Starting phenix.real_space_refine on Sat Sep 12 14:53:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t9o_10419/09_2026/6t9o_10419.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9o_10419/09_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_10419/09_2026/6t9o_10419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9o_10419/09_2026/6t9o_10419.map" model { file = "/net/cci-nas-00/data/ceres_data/6t9o_10419/09_2026/6t9o_10419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9o_10419/09_2026/6t9o_10419.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6t9o_10419/09_2026/6t9o_10419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t9o_10419/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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: 3 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: 3 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: 3 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: 3 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 3.62, per 1000 atoms: 0.22 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: 1.45 Conformation dependent library (CDL) restraints added in 698.6 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: 0.43 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: 2.75 Time building geometry restraints manager: 1.94 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: 8598 13.23 - 26.46: 662 26.46 - 39.69: 136 39.69 - 52.92: 40 52.92 - 66.15: 28 Dihedral angle restraints: 9464 sinusoidal: 3756 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 9461 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: 0.730 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 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 : 10.823 66.146 5756 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/Z covalent geometry : bond 0.00954 / 0.41 (16912) covalent geometry : angle 1.00740 / 0.51 (22956) SS BOND : bond 0.00820 / 0.41 ( 4) SS BOND : angle 3.93723 / 2.13 ( 8) hydrogen bonds : bond 0.15137 / 9.56 ( 936) hydrogen bonds : angle 6.34646 / 4.37 ( 2712) link_BETA1-4 : bond 0.00052 / 0.03 ( 4) link_BETA1-4 : angle 2.05842 / 1.30 ( 12) link_NAG-ASN : bond 0.00841 / 0.56 ( 12) link_NAG-ASN : angle 4.81826 / 3.35 ( 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 : 0.638 Fit side-chains 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: 0.8509 (pt) REVERT: A 398 THR cc_start: 0.8575 (p) cc_final: 0.8196 (t) 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: 0.7278 (m-30) REVERT: A 648 GLU cc_start: 0.8390 (pt0) cc_final: 0.8156 (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: 0.8048 (p) REVERT: C 489 VAL cc_start: 0.8532 (t) cc_final: 0.8260 (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: 0.8259 (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: 0.7176 (tm-30) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1382 time to fit residues: 89.6419 Evaluate side-chains 232 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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... 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 = 0.137096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109097 restraints weight = 20718.362| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.95 r_work: 0.2903 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16932 Z= 0.165 Angle : 0.560 8.289 23012 Z= 0.297 Chirality : 0.041 0.296 2712 Planarity : 0.004 0.046 2728 Dihedral : 9.509 57.363 2316 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.02 % Rotamer: Outliers : 2.28 % Allowed : 6.35 % Favored : 91.37 % 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: -1.48 (0.17), residues: 1908 helix: -0.20 (0.14), residues: 1100 sheet: -2.04 (0.35), residues: 200 loop : -1.87 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 592 TYR 0.019 0.002 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/Z covalent geometry : bond 0.00365 / 0.16 (16912) covalent geometry : angle 0.54756 / 0.29 (22956) SS BOND : bond 0.00342 / 0.17 ( 4) SS BOND : angle 1.83002 / 1.00 ( 8) hydrogen bonds : bond 0.05085 / 3.24 ( 936) hydrogen bonds : angle 4.59953 / 3.15 ( 2712) link_BETA1-4 : bond 0.00140 / 0.07 ( 4) link_BETA1-4 : angle 1.45876 / 0.91 ( 12) link_NAG-ASN : bond 0.00436 / 0.29 ( 12) link_NAG-ASN : angle 2.85061 / 1.99 ( 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 314 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 SER cc_start: 0.8835 (p) cc_final: 0.8430 (t) REVERT: A 333 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8406 (tp) REVERT: A 367 ILE cc_start: 0.9079 (mt) cc_final: 0.8631 (pt) REVERT: A 488 VAL cc_start: 0.8929 (t) cc_final: 0.8615 (m) REVERT: A 570 TRP cc_start: 0.8689 (m100) cc_final: 0.8288 (m100) REVERT: A 650 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7857 (tt0) REVERT: B 245 ASN cc_start: 0.7925 (m-40) cc_final: 0.7700 (m-40) REVERT: B 275 SER cc_start: 0.8875 (p) cc_final: 0.8408 (t) REVERT: B 367 ILE cc_start: 0.9095 (mt) cc_final: 0.8717 (pt) REVERT: B 444 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8543 (mt-10) REVERT: B 531 ASN cc_start: 0.7985 (t0) cc_final: 0.7575 (t0) REVERT: B 570 TRP cc_start: 0.8651 (m100) cc_final: 0.8422 (m100) REVERT: B 650 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8018 (tt0) REVERT: C 223 GLU cc_start: 0.7292 (pt0) cc_final: 0.6760 (tp30) REVERT: C 275 SER cc_start: 0.8955 (p) cc_final: 0.8405 (t) REVERT: C 444 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8573 (mt-10) REVERT: C 486 TYR cc_start: 0.8480 (t80) cc_final: 0.8192 (t80) REVERT: C 531 ASN cc_start: 0.8062 (t0) cc_final: 0.7586 (t0) REVERT: C 570 TRP cc_start: 0.8655 (m100) cc_final: 0.8351 (m100) REVERT: D 223 GLU cc_start: 0.7223 (pt0) cc_final: 0.6728 (tp30) REVERT: D 275 SER cc_start: 0.8823 (p) cc_final: 0.8440 (t) REVERT: D 570 TRP cc_start: 0.8685 (m100) cc_final: 0.8288 (m100) REVERT: D 650 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7875 (tt0) outliers start: 38 outliers final: 27 residues processed: 306 average time/residue: 0.1123 time to fit residues: 55.7402 Evaluate side-chains 248 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 344 CYS 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 587 SER 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: 2.9990 chunk 187 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109474 restraints weight = 20810.568| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.96 r_work: 0.2943 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.137 Angle : 0.498 8.247 23012 Z= 0.262 Chirality : 0.040 0.278 2712 Planarity : 0.003 0.041 2728 Dihedral : 8.836 59.491 2316 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 2.46 % Allowed : 8.93 % Favored : 88.61 % 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: -0.58 (0.18), residues: 1908 helix: 0.68 (0.15), residues: 1096 sheet: -1.88 (0.34), residues: 200 loop : -1.73 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 592 TYR 0.018 0.001 TYR A 486 PHE 0.022 0.001 PHE C 600 TRP 0.010 0.001 TRP D 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (16912) covalent geometry : angle 0.48840 / 0.26 (22956) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 1.26332 / 0.68 ( 8) hydrogen bonds : bond 0.04574 / 2.94 ( 936) hydrogen bonds : angle 4.24521 / 2.90 ( 2712) link_BETA1-4 : bond 0.00246 / 0.12 ( 4) link_BETA1-4 : angle 1.25250 / 0.78 ( 12) link_NAG-ASN : bond 0.00432 / 0.29 ( 12) link_NAG-ASN : angle 2.35250 / 1.64 ( 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 280 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.621 Fit side-chains REVERT: A 275 SER cc_start: 0.8856 (p) cc_final: 0.8530 (t) REVERT: A 367 ILE cc_start: 0.9092 (mt) cc_final: 0.8833 (tp) REVERT: A 444 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8520 (mt-10) REVERT: A 488 VAL cc_start: 0.8962 (t) cc_final: 0.8650 (m) REVERT: A 570 TRP cc_start: 0.8721 (m100) cc_final: 0.8326 (m100) REVERT: A 650 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7848 (tt0) REVERT: B 275 SER cc_start: 0.8899 (p) cc_final: 0.8522 (t) REVERT: B 367 ILE cc_start: 0.9071 (mt) cc_final: 0.8604 (pt) REVERT: B 444 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8548 (mt-10) REVERT: C 223 GLU cc_start: 0.7165 (pt0) cc_final: 0.6810 (tp30) REVERT: C 275 SER cc_start: 0.8965 (p) cc_final: 0.8549 (t) REVERT: C 444 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8575 (mt-10) REVERT: C 673 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 223 GLU cc_start: 0.7172 (pt0) cc_final: 0.6700 (tp30) REVERT: D 245 ASN cc_start: 0.7852 (m-40) cc_final: 0.7649 (m-40) REVERT: D 275 SER cc_start: 0.8864 (p) cc_final: 0.8527 (t) REVERT: D 570 TRP cc_start: 0.8688 (m100) cc_final: 0.8413 (m100) REVERT: D 650 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7887 (tt0) REVERT: D 673 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8551 (mp) outliers start: 41 outliers final: 32 residues processed: 263 average time/residue: 0.1097 time to fit residues: 47.4652 Evaluate side-chains 249 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 CYS Chi-restraints excluded: chain A residue 268 THR 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 427 SER 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 268 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 522 ILE 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 489 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 427 SER 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 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: 7.9990 chunk 71 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 123 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 D 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.096219 restraints weight = 21090.920| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.11 r_work: 0.2828 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2387 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= 0.204 Angle : 0.538 9.927 23012 Z= 0.276 Chirality : 0.041 0.268 2712 Planarity : 0.003 0.043 2728 Dihedral : 8.595 59.211 2316 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 3.66 % Allowed : 8.69 % 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: -0.21 (0.19), residues: 1908 helix: 0.94 (0.15), residues: 1104 sheet: -1.78 (0.34), residues: 200 loop : -1.48 (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 D 600 TRP 0.012 0.002 TRP A 554 HIS 0.004 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (16912) covalent geometry : angle 0.52998 / 0.27 (22956) SS BOND : bond 0.00039 / 0.02 ( 4) SS BOND : angle 0.86441 / 0.46 ( 8) hydrogen bonds : bond 0.04710 / 3.02 ( 936) hydrogen bonds : angle 4.18730 / 2.86 ( 2712) link_BETA1-4 : bond 0.00305 / 0.15 ( 4) link_BETA1-4 : angle 1.46195 / 0.90 ( 12) link_NAG-ASN : bond 0.00411 / 0.28 ( 12) link_NAG-ASN : angle 2.19137 / 1.53 ( 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 287 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 0.738 Fit side-chains REVERT: A 275 SER cc_start: 0.8902 (p) cc_final: 0.8567 (t) REVERT: A 444 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 570 TRP cc_start: 0.8777 (m100) cc_final: 0.8388 (m100) REVERT: A 650 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8014 (tt0) REVERT: B 245 ASN cc_start: 0.7878 (m-40) cc_final: 0.7039 (p0) REVERT: B 275 SER cc_start: 0.8920 (p) cc_final: 0.8565 (t) REVERT: B 444 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8676 (mt-10) REVERT: B 486 TYR cc_start: 0.8396 (t80) cc_final: 0.8178 (t80) REVERT: B 650 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8052 (tt0) REVERT: C 223 GLU cc_start: 0.7211 (pt0) cc_final: 0.6808 (tp30) REVERT: C 245 ASN cc_start: 0.7883 (m-40) cc_final: 0.7038 (p0) REVERT: C 275 SER cc_start: 0.8992 (p) cc_final: 0.8588 (t) REVERT: C 673 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8793 (mp) REVERT: D 223 GLU cc_start: 0.7164 (pt0) cc_final: 0.6732 (tp30) REVERT: D 245 ASN cc_start: 0.8008 (m-40) cc_final: 0.7805 (m-40) REVERT: D 275 SER cc_start: 0.8910 (p) cc_final: 0.8572 (t) REVERT: D 570 TRP cc_start: 0.8727 (m100) cc_final: 0.8353 (m100) REVERT: D 650 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7986 (tt0) REVERT: D 673 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8656 (mp) outliers start: 61 outliers final: 52 residues processed: 272 average time/residue: 0.1060 time to fit residues: 47.9944 Evaluate side-chains 260 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 269 ASN 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 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 398 THR 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 492 ILE Chi-restraints excluded: chain C residue 494 GLU 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 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: 3.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096488 restraints weight = 20948.017| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.11 r_work: 0.2829 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16932 Z= 0.174 Angle : 0.510 9.535 23012 Z= 0.262 Chirality : 0.040 0.257 2712 Planarity : 0.003 0.040 2728 Dihedral : 8.336 55.645 2316 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 3.06 % Allowed : 10.91 % Favored : 86.03 % 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: 0.06 (0.19), residues: 1908 helix: 1.11 (0.15), residues: 1108 sheet: -1.63 (0.35), residues: 200 loop : -1.30 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 592 TYR 0.019 0.001 TYR A 486 PHE 0.022 0.001 PHE D 600 TRP 0.010 0.001 TRP A 554 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (16912) covalent geometry : angle 0.50325 / 0.26 (22956) SS BOND : bond 0.00108 / 0.05 ( 4) SS BOND : angle 0.75355 / 0.40 ( 8) hydrogen bonds : bond 0.04539 / 2.91 ( 936) hydrogen bonds : angle 4.08611 / 2.80 ( 2712) link_BETA1-4 : bond 0.00230 / 0.11 ( 4) link_BETA1-4 : angle 1.39451 / 0.86 ( 12) link_NAG-ASN : bond 0.00384 / 0.26 ( 12) link_NAG-ASN : angle 2.01349 / 1.40 ( 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 266 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.619 Fit side-chains REVERT: A 245 ASN cc_start: 0.7857 (m-40) cc_final: 0.7030 (p0) REVERT: A 275 SER cc_start: 0.8883 (p) cc_final: 0.8633 (t) REVERT: A 444 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8679 (mt-10) REVERT: A 488 VAL cc_start: 0.8954 (t) cc_final: 0.8690 (m) REVERT: A 570 TRP cc_start: 0.8789 (m100) cc_final: 0.8431 (m100) REVERT: A 650 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8006 (tt0) REVERT: B 245 ASN cc_start: 0.7877 (m-40) cc_final: 0.7127 (p0) REVERT: B 275 SER cc_start: 0.8914 (p) cc_final: 0.8574 (t) REVERT: B 444 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8675 (mt-10) REVERT: B 650 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8038 (tt0) REVERT: C 223 GLU cc_start: 0.7208 (pt0) cc_final: 0.6792 (tp30) REVERT: C 245 ASN cc_start: 0.7897 (m-40) cc_final: 0.7105 (p0) REVERT: C 275 SER cc_start: 0.8960 (p) cc_final: 0.8605 (t) REVERT: C 673 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (mp) REVERT: D 223 GLU cc_start: 0.7087 (pt0) cc_final: 0.6649 (tp30) REVERT: D 245 ASN cc_start: 0.7958 (m-40) cc_final: 0.7745 (m-40) REVERT: D 275 SER cc_start: 0.8930 (p) cc_final: 0.8637 (t) REVERT: D 570 TRP cc_start: 0.8752 (m100) cc_final: 0.8495 (m100) REVERT: D 650 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8001 (tt0) REVERT: D 673 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8713 (mp) outliers start: 51 outliers final: 46 residues processed: 255 average time/residue: 0.1099 time to fit residues: 46.1866 Evaluate side-chains 251 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 269 ASN 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 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 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 427 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 512 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 587 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 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 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 156 optimal weight: 0.0270 chunk 104 optimal weight: 9.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108882 restraints weight = 20807.745| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.95 r_work: 0.2923 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16932 Z= 0.124 Angle : 0.468 9.548 23012 Z= 0.242 Chirality : 0.039 0.248 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.916 53.886 2316 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.57 % Favored : 97.22 % Rotamer: Outliers : 3.06 % Allowed : 11.21 % Favored : 85.73 % 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: 0.40 (0.19), residues: 1908 helix: 1.39 (0.15), residues: 1104 sheet: -1.45 (0.34), residues: 200 loop : -1.17 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 464 TYR 0.021 0.001 TYR B 486 PHE 0.021 0.001 PHE C 600 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16912) covalent geometry : angle 0.46200 / 0.24 (22956) SS BOND : bond 0.00076 / 0.04 ( 4) SS BOND : angle 0.63730 / 0.34 ( 8) hydrogen bonds : bond 0.04258 / 2.73 ( 936) hydrogen bonds : angle 3.95479 / 2.70 ( 2712) link_BETA1-4 : bond 0.00206 / 0.10 ( 4) link_BETA1-4 : angle 1.26091 / 0.78 ( 12) link_NAG-ASN : bond 0.00363 / 0.25 ( 12) link_NAG-ASN : angle 1.86249 / 1.29 ( 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 265 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.638 Fit side-chains REVERT: A 245 ASN cc_start: 0.7844 (m-40) cc_final: 0.7081 (p0) REVERT: A 275 SER cc_start: 0.8889 (p) cc_final: 0.8650 (t) REVERT: A 444 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 488 VAL cc_start: 0.8947 (t) cc_final: 0.8652 (m) REVERT: A 570 TRP cc_start: 0.8790 (m100) cc_final: 0.8508 (m100) REVERT: A 650 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7989 (tt0) REVERT: B 245 ASN cc_start: 0.7755 (m-40) cc_final: 0.7068 (p0) REVERT: B 275 SER cc_start: 0.8939 (p) cc_final: 0.8658 (t) REVERT: B 444 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8563 (mt-10) REVERT: B 650 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7990 (tt0) REVERT: C 223 GLU cc_start: 0.7115 (pt0) cc_final: 0.6779 (tp30) REVERT: C 245 ASN cc_start: 0.7800 (m-40) cc_final: 0.7092 (p0) REVERT: C 275 SER cc_start: 0.8918 (p) cc_final: 0.8602 (t) REVERT: C 673 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8830 (mp) REVERT: D 223 GLU cc_start: 0.6986 (pt0) cc_final: 0.6594 (tp30) REVERT: D 245 ASN cc_start: 0.7837 (m-40) cc_final: 0.7021 (p0) REVERT: D 275 SER cc_start: 0.8914 (p) cc_final: 0.8651 (t) REVERT: D 650 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8280 (tm-30) REVERT: D 673 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8757 (mp) outliers start: 51 outliers final: 43 residues processed: 254 average time/residue: 0.1052 time to fit residues: 44.9750 Evaluate side-chains 252 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 587 SER 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 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 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 373 ASP Chi-restraints excluded: chain C residue 398 THR 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 494 GLU 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 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: 0.4980 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN ** B 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 = 0.3519 r_free = 0.3519 target = 0.136655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108663 restraints weight = 20744.941| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.96 r_work: 0.2907 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.136 Angle : 0.472 9.520 23012 Z= 0.243 Chirality : 0.039 0.241 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.658 52.832 2316 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.94 % Favored : 96.86 % Rotamer: Outliers : 3.06 % Allowed : 11.63 % Favored : 85.31 % 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: 0.58 (0.19), residues: 1908 helix: 1.49 (0.15), residues: 1108 sheet: -1.33 (0.35), residues: 200 loop : -1.03 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.020 0.001 TYR B 486 PHE 0.022 0.001 PHE C 600 TRP 0.008 0.001 TRP B 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16912) covalent geometry : angle 0.46574 / 0.24 (22956) SS BOND : bond 0.00094 / 0.05 ( 4) SS BOND : angle 0.56429 / 0.30 ( 8) hydrogen bonds : bond 0.04241 / 2.72 ( 936) hydrogen bonds : angle 3.89935 / 2.67 ( 2712) link_BETA1-4 : bond 0.00219 / 0.11 ( 4) link_BETA1-4 : angle 1.28425 / 0.80 ( 12) link_NAG-ASN : bond 0.00346 / 0.23 ( 12) link_NAG-ASN : angle 1.78597 / 1.24 ( 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 269 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.619 Fit side-chains REVERT: A 245 ASN cc_start: 0.7820 (m-40) cc_final: 0.7081 (p0) REVERT: A 275 SER cc_start: 0.8873 (p) cc_final: 0.8660 (t) REVERT: A 444 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8514 (mt-10) REVERT: A 488 VAL cc_start: 0.8952 (t) cc_final: 0.8665 (m) REVERT: A 650 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7980 (tt0) REVERT: B 245 ASN cc_start: 0.7763 (m-40) cc_final: 0.7072 (p0) REVERT: B 275 SER cc_start: 0.8909 (p) cc_final: 0.8654 (t) REVERT: B 444 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8589 (mt-10) REVERT: B 650 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7992 (tt0) REVERT: C 223 GLU cc_start: 0.7145 (pt0) cc_final: 0.6824 (tp30) REVERT: C 245 ASN cc_start: 0.7823 (m-40) cc_final: 0.7109 (p0) REVERT: C 275 SER cc_start: 0.8971 (p) cc_final: 0.8668 (t) REVERT: C 673 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8821 (mp) REVERT: D 223 GLU cc_start: 0.6972 (pt0) cc_final: 0.6755 (tp30) REVERT: D 245 ASN cc_start: 0.7913 (m-40) cc_final: 0.7066 (p0) REVERT: D 275 SER cc_start: 0.8908 (p) cc_final: 0.8676 (t) REVERT: D 488 VAL cc_start: 0.8978 (t) cc_final: 0.8740 (m) REVERT: D 650 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7978 (tt0) REVERT: D 673 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8744 (mp) outliers start: 51 outliers final: 47 residues processed: 259 average time/residue: 0.1084 time to fit residues: 46.7426 Evaluate side-chains 255 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 489 VAL 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 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 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 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 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 373 ASP Chi-restraints excluded: chain C residue 398 THR 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 494 GLU Chi-restraints excluded: chain C residue 512 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 587 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 425 ASP Chi-restraints excluded: chain D residue 427 SER 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 587 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: 0.9980 chunk 160 optimal weight: 8.9990 chunk 5 optimal weight: 0.0170 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3533 r_free = 0.3533 target = 0.137720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109866 restraints weight = 20730.766| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.95 r_work: 0.2935 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2893 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= 0.116 Angle : 0.459 9.354 23012 Z= 0.236 Chirality : 0.038 0.235 2712 Planarity : 0.003 0.035 2728 Dihedral : 7.381 51.638 2316 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.36 % Favored : 97.43 % Rotamer: Outliers : 2.88 % Allowed : 12.35 % Favored : 84.77 % 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: 1.66 (0.15), residues: 1100 sheet: -1.15 (0.35), residues: 200 loop : -0.98 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.019 0.001 TYR B 486 PHE 0.021 0.001 PHE C 600 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16912) covalent geometry : angle 0.45328 / 0.24 (22956) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 0.47504 / 0.25 ( 8) hydrogen bonds : bond 0.04110 / 2.64 ( 936) hydrogen bonds : angle 3.82707 / 2.62 ( 2712) link_BETA1-4 : bond 0.00273 / 0.14 ( 4) link_BETA1-4 : angle 1.23951 / 0.77 ( 12) link_NAG-ASN : bond 0.00343 / 0.23 ( 12) link_NAG-ASN : angle 1.68718 / 1.17 ( 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 255 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.619 Fit side-chains REVERT: A 245 ASN cc_start: 0.7748 (m-40) cc_final: 0.7085 (p0) REVERT: A 444 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8562 (mt-10) REVERT: A 488 VAL cc_start: 0.8934 (t) cc_final: 0.8633 (m) REVERT: B 224 LEU cc_start: 0.7817 (tt) cc_final: 0.7539 (tt) REVERT: B 245 ASN cc_start: 0.7669 (m-40) cc_final: 0.7079 (p0) REVERT: B 275 SER cc_start: 0.8935 (p) cc_final: 0.8711 (t) REVERT: B 444 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8515 (mt-10) REVERT: C 223 GLU cc_start: 0.7110 (pt0) cc_final: 0.6821 (tp30) REVERT: C 245 ASN cc_start: 0.7740 (m-40) cc_final: 0.7122 (p0) REVERT: C 275 SER cc_start: 0.8945 (p) cc_final: 0.8684 (t) REVERT: C 673 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8827 (mp) REVERT: D 223 GLU cc_start: 0.7023 (pt0) cc_final: 0.6779 (tp30) REVERT: D 245 ASN cc_start: 0.7902 (m-40) cc_final: 0.7124 (p0) REVERT: D 488 VAL cc_start: 0.8959 (t) cc_final: 0.8701 (m) REVERT: D 673 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8735 (mp) outliers start: 48 outliers final: 44 residues processed: 246 average time/residue: 0.1012 time to fit residues: 41.6207 Evaluate side-chains 243 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 584 SER 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 269 ASN 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 511 ASP Chi-restraints excluded: chain B residue 512 VAL 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 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 494 GLU 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 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 498 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 = 0.3461 r_free = 0.3461 target = 0.132148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103477 restraints weight = 20857.807| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.05 r_work: 0.2850 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 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 : 0.004 0.031 16932 Z= 0.174 Angle : 0.510 10.250 23012 Z= 0.258 Chirality : 0.040 0.228 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.469 52.431 2316 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 3.12 % Allowed : 12.83 % Favored : 84.05 % 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: 0.67 (0.19), residues: 1908 helix: 1.56 (0.15), residues: 1108 sheet: -1.26 (0.35), residues: 200 loop : -1.01 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.018 0.001 TYR B 486 PHE 0.023 0.001 PHE C 600 TRP 0.010 0.001 TRP A 554 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (16912) covalent geometry : angle 0.50512 / 0.26 (22956) SS BOND : bond 0.00091 / 0.05 ( 4) SS BOND : angle 0.52925 / 0.28 ( 8) hydrogen bonds : bond 0.04371 / 2.81 ( 936) hydrogen bonds : angle 3.89149 / 2.66 ( 2712) link_BETA1-4 : bond 0.00300 / 0.15 ( 4) link_BETA1-4 : angle 1.37424 / 0.85 ( 12) link_NAG-ASN : bond 0.00322 / 0.22 ( 12) link_NAG-ASN : angle 1.67905 / 1.16 ( 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 261 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.640 Fit side-chains REVERT: A 245 ASN cc_start: 0.7820 (m-40) cc_final: 0.7130 (p0) REVERT: A 488 VAL cc_start: 0.8900 (t) cc_final: 0.8611 (m) REVERT: A 650 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7990 (tt0) REVERT: B 245 ASN cc_start: 0.7742 (m-40) cc_final: 0.7094 (p0) REVERT: B 275 SER cc_start: 0.8906 (p) cc_final: 0.8692 (t) REVERT: B 650 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7958 (tt0) REVERT: C 223 GLU cc_start: 0.7125 (pt0) cc_final: 0.6827 (tp30) REVERT: C 245 ASN cc_start: 0.7847 (m-40) cc_final: 0.7156 (p0) REVERT: C 275 SER cc_start: 0.8952 (p) cc_final: 0.8692 (t) REVERT: C 673 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8836 (mp) REVERT: D 223 GLU cc_start: 0.7007 (pt0) cc_final: 0.6744 (tp30) REVERT: D 245 ASN cc_start: 0.7920 (m-40) cc_final: 0.7017 (p0) REVERT: D 488 VAL cc_start: 0.8912 (t) cc_final: 0.8648 (m) REVERT: D 650 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7982 (tt0) REVERT: D 673 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8786 (mp) outliers start: 52 outliers final: 47 residues processed: 253 average time/residue: 0.1078 time to fit residues: 45.6939 Evaluate side-chains 252 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 489 VAL Chi-restraints excluded: chain A residue 511 ASP 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 584 SER Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 269 ASN 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 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 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 494 GLU 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 587 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 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 587 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 55 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN A 636 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106891 restraints weight = 20754.122| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.94 r_work: 0.2912 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16932 Z= 0.131 Angle : 0.484 10.010 23012 Z= 0.246 Chirality : 0.038 0.225 2712 Planarity : 0.003 0.036 2728 Dihedral : 7.326 51.923 2316 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.25 % Favored : 97.54 % Rotamer: Outliers : 3.00 % Allowed : 13.07 % Favored : 83.93 % 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: 0.79 (0.19), residues: 1908 helix: 1.64 (0.15), residues: 1108 sheet: -1.16 (0.36), residues: 200 loop : -0.95 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 464 TYR 0.019 0.001 TYR B 486 PHE 0.022 0.001 PHE B 600 TRP 0.008 0.001 TRP A 554 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16912) covalent geometry : angle 0.47891 / 0.24 (22956) SS BOND : bond 0.00073 / 0.04 ( 4) SS BOND : angle 0.49116 / 0.26 ( 8) hydrogen bonds : bond 0.04196 / 2.69 ( 936) hydrogen bonds : angle 3.83806 / 2.63 ( 2712) link_BETA1-4 : bond 0.00144 / 0.07 ( 4) link_BETA1-4 : angle 1.28696 / 0.80 ( 12) link_NAG-ASN : bond 0.00323 / 0.22 ( 12) link_NAG-ASN : angle 1.61510 / 1.12 ( 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 258 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.686 Fit side-chains REVERT: A 245 ASN cc_start: 0.7668 (m-40) cc_final: 0.7086 (p0) REVERT: A 267 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8267 (tptp) REVERT: A 488 VAL cc_start: 0.8921 (t) cc_final: 0.8628 (m) REVERT: A 650 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7983 (tt0) REVERT: B 224 LEU cc_start: 0.7812 (tt) cc_final: 0.7567 (tt) REVERT: B 245 ASN cc_start: 0.7611 (m-40) cc_final: 0.7071 (p0) REVERT: B 275 SER cc_start: 0.8904 (p) cc_final: 0.8666 (t) REVERT: B 650 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7944 (tt0) REVERT: C 223 GLU cc_start: 0.7065 (pt0) cc_final: 0.6805 (tp30) REVERT: C 245 ASN cc_start: 0.7710 (m-40) cc_final: 0.7125 (p0) REVERT: C 275 SER cc_start: 0.8943 (p) cc_final: 0.8690 (t) REVERT: C 673 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8834 (mp) REVERT: D 223 GLU cc_start: 0.6983 (pt0) cc_final: 0.6749 (tp30) REVERT: D 245 ASN cc_start: 0.7969 (m-40) cc_final: 0.7176 (p0) REVERT: D 488 VAL cc_start: 0.8955 (t) cc_final: 0.8686 (m) REVERT: D 650 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7979 (tt0) REVERT: D 673 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8760 (mp) outliers start: 50 outliers final: 46 residues processed: 249 average time/residue: 0.1126 time to fit residues: 45.7291 Evaluate side-chains 249 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 513 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 587 SER Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 269 ASN 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 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 587 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 425 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 498 HIS Chi-restraints excluded: chain D residue 511 ASP 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 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 135 optimal weight: 0.0000 chunk 5 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110255 restraints weight = 20591.305| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.93 r_work: 0.2962 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16932 Z= 0.097 Angle : 0.453 9.271 23012 Z= 0.232 Chirality : 0.037 0.223 2712 Planarity : 0.003 0.035 2728 Dihedral : 6.902 53.410 2316 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.46 % Favored : 97.33 % Rotamer: Outliers : 2.52 % Allowed : 13.61 % Favored : 83.87 % 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: 0.98 (0.19), residues: 1908 helix: 1.82 (0.15), residues: 1100 sheet: -0.96 (0.36), residues: 200 loop : -0.94 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 464 TYR 0.019 0.001 TYR B 486 PHE 0.020 0.001 PHE B 600 TRP 0.006 0.001 TRP A 414 HIS 0.002 0.000 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (16912) covalent geometry : angle 0.44896 / 0.23 (22956) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 0.34503 / 0.18 ( 8) hydrogen bonds : bond 0.03924 / 2.53 ( 936) hydrogen bonds : angle 3.74763 / 2.57 ( 2712) link_BETA1-4 : bond 0.00198 / 0.10 ( 4) link_BETA1-4 : angle 1.16972 / 0.73 ( 12) link_NAG-ASN : bond 0.00320 / 0.22 ( 12) link_NAG-ASN : angle 1.50076 / 1.04 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.60 seconds wall clock time: 63 minutes 1.23 seconds (3781.23 seconds total)