Starting phenix.real_space_refine on Thu Sep 18 02:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlr_38456/09_2025/8xlr_38456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlr_38456/09_2025/8xlr_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_38456/09_2025/8xlr_38456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlr_38456/09_2025/8xlr_38456.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xlr_38456/09_2025/8xlr_38456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlr_38456/09_2025/8xlr_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-2.0-5805/lib/python3.9/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, 428 Unusual residues: {' CA': 2, 'C14': 24, 'HEX': 1, 'JGX': 1, 'NAG': 4} Classifications: {'undetermined': 32} Link IDs: {None: 31} 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, 456 Unusual residues: {' CA': 2, 'C14': 26, 'HEX': 1, 'JGX': 1, 'NAG': 4} Classifications: {'undetermined': 34} Link IDs: {None: 33} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.95, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 542.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.37 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: 1.13 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 2.510 ... (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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 aren 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 covalent geometry : bond 0.00521 (13602) covalent geometry : angle 0.71680 (18108) SS BOND : bond 0.00152 ( 8) SS BOND : angle 0.60398 ( 16) hydrogen bonds : bond 0.16621 ( 587) hydrogen bonds : angle 5.14781 ( 1731) link_NAG-ASN : bond 0.00641 ( 8) link_NAG-ASN : angle 2.60985 ( 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 : 0.378 Fit side-chains REVERT: B 904 MET cc_start: 0.3700 (ttt) cc_final: 0.2951 (ptp) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.5063 time to fit residues: 60.7240 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4297 r_free = 0.4297 target = 0.205400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157459 restraints weight = 13523.222| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.93 r_work: 0.3484 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13618 Z= 0.139 Angle : 0.516 6.485 18148 Z= 0.273 Chirality : 0.041 0.288 1934 Planarity : 0.005 0.077 2166 Dihedral : 10.787 75.135 2446 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.60 % Allowed : 20.55 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1490 helix: 1.52 (0.17), residues: 842 sheet: 0.83 (0.66), residues: 56 loop : -1.27 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 842 TYR 0.013 0.001 TYR B 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 covalent geometry : bond 0.00293 (13602) covalent geometry : angle 0.50616 (18108) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.94605 ( 16) hydrogen bonds : bond 0.06925 ( 587) hydrogen bonds : angle 3.94535 ( 1731) link_NAG-ASN : bond 0.00547 ( 8) link_NAG-ASN : angle 2.76741 ( 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 130 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.372 Fit side-chains REVERT: A 391 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7202 (ttm) REVERT: A 647 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7895 (tt) REVERT: A 657 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6778 (mm) REVERT: B 391 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7187 (ttm) REVERT: B 647 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7877 (tt) REVERT: B 657 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6709 (mm) REVERT: B 797 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: B 874 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8393 (mp) outliers start: 35 outliers final: 9 residues processed: 121 average time/residue: 0.4918 time to fit residues: 66.0691 Evaluate side-chains 110 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 391 MET 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 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 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: 1.9990 chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 131 optimal weight: 0.0000 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 0.0270 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A 913 GLN B 692 ASN B 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.207913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155283 restraints weight = 13800.093| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.95 r_work: 0.3390 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13618 Z= 0.109 Angle : 0.461 6.587 18148 Z= 0.242 Chirality : 0.039 0.276 1934 Planarity : 0.004 0.068 2166 Dihedral : 10.095 73.717 2444 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.52 % Allowed : 19.73 % Favored : 77.74 % 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 aren not related in a simple way. whole: 0.85 (0.21), residues: 1490 helix: 1.62 (0.17), residues: 868 sheet: 1.14 (0.66), residues: 56 loop : -1.21 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.017 0.001 TYR B 68 PHE 0.012 0.001 PHE B 415 TRP 0.006 0.001 TRP A 305 HIS 0.013 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00210 (13602) covalent geometry : angle 0.45095 (18108) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.74758 ( 16) hydrogen bonds : bond 0.05631 ( 587) hydrogen bonds : angle 3.76870 ( 1731) link_NAG-ASN : bond 0.00601 ( 8) link_NAG-ASN : angle 2.67340 ( 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 127 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: A 130 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: A 647 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7689 (tt) REVERT: A 657 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6096 (mm) REVERT: A 797 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: A 913 GLN cc_start: 0.2826 (OUTLIER) cc_final: 0.2274 (mm-40) REVERT: B 130 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: B 647 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 657 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.6038 (mm) REVERT: B 874 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (mp) outliers start: 34 outliers final: 15 residues processed: 120 average time/residue: 0.5165 time to fit residues: 68.6812 Evaluate side-chains 114 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 170 GLU Chi-restraints excluded: chain A residue 406 ASN 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 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 913 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 406 ASN 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 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 874 LEU 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: 7.9990 chunk 126 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A 913 GLN B 692 ASN B 824 ASN B 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.209342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170402 restraints weight = 13721.899| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.65 r_work: 0.3570 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13618 Z= 0.119 Angle : 0.479 7.351 18148 Z= 0.250 Chirality : 0.040 0.286 1934 Planarity : 0.004 0.061 2166 Dihedral : 10.005 71.193 2444 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.52 % Allowed : 19.81 % Favored : 77.67 % 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 aren not related in a simple way. whole: 0.89 (0.21), residues: 1490 helix: 1.67 (0.17), residues: 868 sheet: 1.26 (0.67), residues: 56 loop : -1.23 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 321 TYR 0.014 0.001 TYR A 68 PHE 0.013 0.001 PHE B 415 TRP 0.007 0.001 TRP A 305 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00240 (13602) covalent geometry : angle 0.46823 (18108) SS BOND : bond 0.00177 ( 8) SS BOND : angle 0.77520 ( 16) hydrogen bonds : bond 0.06032 ( 587) hydrogen bonds : angle 3.70004 ( 1731) link_NAG-ASN : bond 0.00558 ( 8) link_NAG-ASN : angle 2.72288 ( 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 125 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: A 588 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7472 (tttp) REVERT: A 647 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8028 (tt) REVERT: A 657 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6901 (mm) REVERT: A 797 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: A 874 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 895 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: B 362 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: B 588 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7467 (tttp) REVERT: B 647 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8024 (tt) REVERT: B 657 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6821 (mm) REVERT: B 874 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 895 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6567 (tm-30) outliers start: 34 outliers final: 13 residues processed: 117 average time/residue: 0.5355 time to fit residues: 69.1950 Evaluate side-chains 115 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU 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 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 811 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 362 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 750 VAL Chi-restraints excluded: chain B residue 794 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 69 HIS B 692 ASN B 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.209367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172317 restraints weight = 13702.123| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.57 r_work: 0.3595 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1133 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= 0.115 Angle : 0.474 7.549 18148 Z= 0.247 Chirality : 0.039 0.284 1934 Planarity : 0.004 0.058 2166 Dihedral : 9.518 61.097 2444 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.78 % Allowed : 18.92 % Favored : 77.30 % 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 aren not related in a simple way. whole: 0.96 (0.21), residues: 1490 helix: 1.76 (0.17), residues: 866 sheet: 1.23 (0.66), residues: 56 loop : -1.25 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 321 TYR 0.011 0.001 TYR B 68 PHE 0.013 0.001 PHE B 415 TRP 0.007 0.001 TRP B 389 HIS 0.004 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00233 (13602) covalent geometry : angle 0.46309 (18108) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.76952 ( 16) hydrogen bonds : bond 0.05918 ( 587) hydrogen bonds : angle 3.65731 ( 1731) link_NAG-ASN : bond 0.00547 ( 8) link_NAG-ASN : angle 2.72735 ( 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 148 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 0.515 Fit side-chains REVERT: A 362 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: A 391 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7237 (ttm) REVERT: A 588 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7481 (tttp) REVERT: A 657 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6846 (mm) REVERT: A 874 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 895 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: B 362 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: B 391 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7193 (ttm) REVERT: B 588 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7449 (tttp) REVERT: B 657 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6809 (mm) REVERT: B 797 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: B 874 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8372 (mp) REVERT: B 895 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6692 (tm-30) outliers start: 51 outliers final: 23 residues processed: 135 average time/residue: 0.5029 time to fit residues: 75.3812 Evaluate side-chains 126 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 586 LEU Chi-restraints excluded: chain A residue 588 LYS 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 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 874 LEU 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 362 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 406 ASN 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 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 797 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4328 r_free = 0.4328 target = 0.208691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170136 restraints weight = 13655.125| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.62 r_work: 0.3572 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1233 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= 0.124 Angle : 0.500 7.937 18148 Z= 0.258 Chirality : 0.040 0.290 1934 Planarity : 0.004 0.057 2166 Dihedral : 9.417 61.714 2444 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.86 % Allowed : 18.99 % Favored : 77.15 % 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 aren not related in a simple way. whole: 0.93 (0.21), residues: 1490 helix: 1.74 (0.17), residues: 866 sheet: 1.28 (0.66), residues: 56 loop : -1.26 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 321 TYR 0.011 0.001 TYR B 68 PHE 0.013 0.001 PHE B 415 TRP 0.007 0.001 TRP B 389 HIS 0.005 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00257 (13602) covalent geometry : angle 0.48927 (18108) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.80359 ( 16) hydrogen bonds : bond 0.06190 ( 587) hydrogen bonds : angle 3.64942 ( 1731) link_NAG-ASN : bond 0.00541 ( 8) link_NAG-ASN : angle 2.77793 ( 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 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: A 362 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: A 391 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7209 (ttm) REVERT: A 588 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7477 (tttp) REVERT: A 657 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6804 (mm) REVERT: A 702 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: A 797 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: A 874 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 895 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: B 362 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: B 391 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7224 (ttm) REVERT: B 588 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7478 (tttp) REVERT: B 657 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6803 (mm) REVERT: B 702 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: B 797 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: B 874 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 895 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6680 (tm-30) outliers start: 52 outliers final: 29 residues processed: 132 average time/residue: 0.5346 time to fit residues: 77.6747 Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR 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 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 874 LEU 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 248 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 391 MET 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 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 797 GLN 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=2.50 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4302 r_free = 0.4302 target = 0.206070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167045 restraints weight = 13561.746| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.61 r_work: 0.3534 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13618 Z= 0.158 Angle : 0.555 8.360 18148 Z= 0.289 Chirality : 0.042 0.321 1934 Planarity : 0.004 0.056 2166 Dihedral : 10.172 65.719 2444 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.71 % Allowed : 19.21 % 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 aren not related in a simple way. whole: 0.77 (0.21), residues: 1490 helix: 1.63 (0.17), residues: 854 sheet: 1.39 (0.67), residues: 56 loop : -1.34 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 321 TYR 0.011 0.001 TYR A 838 PHE 0.016 0.002 PHE A 582 TRP 0.008 0.001 TRP B 389 HIS 0.006 0.001 HIS B 807 Details of bonding type rmsd covalent geometry : bond 0.00349 (13602) covalent geometry : angle 0.54368 (18108) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.04745 ( 16) hydrogen bonds : bond 0.07652 ( 587) hydrogen bonds : angle 3.74611 ( 1731) link_NAG-ASN : bond 0.00473 ( 8) link_NAG-ASN : angle 3.03375 ( 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 146 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: A 391 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7379 (ttm) REVERT: A 588 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7393 (tttp) REVERT: A 657 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6907 (mm) REVERT: A 702 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: A 874 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8474 (mp) REVERT: A 895 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: B 362 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: B 391 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7328 (ttm) REVERT: B 588 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7402 (tttp) REVERT: B 657 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6923 (mm) REVERT: B 702 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 797 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: B 874 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 895 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6677 (tm-30) outliers start: 50 outliers final: 27 residues processed: 134 average time/residue: 0.5358 time to fit residues: 78.9591 Evaluate side-chains 136 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 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 874 LEU 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 153 VAL 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 491 PHE 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 797 GLN 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: 0.9980 chunk 66 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4322 r_free = 0.4322 target = 0.208188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.169312 restraints weight = 13575.161| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.56 r_work: 0.3565 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1396 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= 0.122 Angle : 0.491 7.577 18148 Z= 0.256 Chirality : 0.040 0.297 1934 Planarity : 0.004 0.055 2166 Dihedral : 9.374 64.758 2444 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.26 % Allowed : 19.81 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1490 helix: 1.67 (0.17), residues: 868 sheet: 1.37 (0.67), residues: 56 loop : -1.29 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 321 TYR 0.009 0.001 TYR A 838 PHE 0.014 0.001 PHE A 415 TRP 0.007 0.001 TRP A 305 HIS 0.005 0.001 HIS B 807 Details of bonding type rmsd covalent geometry : bond 0.00248 (13602) covalent geometry : angle 0.47954 (18108) SS BOND : bond 0.00204 ( 8) SS BOND : angle 0.80464 ( 16) hydrogen bonds : bond 0.06198 ( 587) hydrogen bonds : angle 3.64973 ( 1731) link_NAG-ASN : bond 0.00573 ( 8) link_NAG-ASN : angle 2.87166 ( 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 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: A 362 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: A 391 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7308 (ttm) REVERT: A 588 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7527 (tttp) REVERT: A 657 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6772 (mm) REVERT: A 702 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 874 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 895 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: B 64 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: B 69 HIS cc_start: 0.7989 (m-70) cc_final: 0.7781 (OUTLIER) REVERT: B 362 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: B 391 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7261 (ttm) REVERT: B 588 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7531 (tttp) REVERT: B 657 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6818 (mm) REVERT: B 702 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 797 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: B 874 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 895 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6665 (tm-30) outliers start: 44 outliers final: 21 residues processed: 128 average time/residue: 0.5623 time to fit residues: 79.1830 Evaluate side-chains 131 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR 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 874 LEU 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 153 VAL 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 797 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4324 r_free = 0.4324 target = 0.208383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171314 restraints weight = 13716.876| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.54 r_work: 0.3582 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13618 Z= 0.120 Angle : 0.498 10.538 18148 Z= 0.255 Chirality : 0.040 0.288 1934 Planarity : 0.004 0.054 2166 Dihedral : 9.023 64.932 2444 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.97 % Allowed : 20.18 % 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 aren not related in a simple way. whole: 0.93 (0.21), residues: 1490 helix: 1.75 (0.17), residues: 868 sheet: 0.80 (0.67), residues: 60 loop : -1.26 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.009 0.001 TYR A 838 PHE 0.012 0.001 PHE A 415 TRP 0.008 0.001 TRP A 305 HIS 0.005 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00244 (13602) covalent geometry : angle 0.48789 (18108) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.80006 ( 16) hydrogen bonds : bond 0.06113 ( 587) hydrogen bonds : angle 3.61085 ( 1731) link_NAG-ASN : bond 0.00536 ( 8) link_NAG-ASN : angle 2.79922 ( 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 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: A 362 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: A 391 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7308 (ttm) REVERT: A 588 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7487 (tttp) REVERT: A 657 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6826 (mm) REVERT: A 702 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 874 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8397 (mp) REVERT: A 895 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: A 904 MET cc_start: 0.3727 (ttt) cc_final: 0.3210 (ppp) REVERT: B 64 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: B 362 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: B 391 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7216 (ttm) REVERT: B 588 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7452 (tttp) REVERT: B 657 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6780 (mm) REVERT: B 702 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: B 874 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8374 (mp) REVERT: B 895 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6729 (tm-30) outliers start: 40 outliers final: 20 residues processed: 125 average time/residue: 0.5242 time to fit residues: 72.2910 Evaluate side-chains 128 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR 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 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 874 LEU 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 153 VAL 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 895 GLN Chi-restraints excluded: chain B residue 912 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4349 r_free = 0.4349 target = 0.210904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172506 restraints weight = 13751.954| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.57 r_work: 0.3609 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1483 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= 0.098 Angle : 0.455 9.094 18148 Z= 0.232 Chirality : 0.039 0.267 1934 Planarity : 0.004 0.054 2166 Dihedral : 8.296 63.198 2444 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 21.14 % Favored : 76.78 % 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 aren not related in a simple way. whole: 1.15 (0.21), residues: 1490 helix: 1.93 (0.17), residues: 870 sheet: 0.68 (0.66), residues: 60 loop : -1.16 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 321 TYR 0.007 0.001 TYR B 68 PHE 0.012 0.001 PHE B 589 TRP 0.007 0.001 TRP A 427 HIS 0.003 0.001 HIS B 807 Details of bonding type rmsd covalent geometry : bond 0.00188 (13602) covalent geometry : angle 0.44534 (18108) SS BOND : bond 0.00152 ( 8) SS BOND : angle 0.65410 ( 16) hydrogen bonds : bond 0.04820 ( 587) hydrogen bonds : angle 3.51481 ( 1731) link_NAG-ASN : bond 0.00616 ( 8) link_NAG-ASN : angle 2.60217 ( 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 124 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: A 266 MET cc_start: 0.4878 (mtm) cc_final: 0.4642 (mtt) REVERT: A 362 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: A 588 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7494 (tttp) REVERT: A 657 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6773 (mm) REVERT: A 702 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: A 895 GLN cc_start: 0.7023 (tp-100) cc_final: 0.6711 (tm-30) REVERT: B 64 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: B 362 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: B 588 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7482 (tttp) REVERT: B 657 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6744 (mm) REVERT: B 702 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: B 874 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 895 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: B 904 MET cc_start: 0.3791 (ttt) cc_final: 0.3234 (ppp) outliers start: 28 outliers final: 12 residues processed: 121 average time/residue: 0.5071 time to fit residues: 67.9884 Evaluate side-chains 116 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 564 LEU 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 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 564 LEU 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 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4331 r_free = 0.4331 target = 0.209083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.167748 restraints weight = 13702.014| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.71 r_work: 0.3545 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1521 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= 0.115 Angle : 0.486 9.417 18148 Z= 0.249 Chirality : 0.040 0.284 1934 Planarity : 0.004 0.054 2166 Dihedral : 8.584 64.007 2444 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.30 % Allowed : 20.92 % Favored : 76.78 % 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 aren not related in a simple way. whole: 1.07 (0.21), residues: 1490 helix: 1.88 (0.17), residues: 868 sheet: 0.72 (0.66), residues: 60 loop : -1.22 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 321 TYR 0.009 0.001 TYR A 838 PHE 0.012 0.001 PHE B 415 TRP 0.008 0.001 TRP A 305 HIS 0.005 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00236 (13602) covalent geometry : angle 0.47635 (18108) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.78439 ( 16) hydrogen bonds : bond 0.05798 ( 587) hydrogen bonds : angle 3.53292 ( 1731) link_NAG-ASN : bond 0.00520 ( 8) link_NAG-ASN : angle 2.71032 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.94 seconds wall clock time: 61 minutes 8.14 seconds (3668.14 seconds total)