Starting phenix.real_space_refine on Fri Jul 3 09:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlr_38456/07_2026/8xlr_38456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlr_38456/07_2026/8xlr_38456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xlr_38456/07_2026/8xlr_38456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlr_38456/07_2026/8xlr_38456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xlr_38456/07_2026/8xlr_38456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlr_38456/07_2026/8xlr_38456.map" } resolution = 2.93 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= 0.002 sd= 0.160 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 4 9.91 5 S 78 5.16 5 C 8966 2.51 5 N 2064 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6227 Classifications: {'peptide': 757} Link IDs: {'PTRANS': 29, 'TRANS': 727} Chain breaks: 5 Chain: "B" Number of atoms: 6227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6227 Classifications: {'peptide': 757} Link IDs: {'PTRANS': 29, 'TRANS': 727} Chain breaks: 5 Chain: "A" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 426 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 24, 'HEX': 1, 'JGX': 1, 'NAG': 4} Classifications: {'undetermined': 30} Link IDs: {None: 28} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 454 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'C14': 26, 'HEX': 1, 'JGX': 1, 'NAG': 4} Classifications: {'undetermined': 32} Link IDs: {None: 30} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.03, per 1000 atoms: 0.23 Number of scatterers: 13338 At special positions: 0 Unit cell: (112.66, 124.7, 124.7, 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 4 19.99 S 78 16.00 O 2226 8.00 N 2064 7.00 C 8966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 813 " " NAG A1002 " - " ASN A 806 " " NAG A1003 " - " ASN A 798 " " NAG A1004 " - " ASN A 375 " " NAG B1003 " - " ASN B 813 " " NAG B1004 " - " ASN B 806 " " NAG B1005 " - " ASN B 798 " " NAG B1006 " - " ASN B 375 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 555.2 milliseconds 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 63.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 119 through 139 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.528A pdb=" N LEU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.645A pdb=" N ASN A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.896A pdb=" N PHE A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.712A pdb=" N ILE A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 removed outlier: 4.478A pdb=" N SER A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.582A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 359 removed outlier: 4.171A pdb=" N ALA A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.535A pdb=" N MET A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.699A pdb=" N HIS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 438 removed outlier: 3.628A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 526 removed outlier: 3.825A pdb=" N GLY A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 568 removed outlier: 3.746A pdb=" N VAL A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 602 removed outlier: 3.840A pdb=" N PHE A 576 " --> pdb=" O THR A 572 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 594 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix removed outlier: 3.618A pdb=" N TYR A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 removed outlier: 4.210A pdb=" N LEU A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 670 Proline residue: A 658 - end of helix removed outlier: 3.609A pdb=" N LYS A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 691 Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.652A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 745 removed outlier: 3.626A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 730 " --> pdb=" O PHE A 726 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 735 " --> pdb=" O ASN A 731 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 740 " --> pdb=" O ARG A 736 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.756A pdb=" N ILE A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 803 through 808 Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 854 through 886 removed outlier: 4.275A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 859 " --> pdb=" O LYS A 855 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 860 " --> pdb=" O ASP A 856 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 862 " --> pdb=" O TRP A 858 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 868 " --> pdb=" O ARG A 864 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 882 " --> pdb=" O MET A 878 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 913 removed outlier: 3.622A pdb=" N ILE A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 139 Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.528A pdb=" N LEU B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.646A pdb=" N ASN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.896A pdb=" N PHE B 241 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.712A pdb=" N ILE B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 275 removed outlier: 4.479A pdb=" N SER B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.581A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 359 removed outlier: 4.171A pdb=" N ALA B 345 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.535A pdb=" N MET B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.700A pdb=" N HIS B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 438 removed outlier: 3.628A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 413 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 526 removed outlier: 3.826A pdb=" N GLY B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 568 removed outlier: 3.747A pdb=" N VAL B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 602 removed outlier: 3.840A pdb=" N PHE B 576 " --> pdb=" O THR B 572 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 594 " --> pdb=" O VAL B 590 " (cutoff:3.500A) Proline residue: B 595 - end of helix removed outlier: 3.618A pdb=" N TYR B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 599 " --> pdb=" O PRO B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 removed outlier: 4.210A pdb=" N LEU B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 670 Proline residue: B 658 - end of helix removed outlier: 3.610A pdb=" N LYS B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 691 Processing helix chain 'B' and resid 699 through 716 removed outlier: 3.652A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 712 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 714 " --> pdb=" O PHE B 710 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 745 removed outlier: 3.625A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 728 " --> pdb=" O PRO B 724 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 729 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 730 " --> pdb=" O PHE B 726 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 740 " --> pdb=" O ARG B 736 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 741 " --> pdb=" O LEU B 737 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 742 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.756A pdb=" N ILE B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 Processing helix chain 'B' and resid 803 through 808 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 854 through 886 removed outlier: 4.275A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 860 " --> pdb=" O ASP B 856 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 862 " --> pdb=" O TRP B 858 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 863 " --> pdb=" O ALA B 859 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B 868 " --> pdb=" O ARG B 864 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 873 " --> pdb=" O ILE B 869 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 882 " --> pdb=" O MET B 878 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 913 removed outlier: 3.622A pdb=" N ILE B 897 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS B 898 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 912 " --> pdb=" O PHE B 908 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 145 removed outlier: 3.561A pdb=" N GLU A 143 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 64 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 65 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA A 280 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 67 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 183 removed outlier: 6.868A pdb=" N THR A 178 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR A 222 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 180 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 182 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.668A pdb=" N TRP A 389 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AA6, first strand: chain 'A' and resid 809 through 813 removed outlier: 3.511A pdb=" N CYS A 836 " --> pdb=" O PHE A 812 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 145 removed outlier: 3.562A pdb=" N GLU B 143 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 64 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 65 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA B 280 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 67 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 183 removed outlier: 3.902A pdb=" N LEU B 220 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 180 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS B 218 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 377 through 378 removed outlier: 3.668A pdb=" N TRP B 389 " --> pdb=" O MET B 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AB2, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AB3, first strand: chain 'B' and resid 809 through 813 removed outlier: 3.512A pdb=" N CYS B 836 " --> pdb=" O PHE B 812 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1731 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: 2.09 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1950 1.27 - 1.41: 3505 1.41 - 1.55: 8008 1.55 - 1.68: 15 1.68 - 1.82: 124 Bond restraints: 13602 Sorted by residual: bond pdb=" C TYR A 838 " pdb=" O TYR A 838 " ideal model delta sigma weight residual 1.234 1.138 0.096 1.24e-02 6.50e+03 5.97e+01 bond pdb=" C TYR B 838 " pdb=" O TYR B 838 " ideal model delta sigma weight residual 1.234 1.138 0.096 1.24e-02 6.50e+03 5.95e+01 bond pdb=" C20 JGX B1034 " pdb=" S22 JGX B1034 " ideal model delta sigma weight residual 1.771 1.618 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" C20 JGX A1031 " pdb=" S22 JGX A1031 " ideal model delta sigma weight residual 1.771 1.618 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" C ARG A 609 " pdb=" O ARG A 609 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.05e-02 9.07e+03 4.55e+01 ... (remaining 13597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 17829 2.66 - 5.33: 227 5.33 - 7.99: 42 7.99 - 10.66: 8 10.66 - 13.32: 2 Bond angle restraints: 18108 Sorted by residual: angle pdb=" CA LEU B 861 " pdb=" C LEU B 861 " pdb=" O LEU B 861 " ideal model delta sigma weight residual 120.63 113.08 7.55 1.08e+00 8.57e-01 4.89e+01 angle pdb=" CA LEU A 861 " pdb=" C LEU A 861 " pdb=" O LEU A 861 " ideal model delta sigma weight residual 120.63 113.14 7.49 1.08e+00 8.57e-01 4.80e+01 angle pdb=" CA LEU B 861 " pdb=" C LEU B 861 " pdb=" N ALA B 862 " ideal model delta sigma weight residual 117.22 124.48 -7.26 1.17e+00 7.31e-01 3.85e+01 angle pdb=" CA LEU A 861 " pdb=" C LEU A 861 " pdb=" N ALA A 862 " ideal model delta sigma weight residual 117.22 124.47 -7.25 1.17e+00 7.31e-01 3.84e+01 angle pdb=" C PRO B 610 " pdb=" CA PRO B 610 " pdb=" CB PRO B 610 " ideal model delta sigma weight residual 111.56 121.63 -10.07 1.65e+00 3.67e-01 3.72e+01 ... (remaining 18103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 7018 16.12 - 32.24: 922 32.24 - 48.36: 314 48.36 - 64.47: 84 64.47 - 80.59: 34 Dihedral angle restraints: 8372 sinusoidal: 3892 harmonic: 4480 Sorted by residual: dihedral pdb=" C PRO B 610 " pdb=" N PRO B 610 " pdb=" CA PRO B 610 " pdb=" CB PRO B 610 " ideal model delta harmonic sigma weight residual -120.70 -132.22 11.52 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C PRO A 610 " pdb=" N PRO A 610 " pdb=" CA PRO A 610 " pdb=" CB PRO A 610 " ideal model delta harmonic sigma weight residual -120.70 -132.17 11.47 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" CA ASN A 798 " pdb=" C ASN A 798 " pdb=" N GLY A 799 " pdb=" CA GLY A 799 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1844 0.090 - 0.180: 70 0.180 - 0.271: 16 0.271 - 0.361: 2 0.361 - 0.451: 2 Chirality restraints: 1934 Sorted by residual: chirality pdb=" CA PRO B 610 " pdb=" N PRO B 610 " pdb=" C PRO B 610 " pdb=" CB PRO B 610 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PRO A 610 " pdb=" N PRO A 610 " pdb=" C PRO A 610 " pdb=" CB PRO A 610 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA ARG A 128 " pdb=" N ARG A 128 " pdb=" C ARG A 128 " pdb=" CB ARG A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1931 not shown) Planarity restraints: 2174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 222 " 0.071 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 223 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 222 " 0.071 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO B 223 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 860 " 0.014 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C VAL B 860 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 860 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 861 " 0.017 2.00e-02 2.50e+03 ... (remaining 2171 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3557 2.81 - 3.34: 10751 3.34 - 3.86: 18565 3.86 - 4.38: 21103 4.38 - 4.90: 39111 Nonbonded interactions: 93087 Sorted by model distance: nonbonded pdb=" O VAL A 590 " pdb=" OG1 THR A 594 " model vdw 2.293 3.040 nonbonded pdb=" O VAL B 590 " pdb=" OG1 THR B 594 " model vdw 2.294 3.040 nonbonded pdb=" O GLN B 818 " pdb=" OG1 THR B 821 " model vdw 2.330 3.040 nonbonded pdb=" O GLN A 818 " pdb=" OG1 THR A 821 " model vdw 2.330 3.040 nonbonded pdb=" OE2 GLU B 734 " pdb="CA CA B1033 " model vdw 2.353 3.250 ... (remaining 93082 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 47 through 913 or resid 1003 through 1004 or resid 1007 th \ rough 1028)) selection = (chain 'B' and (resid 47 through 913 or resid 1003 through 1004 or resid 1007 th \ rough 1028)) } 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: 5.460 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 13618 Z= 0.325 Angle : 0.722 13.320 18148 Z= 0.433 Chirality : 0.047 0.451 1934 Planarity : 0.005 0.106 2166 Dihedral : 17.010 80.592 5456 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.59 % Allowed : 22.26 % Favored : 77.15 % Cbeta Deviations : 0.14 % 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: 0.05 (0.20), residues: 1490 helix: 0.84 (0.17), residues: 862 sheet: 1.07 (0.66), residues: 42 loop : -1.25 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 842 TYR 0.042 0.001 TYR B 838 PHE 0.026 0.001 PHE B 857 TRP 0.007 0.001 TRP A 563 HIS 0.003 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.33 (13602) covalent geometry : angle 0.71680 / 0.43 (18108) SS BOND : bond 0.00152 / 0.10 ( 8) SS BOND : angle 0.60398 / 0.31 ( 16) hydrogen bonds : bond 0.16621 / 11.63 ( 587) hydrogen bonds : angle 5.14781 / 3.60 ( 1731) link_NAG-ASN : bond 0.00641 / 0.36 ( 8) link_NAG-ASN : angle 2.60985 / 1.59 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.457 Fit side-chains REVERT: B 904 MET cc_start: 0.3700 (ttt) cc_final: 0.2950 (ptp) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.4904 time to fit residues: 58.7008 Evaluate side-chains 96 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 902 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN A 159 HIS A 692 ASN B 144 ASN B 159 HIS B 692 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.205587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149322 restraints weight = 13511.132| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.17 r_work: 0.3427 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13618 Z= 0.140 Angle : 0.517 6.473 18148 Z= 0.273 Chirality : 0.041 0.288 1934 Planarity : 0.005 0.076 2166 Dihedral : 10.786 75.320 2446 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.74 % Allowed : 20.40 % Favored : 76.85 % 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: 0.66 (0.21), residues: 1490 helix: 1.53 (0.17), residues: 844 sheet: 0.83 (0.66), residues: 56 loop : -1.25 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 842 TYR 0.014 0.001 TYR A 68 PHE 0.014 0.001 PHE B 710 TRP 0.007 0.001 TRP A 389 HIS 0.006 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (13602) covalent geometry : angle 0.50645 / 0.27 (18108) SS BOND : bond 0.00222 / 0.13 ( 8) SS BOND : angle 0.94301 / 0.51 ( 16) hydrogen bonds : bond 0.06923 / 4.60 ( 587) hydrogen bonds : angle 3.94080 / 2.76 ( 1731) link_NAG-ASN : bond 0.00554 / 0.30 ( 8) link_NAG-ASN : angle 2.77189 / 1.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.332 Fit side-chains REVERT: A 647 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7834 (tt) REVERT: A 657 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6700 (mm) REVERT: B 391 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7330 (ttm) REVERT: B 647 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7772 (tt) REVERT: B 657 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6642 (mm) REVERT: B 797 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: B 874 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8441 (mp) outliers start: 37 outliers final: 11 residues processed: 121 average time/residue: 0.4804 time to fit residues: 64.4623 Evaluate side-chains 112 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 GLN B 692 ASN B 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.204808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153024 restraints weight = 13734.263| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.90 r_work: 0.3340 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13618 Z= 0.149 Angle : 0.533 7.131 18148 Z= 0.281 Chirality : 0.041 0.315 1934 Planarity : 0.005 0.069 2166 Dihedral : 10.932 80.010 2444 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.12 % Allowed : 19.44 % Favored : 77.45 % 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: 0.61 (0.21), residues: 1490 helix: 1.42 (0.17), residues: 866 sheet: 1.19 (0.67), residues: 56 loop : -1.32 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 321 TYR 0.016 0.001 TYR B 68 PHE 0.014 0.002 PHE A 710 TRP 0.008 0.001 TRP B 389 HIS 0.013 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (13602) covalent geometry : angle 0.52156 / 0.28 (18108) SS BOND : bond 0.00214 / 0.13 ( 8) SS BOND : angle 0.99389 / 0.54 ( 16) hydrogen bonds : bond 0.07384 / 4.91 ( 587) hydrogen bonds : angle 3.85653 / 2.71 ( 1731) link_NAG-ASN : bond 0.00517 / 0.28 ( 8) link_NAG-ASN : angle 2.95248 / 1.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.496 Fit side-chains REVERT: A 391 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7158 (ttm) REVERT: A 647 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 657 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6264 (mm) REVERT: A 797 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: B 130 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: B 391 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7419 (ttm) REVERT: B 647 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 657 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6210 (mm) REVERT: B 874 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8156 (mp) outliers start: 42 outliers final: 22 residues processed: 122 average time/residue: 0.5440 time to fit residues: 73.3873 Evaluate side-chains 122 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 5 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN B 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.204529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153352 restraints weight = 13667.637| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.95 r_work: 0.3310 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13618 Z= 0.150 Angle : 0.535 7.674 18148 Z= 0.281 Chirality : 0.041 0.322 1934 Planarity : 0.005 0.063 2166 Dihedral : 10.980 81.324 2444 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.08 % Allowed : 18.84 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1490 helix: 1.57 (0.17), residues: 854 sheet: 1.37 (0.68), residues: 56 loop : -1.37 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 321 TYR 0.016 0.001 TYR A 68 PHE 0.014 0.002 PHE A 415 TRP 0.008 0.001 TRP B 389 HIS 0.010 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (13602) covalent geometry : angle 0.52371 / 0.28 (18108) SS BOND : bond 0.00219 / 0.13 ( 8) SS BOND : angle 0.99806 / 0.53 ( 16) hydrogen bonds : bond 0.07356 / 4.87 ( 587) hydrogen bonds : angle 3.80749 / 2.68 ( 1731) link_NAG-ASN : bond 0.00531 / 0.29 ( 8) link_NAG-ASN : angle 3.02625 / 1.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 94 time to evaluate : 0.491 Fit side-chains REVERT: A 130 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: A 362 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: A 391 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7144 (ttm) REVERT: A 588 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6961 (tttp) REVERT: A 657 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6127 (mm) REVERT: A 702 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: A 797 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: B 130 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: B 362 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: B 391 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: B 588 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.6898 (tttp) REVERT: B 657 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.6132 (mm) REVERT: B 702 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: B 874 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 895 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.5747 (tm-30) outliers start: 55 outliers final: 27 residues processed: 136 average time/residue: 0.4838 time to fit residues: 72.7758 Evaluate side-chains 135 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.205657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153854 restraints weight = 13655.896| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.99 r_work: 0.3338 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13618 Z= 0.125 Angle : 0.504 7.563 18148 Z= 0.262 Chirality : 0.040 0.307 1934 Planarity : 0.004 0.060 2166 Dihedral : 10.558 79.004 2444 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.64 % Allowed : 19.66 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1490 helix: 1.60 (0.17), residues: 868 sheet: 1.40 (0.67), residues: 56 loop : -1.32 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.013 0.001 TYR A 68 PHE 0.014 0.001 PHE B 415 TRP 0.008 0.001 TRP A 305 HIS 0.009 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (13602) covalent geometry : angle 0.49223 / 0.26 (18108) SS BOND : bond 0.00207 / 0.13 ( 8) SS BOND : angle 0.86817 / 0.46 ( 16) hydrogen bonds : bond 0.06456 / 4.27 ( 587) hydrogen bonds : angle 3.74282 / 2.63 ( 1731) link_NAG-ASN : bond 0.00580 / 0.31 ( 8) link_NAG-ASN : angle 2.95095 / 1.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: A 130 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: A 362 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: A 588 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6954 (tttp) REVERT: A 657 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.6169 (mm) REVERT: A 702 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 797 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: A 895 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.5802 (tm-30) REVERT: B 69 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7856 (t-170) REVERT: B 362 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: B 391 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7402 (ttm) REVERT: B 588 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6969 (tttp) REVERT: B 657 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6126 (mm) REVERT: B 702 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 874 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 895 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.5796 (tm-30) outliers start: 49 outliers final: 27 residues processed: 138 average time/residue: 0.4928 time to fit residues: 75.4909 Evaluate side-chains 135 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.206482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155542 restraints weight = 13650.318| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.96 r_work: 0.3374 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13618 Z= 0.116 Angle : 0.482 7.373 18148 Z= 0.251 Chirality : 0.040 0.295 1934 Planarity : 0.004 0.057 2166 Dihedral : 10.052 72.677 2444 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.01 % Allowed : 19.66 % Favored : 76.34 % 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: 0.92 (0.21), residues: 1490 helix: 1.73 (0.17), residues: 868 sheet: 1.36 (0.67), residues: 56 loop : -1.30 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 842 TYR 0.012 0.001 TYR A 68 PHE 0.013 0.001 PHE B 415 TRP 0.008 0.001 TRP A 305 HIS 0.009 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (13602) covalent geometry : angle 0.47022 / 0.25 (18108) SS BOND : bond 0.00196 / 0.12 ( 8) SS BOND : angle 0.78947 / 0.41 ( 16) hydrogen bonds : bond 0.05958 / 3.94 ( 587) hydrogen bonds : angle 3.67759 / 2.59 ( 1731) link_NAG-ASN : bond 0.00587 / 0.32 ( 8) link_NAG-ASN : angle 2.84910 / 1.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 130 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6435 (tm-30) REVERT: A 362 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: A 391 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7143 (ttm) REVERT: A 588 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6955 (tttp) REVERT: A 657 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6231 (mm) REVERT: A 702 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 895 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: B 64 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: B 69 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7911 (t-170) REVERT: B 130 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: B 362 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 588 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6971 (tttp) REVERT: B 647 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 657 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6216 (mm) REVERT: B 702 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: B 874 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 895 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.5917 (tm-30) outliers start: 54 outliers final: 23 residues processed: 140 average time/residue: 0.5024 time to fit residues: 78.1038 Evaluate side-chains 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.202782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148658 restraints weight = 13578.170| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.03 r_work: 0.3284 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13618 Z= 0.178 Angle : 0.590 8.498 18148 Z= 0.307 Chirality : 0.043 0.339 1934 Planarity : 0.005 0.058 2166 Dihedral : 10.973 74.069 2444 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.08 % Allowed : 19.73 % Favored : 76.19 % 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: 0.66 (0.21), residues: 1490 helix: 1.52 (0.17), residues: 856 sheet: 1.45 (0.68), residues: 56 loop : -1.38 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 842 TYR 0.011 0.002 TYR A 838 PHE 0.016 0.002 PHE B 710 TRP 0.009 0.001 TRP B 389 HIS 0.007 0.001 HIS B 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (13602) covalent geometry : angle 0.57794 / 0.30 (18108) SS BOND : bond 0.00258 / 0.15 ( 8) SS BOND : angle 1.15742 / 0.64 ( 16) hydrogen bonds : bond 0.08174 / 5.43 ( 587) hydrogen bonds : angle 3.79023 / 2.67 ( 1731) link_NAG-ASN : bond 0.00452 / 0.24 ( 8) link_NAG-ASN : angle 3.15925 / 1.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 96 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: A 362 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: A 391 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7311 (ttm) REVERT: A 588 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6936 (tttp) REVERT: A 657 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.6098 (mm) REVERT: A 702 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: A 895 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: B 130 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: B 362 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: B 588 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6935 (tttp) REVERT: B 657 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6143 (mm) REVERT: B 702 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 874 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 895 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5882 (tm-30) outliers start: 55 outliers final: 28 residues processed: 138 average time/residue: 0.5010 time to fit residues: 76.4069 Evaluate side-chains 135 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 67 optimal weight: 0.0050 chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.206891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153646 restraints weight = 13593.304| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.89 r_work: 0.3383 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13618 Z= 0.110 Angle : 0.475 8.938 18148 Z= 0.246 Chirality : 0.040 0.293 1934 Planarity : 0.004 0.055 2166 Dihedral : 9.771 67.500 2444 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.41 % Allowed : 20.62 % Favored : 75.96 % 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: 0.92 (0.21), residues: 1490 helix: 1.73 (0.17), residues: 868 sheet: 1.35 (0.67), residues: 56 loop : -1.29 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.009 0.001 TYR B 68 PHE 0.012 0.001 PHE A 415 TRP 0.008 0.001 TRP A 305 HIS 0.010 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (13602) covalent geometry : angle 0.46293 / 0.24 (18108) SS BOND : bond 0.00180 / 0.11 ( 8) SS BOND : angle 0.75068 / 0.38 ( 16) hydrogen bonds : bond 0.05574 / 3.68 ( 587) hydrogen bonds : angle 3.65631 / 2.57 ( 1731) link_NAG-ASN : bond 0.00629 / 0.34 ( 8) link_NAG-ASN : angle 2.89295 / 1.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.446 Fit side-chains REVERT: A 64 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 130 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: A 362 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: A 391 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7213 (ttm) REVERT: A 588 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7098 (tttp) REVERT: A 647 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 657 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.5974 (mm) REVERT: A 702 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: A 895 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.5800 (tm-30) REVERT: B 64 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 69 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7823 (t-170) REVERT: B 130 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: B 362 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: B 588 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7101 (tttp) REVERT: B 657 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.5937 (mm) REVERT: B 702 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: B 874 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 895 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.5777 (tm-30) outliers start: 46 outliers final: 16 residues processed: 130 average time/residue: 0.5582 time to fit residues: 79.5249 Evaluate side-chains 128 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 121 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.206294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148736 restraints weight = 13733.781| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.10 r_work: 0.3341 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13618 Z= 0.116 Angle : 0.491 8.458 18148 Z= 0.254 Chirality : 0.040 0.296 1934 Planarity : 0.004 0.055 2166 Dihedral : 9.523 69.388 2444 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 21.74 % Favored : 75.74 % 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: 0.96 (0.21), residues: 1490 helix: 1.77 (0.17), residues: 868 sheet: 0.85 (0.67), residues: 60 loop : -1.25 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.010 0.001 TYR A 68 PHE 0.012 0.001 PHE B 415 TRP 0.009 0.001 TRP A 305 HIS 0.005 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (13602) covalent geometry : angle 0.47955 / 0.25 (18108) SS BOND : bond 0.00197 / 0.12 ( 8) SS BOND : angle 0.79492 / 0.41 ( 16) hydrogen bonds : bond 0.05971 / 3.96 ( 587) hydrogen bonds : angle 3.63188 / 2.56 ( 1731) link_NAG-ASN : bond 0.00562 / 0.31 ( 8) link_NAG-ASN : angle 2.84571 / 1.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.588 Fit side-chains REVERT: A 64 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: A 130 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: A 362 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: A 391 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7215 (ttm) REVERT: A 588 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6962 (tttp) REVERT: A 647 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 657 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6096 (mm) REVERT: A 702 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: A 895 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: B 64 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: B 130 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: B 362 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: B 588 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6982 (tttp) REVERT: B 657 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6099 (mm) REVERT: B 702 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: B 874 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 895 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: B 904 MET cc_start: 0.3295 (ttt) cc_final: 0.2553 (ppp) outliers start: 34 outliers final: 16 residues processed: 122 average time/residue: 0.5450 time to fit residues: 72.9429 Evaluate side-chains 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.206418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149002 restraints weight = 13697.240| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.06 r_work: 0.3371 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13618 Z= 0.116 Angle : 0.487 8.375 18148 Z= 0.252 Chirality : 0.040 0.295 1934 Planarity : 0.004 0.054 2166 Dihedral : 9.335 68.560 2444 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.37 % Allowed : 21.88 % Favored : 75.74 % 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: 1.00 (0.21), residues: 1490 helix: 1.79 (0.17), residues: 868 sheet: 1.20 (0.74), residues: 42 loop : -1.17 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.009 0.001 TYR B 68 PHE 0.012 0.001 PHE A 415 TRP 0.008 0.001 TRP A 305 HIS 0.004 0.001 HIS B 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (13602) covalent geometry : angle 0.47545 / 0.25 (18108) SS BOND : bond 0.00196 / 0.12 ( 8) SS BOND : angle 0.78187 / 0.41 ( 16) hydrogen bonds : bond 0.05869 / 3.89 ( 587) hydrogen bonds : angle 3.61824 / 2.55 ( 1731) link_NAG-ASN : bond 0.00570 / 0.31 ( 8) link_NAG-ASN : angle 2.84937 / 1.75 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.518 Fit side-chains REVERT: A 64 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: A 130 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: A 362 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: A 391 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7290 (ttm) REVERT: A 588 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7112 (tttp) REVERT: A 647 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8020 (tt) REVERT: A 657 ILE cc_start: 0.6314 (OUTLIER) cc_final: 0.5987 (mm) REVERT: A 702 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: A 895 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.5798 (tm-30) REVERT: B 64 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: B 130 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: B 362 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: B 588 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7121 (tttp) REVERT: B 657 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.5997 (mm) REVERT: B 702 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: B 874 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 895 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.5806 (tm-30) outliers start: 32 outliers final: 15 residues processed: 123 average time/residue: 0.5463 time to fit residues: 73.5076 Evaluate side-chains 126 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.207593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154380 restraints weight = 13726.941| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.94 r_work: 0.3388 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13618 Z= 0.107 Angle : 0.467 8.267 18148 Z= 0.240 Chirality : 0.039 0.284 1934 Planarity : 0.004 0.054 2166 Dihedral : 8.595 66.700 2444 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.67 % Allowed : 21.59 % Favored : 75.74 % 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: 1.11 (0.21), residues: 1490 helix: 1.89 (0.18), residues: 868 sheet: 1.18 (0.74), residues: 42 loop : -1.12 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.013 0.001 TYR A 68 PHE 0.012 0.001 PHE B 415 TRP 0.008 0.001 TRP A 305 HIS 0.004 0.001 HIS B 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (13602) covalent geometry : angle 0.45653 / 0.24 (18108) SS BOND : bond 0.00178 / 0.11 ( 8) SS BOND : angle 0.73406 / 0.37 ( 16) hydrogen bonds : bond 0.05298 / 3.51 ( 587) hydrogen bonds : angle 3.54717 / 2.50 ( 1731) link_NAG-ASN : bond 0.00583 / 0.32 ( 8) link_NAG-ASN : angle 2.69164 / 1.64 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.98 seconds wall clock time: 67 minutes 2.67 seconds (4022.67 seconds total)