Starting phenix.real_space_refine on Wed Mar 4 21:22:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9o_10419/03_2026/6t9o_10419.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9o_10419/03_2026/6t9o_10419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t9o_10419/03_2026/6t9o_10419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9o_10419/03_2026/6t9o_10419.map" model { file = "/net/cci-nas-00/data/ceres_data/6t9o_10419/03_2026/6t9o_10419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9o_10419/03_2026/6t9o_10419.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 76 5.16 5 C 10924 2.51 5 N 2472 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 16481 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3903 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Unusual residues: {' CA': 1, 'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 1, 'NAG': 2, 'UMQ': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 3.87, per 1000 atoms: 0.23 Number of scatterers: 16481 At special positions: 0 Unit cell: (115.056, 115.056, 111.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 76 16.00 O 3008 8.00 N 2472 7.00 C 10924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.02 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.02 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.02 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 375 " " NAG G 1 " - " ASN C 375 " " NAG H 1 " - " ASN D 375 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 703.5 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 61.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 215 through 241 removed outlier: 3.728A pdb=" N TYR A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.639A pdb=" N TYR A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.807A pdb=" N ILE A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.643A pdb=" N LEU A 374 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 498 removed outlier: 3.755A pdb=" N ILE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.623A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 593 through 620 Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.787A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 672 through 701 removed outlier: 4.264A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 241 removed outlier: 3.727A pdb=" N TYR B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.639A pdb=" N TYR B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.807A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.643A pdb=" N LEU B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 498 removed outlier: 3.755A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.624A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 593 through 620 Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.787A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 672 through 701 removed outlier: 4.263A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 removed outlier: 3.727A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.640A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.807A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.644A pdb=" N LEU C 374 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 498 removed outlier: 3.755A pdb=" N ILE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 528 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 548 through 573 removed outlier: 3.623A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 593 through 620 Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.787A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 Processing helix chain 'C' and resid 672 through 701 removed outlier: 4.263A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 241 removed outlier: 3.729A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.640A pdb=" N TYR D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.808A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.643A pdb=" N LEU D 374 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 498 removed outlier: 3.754A pdb=" N ILE D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 528 Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 548 through 573 removed outlier: 3.624A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 580 through 593 Processing helix chain 'D' and resid 593 through 620 Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.788A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 667 Processing helix chain 'D' and resid 672 through 701 removed outlier: 4.264A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.527A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.527A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.527A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.528A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 952 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4690 1.34 - 1.45: 3558 1.45 - 1.57: 8548 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 16912 Sorted by residual: bond pdb=" C2' UMQ A 809 " pdb=" C3' UMQ A 809 " ideal model delta sigma weight residual 1.521 1.564 -0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C2' UMQ C 809 " pdb=" C3' UMQ C 809 " ideal model delta sigma weight residual 1.521 1.564 -0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C2' UMQ D 809 " pdb=" C3' UMQ D 809 " ideal model delta sigma weight residual 1.521 1.563 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" C2' UMQ B 809 " pdb=" C3' UMQ B 809 " ideal model delta sigma weight residual 1.521 1.563 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C5 UMQ B 806 " pdb=" O5 UMQ B 806 " ideal model delta sigma weight residual 1.421 1.379 0.042 2.00e-02 2.50e+03 4.44e+00 ... (remaining 16907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21743 2.10 - 4.21: 1041 4.21 - 6.31: 141 6.31 - 8.41: 15 8.41 - 10.52: 16 Bond angle restraints: 22956 Sorted by residual: angle pdb=" C1 UMQ C 806 " pdb=" O1 UMQ C 806 " pdb=" C4' UMQ C 806 " ideal model delta sigma weight residual 119.70 110.26 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" C1 UMQ B 806 " pdb=" O1 UMQ B 806 " pdb=" C4' UMQ B 806 " ideal model delta sigma weight residual 119.70 110.31 9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" C1 UMQ D 806 " pdb=" O1 UMQ D 806 " pdb=" C4' UMQ D 806 " ideal model delta sigma weight residual 119.70 110.32 9.38 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C1 UMQ A 806 " pdb=" O1 UMQ A 806 " pdb=" C4' UMQ A 806 " ideal model delta sigma weight residual 119.70 110.35 9.35 3.00e+00 1.11e-01 9.72e+00 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 126.82 -10.52 3.50e+00 8.16e-02 9.03e+00 ... (remaining 22951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.23: 9656 13.23 - 26.46: 732 26.46 - 39.69: 216 39.69 - 52.92: 80 52.92 - 66.15: 28 Dihedral angle restraints: 10712 sinusoidal: 5004 harmonic: 5708 Sorted by residual: dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 344 " pdb=" CB CYS A 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.54 65.54 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -151.52 65.52 1 1.00e+01 1.00e-02 5.62e+01 ... (remaining 10709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2138 0.071 - 0.142: 443 0.142 - 0.213: 111 0.213 - 0.284: 16 0.284 - 0.355: 4 Chirality restraints: 2712 Sorted by residual: chirality pdb=" C1 NAG C 802 " pdb=" ND2 ASN C 362 " pdb=" C2 NAG C 802 " pdb=" O5 NAG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C1 NAG D 802 " pdb=" ND2 ASN D 362 " pdb=" C2 NAG D 802 " pdb=" O5 NAG D 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 2709 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 634 " -0.034 2.00e-02 2.50e+03 2.18e-02 8.33e+00 pdb=" CG PHE D 634 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 634 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 634 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 634 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 634 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 634 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 634 " 0.034 2.00e-02 2.50e+03 2.18e-02 8.32e+00 pdb=" CG PHE C 634 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 634 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 634 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 634 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 634 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 634 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 634 " 0.033 2.00e-02 2.50e+03 2.17e-02 8.23e+00 pdb=" CG PHE B 634 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 634 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 634 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 634 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 634 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 634 " 0.025 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1723 2.74 - 3.28: 15366 3.28 - 3.82: 26975 3.82 - 4.36: 32747 4.36 - 4.90: 57286 Nonbonded interactions: 134097 Sorted by model distance: nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLU D 491 " pdb=" OH TYR D 502 " model vdw 2.271 3.040 ... (remaining 134092 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 214 through 810) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.800 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.010 0.064 16932 Z= 0.414 Angle : 1.028 10.515 23012 Z= 0.513 Chirality : 0.066 0.355 2712 Planarity : 0.006 0.054 2728 Dihedral : 11.321 66.146 7004 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.71 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.15), residues: 1908 helix: -2.29 (0.11), residues: 1108 sheet: -2.34 (0.35), residues: 192 loop : -2.53 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.039 0.003 TYR B 249 PHE 0.034 0.003 PHE C 634 TRP 0.027 0.004 TRP A 507 HIS 0.005 0.002 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00954 (16912) covalent geometry : angle 1.00740 (22956) SS BOND : bond 0.00820 ( 4) SS BOND : angle 3.93723 ( 8) hydrogen bonds : bond 0.15137 ( 936) hydrogen bonds : angle 6.34646 ( 2712) link_BETA1-4 : bond 0.00052 ( 4) link_BETA1-4 : angle 2.05842 ( 12) link_NAG-ASN : bond 0.00841 ( 12) link_NAG-ASN : angle 4.81826 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 SER cc_start: 0.8764 (p) cc_final: 0.8254 (t) REVERT: A 367 ILE cc_start: 0.8962 (mt) cc_final: 0.8511 (pt) REVERT: A 489 VAL cc_start: 0.8598 (t) cc_final: 0.8322 (p) REVERT: A 570 TRP cc_start: 0.8517 (m100) cc_final: 0.8089 (m100) REVERT: A 625 ASP cc_start: 0.7488 (m-30) cc_final: 0.7277 (m-30) REVERT: A 648 GLU cc_start: 0.8390 (pt0) cc_final: 0.8155 (pt0) REVERT: A 650 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7407 (tt0) REVERT: B 275 SER cc_start: 0.8804 (p) cc_final: 0.8269 (t) REVERT: B 367 ILE cc_start: 0.9004 (mt) cc_final: 0.8674 (pt) REVERT: B 398 THR cc_start: 0.8485 (p) cc_final: 0.7832 (p) REVERT: B 444 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 570 TRP cc_start: 0.8436 (m100) cc_final: 0.7993 (m100) REVERT: B 650 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7646 (tt0) REVERT: C 223 GLU cc_start: 0.6938 (pt0) cc_final: 0.6696 (tp30) REVERT: C 367 ILE cc_start: 0.8970 (mt) cc_final: 0.8609 (pt) REVERT: C 398 THR cc_start: 0.8464 (p) cc_final: 0.8049 (p) REVERT: C 489 VAL cc_start: 0.8532 (t) cc_final: 0.8261 (p) REVERT: C 531 ASN cc_start: 0.7892 (t0) cc_final: 0.7678 (t0) REVERT: C 570 TRP cc_start: 0.8468 (m100) cc_final: 0.8052 (m100) REVERT: D 223 GLU cc_start: 0.6875 (pt0) cc_final: 0.6647 (tp30) REVERT: D 271 LYS cc_start: 0.8903 (mttt) cc_final: 0.8624 (mttm) REVERT: D 275 SER cc_start: 0.8755 (p) cc_final: 0.8251 (t) REVERT: D 398 THR cc_start: 0.8597 (p) cc_final: 0.8179 (t) REVERT: D 489 VAL cc_start: 0.8617 (t) cc_final: 0.8374 (p) REVERT: D 570 TRP cc_start: 0.8501 (m100) cc_final: 0.8138 (m100) REVERT: D 587 SER cc_start: 0.8468 (m) cc_final: 0.8260 (t) REVERT: D 650 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1325 time to fit residues: 84.9384 Evaluate side-chains 231 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 HIS A 636 GLN A 653 ASN B 255 GLN B 313 ASN B 323 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS B 636 GLN B 653 ASN C 255 GLN C 323 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 636 GLN C 653 ASN D 323 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 ASN D 550 HIS D 636 GLN D 653 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109051 restraints weight = 20726.946| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.95 r_work: 0.2921 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16932 Z= 0.164 Angle : 0.560 8.172 23012 Z= 0.297 Chirality : 0.041 0.315 2712 Planarity : 0.004 0.045 2728 Dihedral : 9.857 58.267 3564 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 2.34 % Allowed : 6.35 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 1908 helix: -0.21 (0.14), residues: 1100 sheet: -2.02 (0.35), residues: 200 loop : -1.86 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 592 TYR 0.020 0.001 TYR D 486 PHE 0.022 0.002 PHE C 600 TRP 0.013 0.002 TRP D 554 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00365 (16912) covalent geometry : angle 0.54622 (22956) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.97218 ( 8) hydrogen bonds : bond 0.05174 ( 936) hydrogen bonds : angle 4.61813 ( 2712) link_BETA1-4 : bond 0.00173 ( 4) link_BETA1-4 : angle 1.35950 ( 12) link_NAG-ASN : bond 0.00553 ( 12) link_NAG-ASN : angle 2.92338 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.8829 (p) cc_final: 0.8438 (t) REVERT: A 333 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8406 (tp) REVERT: A 367 ILE cc_start: 0.9087 (mt) cc_final: 0.8639 (pt) REVERT: A 488 VAL cc_start: 0.8934 (t) cc_final: 0.8625 (m) REVERT: A 570 TRP cc_start: 0.8682 (m100) cc_final: 0.8281 (m100) REVERT: A 650 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7859 (tt0) REVERT: B 275 SER cc_start: 0.8891 (p) cc_final: 0.8411 (t) REVERT: B 367 ILE cc_start: 0.9098 (mt) cc_final: 0.8700 (pt) REVERT: B 531 ASN cc_start: 0.7965 (t0) cc_final: 0.7570 (t0) REVERT: B 570 TRP cc_start: 0.8658 (m100) cc_final: 0.8428 (m100) REVERT: B 650 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8021 (tt0) REVERT: C 223 GLU cc_start: 0.7351 (pt0) cc_final: 0.6781 (tp30) REVERT: C 275 SER cc_start: 0.8957 (p) cc_final: 0.8400 (t) REVERT: C 444 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8535 (mt-10) REVERT: C 486 TYR cc_start: 0.8479 (t80) cc_final: 0.8184 (t80) REVERT: C 531 ASN cc_start: 0.8113 (t0) cc_final: 0.7652 (t0) REVERT: C 570 TRP cc_start: 0.8672 (m100) cc_final: 0.8367 (m100) REVERT: D 223 GLU cc_start: 0.7248 (pt0) cc_final: 0.6732 (tp30) REVERT: D 275 SER cc_start: 0.8810 (p) cc_final: 0.8418 (t) REVERT: D 444 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8474 (mt-10) REVERT: D 570 TRP cc_start: 0.8688 (m100) cc_final: 0.8284 (m100) REVERT: D 650 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7872 (tt0) outliers start: 39 outliers final: 27 residues processed: 305 average time/residue: 0.1032 time to fit residues: 51.3855 Evaluate side-chains 247 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 56 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 118 optimal weight: 0.0970 chunk 63 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN D 636 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103887 restraints weight = 20940.287| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.06 r_work: 0.2904 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16932 Z= 0.123 Angle : 0.489 8.473 23012 Z= 0.258 Chirality : 0.039 0.290 2712 Planarity : 0.003 0.039 2728 Dihedral : 8.591 59.433 3564 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.02 % Rotamer: Outliers : 2.46 % Allowed : 9.05 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 1908 helix: 0.70 (0.15), residues: 1096 sheet: -1.82 (0.34), residues: 200 loop : -1.67 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 592 TYR 0.018 0.001 TYR D 486 PHE 0.021 0.001 PHE A 600 TRP 0.010 0.001 TRP A 507 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00268 (16912) covalent geometry : angle 0.47965 (22956) SS BOND : bond 0.00140 ( 4) SS BOND : angle 1.17346 ( 8) hydrogen bonds : bond 0.04463 ( 936) hydrogen bonds : angle 4.20461 ( 2712) link_BETA1-4 : bond 0.00542 ( 4) link_BETA1-4 : angle 1.15326 ( 12) link_NAG-ASN : bond 0.00491 ( 12) link_NAG-ASN : angle 2.38520 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.608 Fit side-chains REVERT: A 245 ASN cc_start: 0.7848 (m-40) cc_final: 0.7645 (m-40) REVERT: A 275 SER cc_start: 0.8830 (p) cc_final: 0.8526 (t) REVERT: A 367 ILE cc_start: 0.9071 (mt) cc_final: 0.8817 (tp) REVERT: A 488 VAL cc_start: 0.8948 (t) cc_final: 0.8629 (m) REVERT: A 537 GLN cc_start: 0.7361 (tt0) cc_final: 0.7156 (mt0) REVERT: A 570 TRP cc_start: 0.8721 (m100) cc_final: 0.8348 (m100) REVERT: A 650 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7808 (tt0) REVERT: B 245 ASN cc_start: 0.7828 (m-40) cc_final: 0.6981 (p0) REVERT: B 275 SER cc_start: 0.8866 (p) cc_final: 0.8523 (t) REVERT: B 367 ILE cc_start: 0.9080 (mt) cc_final: 0.8810 (tp) REVERT: C 223 GLU cc_start: 0.7158 (pt0) cc_final: 0.6813 (tp30) REVERT: C 275 SER cc_start: 0.8925 (p) cc_final: 0.8534 (t) REVERT: C 444 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8602 (mt-10) REVERT: C 673 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8624 (mp) REVERT: D 223 GLU cc_start: 0.7121 (pt0) cc_final: 0.6672 (tp30) REVERT: D 245 ASN cc_start: 0.7896 (m-40) cc_final: 0.7693 (m-40) REVERT: D 275 SER cc_start: 0.8862 (p) cc_final: 0.8543 (t) REVERT: D 650 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7816 (tt0) REVERT: D 673 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8549 (mp) outliers start: 41 outliers final: 30 residues processed: 271 average time/residue: 0.1070 time to fit residues: 47.4182 Evaluate side-chains 248 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.096178 restraints weight = 21094.810| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.10 r_work: 0.2829 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16932 Z= 0.209 Angle : 0.537 7.883 23012 Z= 0.278 Chirality : 0.041 0.275 2712 Planarity : 0.004 0.043 2728 Dihedral : 8.348 57.311 3564 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.46 % Favored : 96.33 % Rotamer: Outliers : 3.48 % Allowed : 8.87 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1908 helix: 0.93 (0.15), residues: 1104 sheet: -1.77 (0.34), residues: 200 loop : -1.44 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 251 TYR 0.021 0.002 TYR A 486 PHE 0.023 0.002 PHE C 600 TRP 0.012 0.002 TRP D 554 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00491 (16912) covalent geometry : angle 0.52946 (22956) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.86216 ( 8) hydrogen bonds : bond 0.04725 ( 936) hydrogen bonds : angle 4.17994 ( 2712) link_BETA1-4 : bond 0.00297 ( 4) link_BETA1-4 : angle 1.39075 ( 12) link_NAG-ASN : bond 0.00458 ( 12) link_NAG-ASN : angle 2.25568 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.619 Fit side-chains REVERT: A 275 SER cc_start: 0.8891 (p) cc_final: 0.8574 (t) REVERT: A 570 TRP cc_start: 0.8761 (m100) cc_final: 0.8374 (m100) REVERT: A 650 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8029 (tt0) REVERT: B 245 ASN cc_start: 0.7980 (m-40) cc_final: 0.7754 (m-40) REVERT: B 275 SER cc_start: 0.8908 (p) cc_final: 0.8572 (t) REVERT: B 650 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8047 (tt0) REVERT: C 223 GLU cc_start: 0.7185 (pt0) cc_final: 0.6790 (tp30) REVERT: C 245 ASN cc_start: 0.7899 (m-40) cc_final: 0.7047 (p0) REVERT: C 275 SER cc_start: 0.8983 (p) cc_final: 0.8599 (t) REVERT: C 673 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8803 (mp) REVERT: D 223 GLU cc_start: 0.7151 (pt0) cc_final: 0.6717 (tp30) REVERT: D 275 SER cc_start: 0.8952 (p) cc_final: 0.8628 (t) REVERT: D 650 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7998 (tt0) REVERT: D 673 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8667 (mp) outliers start: 58 outliers final: 49 residues processed: 269 average time/residue: 0.0986 time to fit residues: 44.1279 Evaluate side-chains 251 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 102 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 636 GLN B 255 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN C 255 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN C 636 GLN D 636 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109961 restraints weight = 20635.907| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.95 r_work: 0.2925 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16932 Z= 0.113 Angle : 0.467 9.029 23012 Z= 0.242 Chirality : 0.039 0.268 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.812 57.854 3564 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.14 % Favored : 96.65 % Rotamer: Outliers : 2.40 % Allowed : 11.33 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1908 helix: 1.25 (0.15), residues: 1104 sheet: -1.53 (0.34), residues: 200 loop : -1.28 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.019 0.001 TYR A 486 PHE 0.021 0.001 PHE D 600 TRP 0.008 0.001 TRP D 554 HIS 0.002 0.001 HIS D 501 Details of bonding type rmsd covalent geometry : bond 0.00242 (16912) covalent geometry : angle 0.45930 (22956) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.71081 ( 8) hydrogen bonds : bond 0.04262 ( 936) hydrogen bonds : angle 3.98532 ( 2712) link_BETA1-4 : bond 0.00235 ( 4) link_BETA1-4 : angle 1.22132 ( 12) link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 2.01331 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.615 Fit side-chains REVERT: A 245 ASN cc_start: 0.7684 (m-40) cc_final: 0.6895 (p0) REVERT: A 275 SER cc_start: 0.8876 (p) cc_final: 0.8639 (t) REVERT: A 488 VAL cc_start: 0.8970 (t) cc_final: 0.8702 (m) REVERT: A 570 TRP cc_start: 0.8757 (m100) cc_final: 0.8453 (m100) REVERT: B 245 ASN cc_start: 0.7725 (m-40) cc_final: 0.6993 (p0) REVERT: B 275 SER cc_start: 0.8886 (p) cc_final: 0.8596 (t) REVERT: C 223 GLU cc_start: 0.7145 (pt0) cc_final: 0.6752 (tp30) REVERT: C 245 ASN cc_start: 0.7738 (m-40) cc_final: 0.7065 (p0) REVERT: C 275 SER cc_start: 0.8922 (p) cc_final: 0.8602 (t) REVERT: C 673 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8798 (mp) REVERT: D 223 GLU cc_start: 0.7045 (pt0) cc_final: 0.6636 (tp30) REVERT: D 245 ASN cc_start: 0.7664 (m-40) cc_final: 0.7012 (p0) REVERT: D 275 SER cc_start: 0.8884 (p) cc_final: 0.8640 (t) REVERT: D 312 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8348 (mm-30) REVERT: D 650 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 673 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8700 (mp) outliers start: 40 outliers final: 30 residues processed: 247 average time/residue: 0.1079 time to fit residues: 44.2013 Evaluate side-chains 232 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109360 restraints weight = 20773.285| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.96 r_work: 0.2934 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16932 Z= 0.110 Angle : 0.456 9.436 23012 Z= 0.235 Chirality : 0.038 0.257 2712 Planarity : 0.003 0.035 2728 Dihedral : 7.392 58.628 3564 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.57 % Favored : 97.22 % Rotamer: Outliers : 2.52 % Allowed : 11.51 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1908 helix: 1.47 (0.15), residues: 1100 sheet: -1.34 (0.34), residues: 200 loop : -1.10 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 464 TYR 0.018 0.001 TYR A 486 PHE 0.021 0.001 PHE D 600 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00235 (16912) covalent geometry : angle 0.44991 (22956) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.58956 ( 8) hydrogen bonds : bond 0.04103 ( 936) hydrogen bonds : angle 3.87668 ( 2712) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.18200 ( 12) link_NAG-ASN : bond 0.00398 ( 12) link_NAG-ASN : angle 1.86125 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.577 Fit side-chains REVERT: A 245 ASN cc_start: 0.7808 (m-40) cc_final: 0.7020 (p0) REVERT: A 488 VAL cc_start: 0.8916 (t) cc_final: 0.8631 (m) REVERT: A 673 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 245 ASN cc_start: 0.7825 (m-40) cc_final: 0.7048 (p0) REVERT: B 275 SER cc_start: 0.8880 (p) cc_final: 0.8648 (t) REVERT: C 223 GLU cc_start: 0.7119 (pt0) cc_final: 0.6760 (tp30) REVERT: C 245 ASN cc_start: 0.7776 (m-40) cc_final: 0.7095 (p0) REVERT: C 275 SER cc_start: 0.8889 (p) cc_final: 0.8638 (t) REVERT: C 673 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8813 (mp) REVERT: D 223 GLU cc_start: 0.7103 (pt0) cc_final: 0.6685 (tp30) REVERT: D 245 ASN cc_start: 0.7712 (m-40) cc_final: 0.7049 (p0) REVERT: D 337 LEU cc_start: 0.8113 (mt) cc_final: 0.7698 (mt) REVERT: D 488 VAL cc_start: 0.8914 (t) cc_final: 0.8649 (m) REVERT: D 673 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8735 (mp) outliers start: 42 outliers final: 36 residues processed: 246 average time/residue: 0.0990 time to fit residues: 41.2654 Evaluate side-chains 239 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 0.0070 chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108769 restraints weight = 20712.192| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.96 r_work: 0.2948 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16932 Z= 0.108 Angle : 0.448 9.680 23012 Z= 0.231 Chirality : 0.038 0.250 2712 Planarity : 0.003 0.034 2728 Dihedral : 7.151 59.965 3564 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.52 % Favored : 97.27 % Rotamer: Outliers : 2.88 % Allowed : 11.75 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1908 helix: 1.61 (0.15), residues: 1100 sheet: -1.16 (0.35), residues: 200 loop : -1.07 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 464 TYR 0.017 0.001 TYR A 486 PHE 0.021 0.001 PHE D 600 TRP 0.007 0.001 TRP D 554 HIS 0.002 0.000 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00231 (16912) covalent geometry : angle 0.44169 (22956) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.51281 ( 8) hydrogen bonds : bond 0.04042 ( 936) hydrogen bonds : angle 3.80933 ( 2712) link_BETA1-4 : bond 0.00310 ( 4) link_BETA1-4 : angle 1.20377 ( 12) link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 1.76446 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.591 Fit side-chains REVERT: A 245 ASN cc_start: 0.7744 (m-40) cc_final: 0.6981 (p0) REVERT: A 488 VAL cc_start: 0.8924 (t) cc_final: 0.8628 (m) REVERT: A 673 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8495 (mp) REVERT: B 245 ASN cc_start: 0.7844 (m-40) cc_final: 0.7147 (p0) REVERT: C 223 GLU cc_start: 0.7083 (pt0) cc_final: 0.6807 (tp30) REVERT: C 245 ASN cc_start: 0.7694 (m-40) cc_final: 0.7094 (p0) REVERT: C 275 SER cc_start: 0.8910 (p) cc_final: 0.8707 (t) REVERT: C 673 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8826 (mp) REVERT: D 223 GLU cc_start: 0.7038 (pt0) cc_final: 0.6793 (tp30) REVERT: D 245 ASN cc_start: 0.7720 (m-40) cc_final: 0.7130 (p0) REVERT: D 337 LEU cc_start: 0.8144 (mt) cc_final: 0.7747 (mt) REVERT: D 488 VAL cc_start: 0.8914 (t) cc_final: 0.8606 (m) REVERT: D 673 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8759 (mp) outliers start: 48 outliers final: 41 residues processed: 244 average time/residue: 0.0958 time to fit residues: 40.2686 Evaluate side-chains 243 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108817 restraints weight = 20739.114| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.93 r_work: 0.2918 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16932 Z= 0.157 Angle : 0.486 10.424 23012 Z= 0.248 Chirality : 0.039 0.246 2712 Planarity : 0.003 0.035 2728 Dihedral : 7.204 59.903 3564 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.73 % Favored : 97.06 % Rotamer: Outliers : 2.88 % Allowed : 12.17 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1908 helix: 1.59 (0.15), residues: 1100 sheet: -1.24 (0.35), residues: 200 loop : -1.10 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.016 0.001 TYR D 486 PHE 0.022 0.001 PHE D 600 TRP 0.009 0.001 TRP A 554 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00363 (16912) covalent geometry : angle 0.48104 (22956) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.56278 ( 8) hydrogen bonds : bond 0.04284 ( 936) hydrogen bonds : angle 3.86523 ( 2712) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 1.36667 ( 12) link_NAG-ASN : bond 0.00370 ( 12) link_NAG-ASN : angle 1.74213 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.616 Fit side-chains REVERT: A 245 ASN cc_start: 0.7827 (m-40) cc_final: 0.7002 (p0) REVERT: A 488 VAL cc_start: 0.8922 (t) cc_final: 0.8628 (m) REVERT: A 673 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 245 ASN cc_start: 0.7851 (m-40) cc_final: 0.7029 (p0) REVERT: C 223 GLU cc_start: 0.7094 (pt0) cc_final: 0.6809 (tp30) REVERT: C 245 ASN cc_start: 0.7791 (m-40) cc_final: 0.7135 (p0) REVERT: C 275 SER cc_start: 0.8915 (p) cc_final: 0.8659 (t) REVERT: C 673 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8832 (mp) REVERT: D 223 GLU cc_start: 0.7094 (pt0) cc_final: 0.6840 (tp30) REVERT: D 245 ASN cc_start: 0.7770 (m-40) cc_final: 0.7108 (p0) REVERT: D 488 VAL cc_start: 0.8934 (t) cc_final: 0.8639 (m) REVERT: D 673 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 48 outliers final: 38 residues processed: 246 average time/residue: 0.0986 time to fit residues: 41.1044 Evaluate side-chains 239 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109954 restraints weight = 20626.245| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.94 r_work: 0.2932 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16932 Z= 0.125 Angle : 0.468 10.224 23012 Z= 0.239 Chirality : 0.038 0.242 2712 Planarity : 0.003 0.035 2728 Dihedral : 7.029 59.814 3564 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.52 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 12.53 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1908 helix: 1.69 (0.15), residues: 1100 sheet: -1.11 (0.35), residues: 200 loop : -1.06 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 464 TYR 0.017 0.001 TYR D 486 PHE 0.022 0.001 PHE B 600 TRP 0.008 0.001 TRP D 414 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00280 (16912) covalent geometry : angle 0.46281 (22956) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.51647 ( 8) hydrogen bonds : bond 0.04128 ( 936) hydrogen bonds : angle 3.79826 ( 2712) link_BETA1-4 : bond 0.00272 ( 4) link_BETA1-4 : angle 1.30730 ( 12) link_NAG-ASN : bond 0.00362 ( 12) link_NAG-ASN : angle 1.66970 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.599 Fit side-chains REVERT: A 245 ASN cc_start: 0.7785 (m-40) cc_final: 0.7059 (p0) REVERT: A 267 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8255 (tptp) REVERT: A 488 VAL cc_start: 0.8907 (t) cc_final: 0.8606 (m) REVERT: A 673 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 245 ASN cc_start: 0.7880 (m-40) cc_final: 0.7164 (p0) REVERT: C 223 GLU cc_start: 0.7107 (pt0) cc_final: 0.6818 (tp30) REVERT: C 245 ASN cc_start: 0.7685 (m-40) cc_final: 0.7105 (p0) REVERT: C 275 SER cc_start: 0.8909 (p) cc_final: 0.8701 (t) REVERT: C 673 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8827 (mp) REVERT: D 223 GLU cc_start: 0.7013 (pt0) cc_final: 0.6780 (tp30) REVERT: D 245 ASN cc_start: 0.7708 (m-40) cc_final: 0.7106 (p0) REVERT: D 267 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8175 (tptp) REVERT: D 488 VAL cc_start: 0.8940 (t) cc_final: 0.8639 (m) REVERT: D 673 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8728 (mp) outliers start: 46 outliers final: 43 residues processed: 242 average time/residue: 0.1004 time to fit residues: 41.0487 Evaluate side-chains 245 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104463 restraints weight = 20743.532| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.09 r_work: 0.2885 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16932 Z= 0.106 Angle : 0.459 9.945 23012 Z= 0.233 Chirality : 0.038 0.237 2712 Planarity : 0.003 0.034 2728 Dihedral : 6.720 59.741 3564 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.36 % Favored : 97.43 % Rotamer: Outliers : 2.88 % Allowed : 12.41 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1908 helix: 1.79 (0.15), residues: 1100 sheet: -1.03 (0.35), residues: 200 loop : -1.03 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.017 0.001 TYR D 486 PHE 0.021 0.001 PHE C 600 TRP 0.007 0.001 TRP A 414 HIS 0.001 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00227 (16912) covalent geometry : angle 0.45463 (22956) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.45017 ( 8) hydrogen bonds : bond 0.03998 ( 936) hydrogen bonds : angle 3.74540 ( 2712) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 1.24092 ( 12) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 1.56513 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.602 Fit side-chains REVERT: A 245 ASN cc_start: 0.7748 (m-40) cc_final: 0.7046 (p0) REVERT: A 253 MET cc_start: 0.9099 (tpp) cc_final: 0.8666 (mmt) REVERT: A 267 LYS cc_start: 0.8774 (mtmm) cc_final: 0.8191 (tptp) REVERT: A 488 VAL cc_start: 0.8804 (t) cc_final: 0.8490 (m) REVERT: A 673 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 245 ASN cc_start: 0.7774 (m-40) cc_final: 0.7085 (p0) REVERT: B 267 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8173 (tptp) REVERT: B 312 GLU cc_start: 0.8612 (tp30) cc_final: 0.8324 (mm-30) REVERT: C 223 GLU cc_start: 0.7036 (pt0) cc_final: 0.6751 (tp30) REVERT: D 223 GLU cc_start: 0.7001 (pt0) cc_final: 0.6636 (tp30) REVERT: D 245 ASN cc_start: 0.7695 (m-40) cc_final: 0.7115 (p0) REVERT: D 267 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8129 (tptp) REVERT: D 488 VAL cc_start: 0.8864 (t) cc_final: 0.8552 (m) REVERT: D 673 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8743 (mp) outliers start: 48 outliers final: 40 residues processed: 245 average time/residue: 0.1087 time to fit residues: 43.5929 Evaluate side-chains 239 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 0.7980 chunk 168 optimal weight: 0.0060 chunk 139 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 176 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114406 restraints weight = 20579.104| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.95 r_work: 0.2956 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16932 Z= 0.089 Angle : 0.441 9.532 23012 Z= 0.227 Chirality : 0.037 0.231 2712 Planarity : 0.003 0.034 2728 Dihedral : 6.289 54.899 3564 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.25 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 13.79 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1908 helix: 1.86 (0.15), residues: 1108 sheet: -0.88 (0.35), residues: 200 loop : -1.00 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 399 TYR 0.017 0.001 TYR D 486 PHE 0.020 0.001 PHE B 600 TRP 0.009 0.001 TRP C 414 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00178 (16912) covalent geometry : angle 0.43656 (22956) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.36245 ( 8) hydrogen bonds : bond 0.03831 ( 936) hydrogen bonds : angle 3.67224 ( 2712) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.16368 ( 12) link_NAG-ASN : bond 0.00351 ( 12) link_NAG-ASN : angle 1.44787 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.44 seconds wall clock time: 60 minutes 51.92 seconds (3651.92 seconds total)