17.611 91.532 4144 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.03 % Favored : 95.78 % Rotamer: Outliers : 1.61 % Allowed : 17.72 % Favored : 80.67 % 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: 0.23 (0.18), residues: 2108 helix: 1.13 (0.14), residues: 1280 sheet: -2.13 (0.48), residues: 84 loop : -1.27 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 213 TYR 0.017 0.002 TYR D 632 PHE 0.019 0.002 PHE A 721 TRP 0.018 0.002 TRP D 273 HIS 0.001 0.000 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00493 (19592) covalent geometry : angle 0.61492 (26196) SS BOND : bond 0.00006 ( 4) SS BOND : angle 0.62903 ( 8) hydrogen bonds : bond 0.04634 ( 996) hydrogen bonds : angle 4.32331 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16757.31 seconds wall clock time: 283 minutes 35.42 seconds (17015.42 seconds total)