Starting phenix.real_space_refine on Mon Dec 30 14:21:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlr_38456/12_2024/8xlr_38456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlr_38456/12_2024/8xlr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xlr_38456/12_2024/8xlr_38456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlr_38456/12_2024/8xlr_38456.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlr_38456/12_2024/8xlr_38456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlr_38456/12_2024/8xlr_38456.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.40, per 1000 atoms: 0.63 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: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 3.96 Time building geometry restraints manager: 3.98 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: 4.960 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.760 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- 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 13602 Z= 0.328 Angle : 0.717 13.320 18108 Z= 0.432 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 563 HIS 0.003 0.001 HIS B 802 PHE 0.026 0.001 PHE B 857 TYR 0.042 0.001 TYR B 838 ARG 0.008 0.001 ARG B 842 *********************** 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 : 1.551 Fit side-chains REVERT: B 904 MET cc_start: 0.3700 (ttt) cc_final: 0.2952 (ptp) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 1.2356 time to fit residues: 148.3635 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 : 1.357 ------------------------------------------------------------------------------- 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 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13602 Z= 0.192 Angle : 0.510 6.476 18108 Z= 0.272 Chirality : 0.041 0.291 1934 Planarity : 0.005 0.076 2166 Dihedral : 10.804 75.410 2446 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.82 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1490 helix: 1.51 (0.17), residues: 842 sheet: 0.82 (0.67), residues: 56 loop : -1.27 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 389 HIS 0.006 0.001 HIS A 807 PHE 0.015 0.001 PHE B 710 TYR 0.014 0.001 TYR A 68 ARG 0.003 0.000 ARG B 842 *********************** 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 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 1.446 Fit side-chains REVERT: A 647 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 657 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6796 (mm) REVERT: A 874 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 391 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7422 (ttm) REVERT: B 647 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7880 (tt) REVERT: B 657 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6783 (mm) REVERT: B 797 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: B 874 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8232 (mp) outliers start: 38 outliers final: 11 residues processed: 122 average time/residue: 1.1551 time to fit residues: 156.9616 Evaluate side-chains 111 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.0470 overall best weight: 1.3484 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13602 Z= 0.224 Angle : 0.536 7.104 18108 Z= 0.287 Chirality : 0.042 0.323 1934 Planarity : 0.005 0.069 2166 Dihedral : 11.144 81.008 2444 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.49 % Allowed : 19.51 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1490 helix: 1.50 (0.17), residues: 840 sheet: 1.16 (0.67), residues: 56 loop : -1.35 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 389 HIS 0.007 0.001 HIS A 807 PHE 0.015 0.002 PHE B 710 TYR 0.013 0.001 TYR B 68 ARG 0.003 0.000 ARG B 842 *********************** 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 141 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 1.480 Fit side-chains REVERT: A 391 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7432 (ttm) REVERT: A 657 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6749 (mm) REVERT: A 874 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 391 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7635 (ttm) REVERT: B 657 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6835 (mm) REVERT: B 797 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: B 874 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8257 (mp) outliers start: 47 outliers final: 22 residues processed: 127 average time/residue: 1.3557 time to fit residues: 189.4179 Evaluate side-chains 121 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 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 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 69 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 248 THR 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 657 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13602 Z= 0.137 Angle : 0.469 7.273 18108 Z= 0.247 Chirality : 0.039 0.289 1934 Planarity : 0.004 0.060 2166 Dihedral : 10.311 77.267 2444 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.12 % Allowed : 19.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1490 helix: 1.65 (0.17), residues: 866 sheet: 1.31 (0.67), residues: 56 loop : -1.28 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.008 0.001 HIS A 69 PHE 0.013 0.001 PHE B 415 TYR 0.014 0.001 TYR A 68 ARG 0.001 0.000 ARG B 226 *********************** 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 136 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 1.429 Fit side-chains REVERT: A 64 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: A 588 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7121 (tttp) REVERT: A 657 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6794 (mm) REVERT: A 874 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 895 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: B 588 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7115 (tttp) REVERT: B 657 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6750 (mm) REVERT: B 874 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 895 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6525 (tm-30) outliers start: 42 outliers final: 21 residues processed: 129 average time/residue: 1.1004 time to fit residues: 158.5335 Evaluate side-chains 121 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE 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 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 0.0050 chunk 123 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 B 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13602 Z= 0.146 Angle : 0.466 7.144 18108 Z= 0.247 Chirality : 0.040 0.288 1934 Planarity : 0.004 0.058 2166 Dihedral : 9.714 67.065 2444 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.19 % Allowed : 20.10 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1490 helix: 1.75 (0.17), residues: 868 sheet: 1.23 (0.65), residues: 56 loop : -1.27 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.004 0.001 HIS A 807 PHE 0.012 0.001 PHE B 415 TYR 0.011 0.001 TYR B 68 ARG 0.001 0.000 ARG A 321 *********************** 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 140 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: A 391 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7385 (ttm) REVERT: A 588 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7098 (tttp) REVERT: A 657 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6756 (mm) REVERT: A 702 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: A 895 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: B 69 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7717 (t-170) REVERT: B 588 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7118 (tttp) REVERT: B 657 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6704 (mm) REVERT: B 702 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: B 874 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 895 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6610 (tm-30) outliers start: 43 outliers final: 23 residues processed: 131 average time/residue: 1.1298 time to fit residues: 164.7240 Evaluate side-chains 123 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 491 PHE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13602 Z= 0.275 Angle : 0.601 8.283 18108 Z= 0.317 Chirality : 0.044 0.346 1934 Planarity : 0.005 0.059 2166 Dihedral : 11.141 68.045 2444 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.08 % Allowed : 19.29 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1490 helix: 1.50 (0.17), residues: 842 sheet: 1.40 (0.68), residues: 56 loop : -1.45 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 389 HIS 0.008 0.001 HIS A 807 PHE 0.018 0.002 PHE B 710 TYR 0.012 0.002 TYR A 838 ARG 0.003 0.000 ARG B 321 *********************** 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 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 94 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7516 (ttm) REVERT: A 588 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.6999 (tttp) REVERT: A 657 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6691 (mm) REVERT: A 702 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: A 797 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6744 (mm-40) REVERT: A 895 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: B 391 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7380 (ttm) REVERT: B 588 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7007 (tttp) REVERT: B 657 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6830 (mm) REVERT: B 702 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: B 874 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8323 (mp) REVERT: B 895 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6629 (tm-30) outliers start: 55 outliers final: 28 residues processed: 135 average time/residue: 1.2167 time to fit residues: 182.0220 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 : 1.500 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain 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 153 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 66 optimal weight: 0.0570 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13602 Z= 0.143 Angle : 0.457 6.679 18108 Z= 0.242 Chirality : 0.039 0.289 1934 Planarity : 0.004 0.056 2166 Dihedral : 9.608 65.720 2444 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.04 % Allowed : 20.47 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1490 helix: 1.68 (0.17), residues: 868 sheet: 0.77 (0.68), residues: 60 loop : -1.26 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 389 HIS 0.004 0.001 HIS A 807 PHE 0.013 0.001 PHE B 415 TYR 0.009 0.001 TYR B 68 ARG 0.001 0.000 ARG A 609 *********************** 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 136 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: A 391 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7294 (ttm) REVERT: A 588 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7125 (tttp) REVERT: A 657 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6670 (mm) REVERT: A 702 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: A 797 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6603 (mm-40) REVERT: A 895 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: B 69 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7553 (m-70) REVERT: B 588 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7131 (tttp) REVERT: B 657 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6691 (mm) REVERT: B 702 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: B 874 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 895 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6655 (tm-30) outliers start: 41 outliers final: 17 residues processed: 129 average time/residue: 1.1763 time to fit residues: 168.1262 Evaluate side-chains 122 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 391 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 564 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 797 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 564 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 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.0050 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13602 Z= 0.143 Angle : 0.475 9.889 18108 Z= 0.247 Chirality : 0.039 0.289 1934 Planarity : 0.004 0.055 2166 Dihedral : 9.209 67.309 2444 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.12 % Allowed : 20.55 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1490 helix: 1.81 (0.17), residues: 868 sheet: 0.71 (0.67), residues: 60 loop : -1.24 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.004 0.001 HIS A 807 PHE 0.012 0.001 PHE B 415 TYR 0.009 0.001 TYR B 68 ARG 0.001 0.000 ARG A 321 *********************** 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 135 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 1.446 Fit side-chains REVERT: A 64 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: A 391 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7397 (ttm) REVERT: A 588 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7117 (tttp) REVERT: A 657 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6746 (mm) REVERT: A 702 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: A 797 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6516 (mm-40) REVERT: A 895 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 904 MET cc_start: 0.3359 (ttt) cc_final: 0.2885 (ppp) REVERT: B 64 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: B 588 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7110 (tttp) REVERT: B 657 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6687 (mm) REVERT: B 702 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: B 874 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 895 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: B 904 MET cc_start: 0.3248 (ttt) cc_final: 0.2885 (ppp) outliers start: 42 outliers final: 17 residues processed: 123 average time/residue: 1.2803 time to fit residues: 173.8636 Evaluate side-chains 122 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 564 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 797 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain 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 564 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 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13602 Z= 0.150 Angle : 0.481 8.882 18108 Z= 0.251 Chirality : 0.040 0.291 1934 Planarity : 0.004 0.053 2166 Dihedral : 9.053 66.230 2444 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.60 % Allowed : 20.99 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1490 helix: 1.77 (0.17), residues: 868 sheet: 0.67 (0.66), residues: 60 loop : -1.23 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.004 0.001 HIS A 807 PHE 0.012 0.001 PHE A 415 TYR 0.009 0.001 TYR B 838 ARG 0.001 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.549 Fit side-chains REVERT: A 64 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: A 391 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7434 (ttm) REVERT: A 588 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7112 (tttp) REVERT: A 657 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6750 (mm) REVERT: A 702 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: A 797 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6554 (mm-40) REVERT: A 895 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: B 64 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: B 391 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7276 (ttm) REVERT: B 588 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7118 (tttp) REVERT: B 657 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6676 (mm) REVERT: B 702 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: B 874 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8199 (mp) REVERT: B 895 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6701 (tm-30) outliers start: 35 outliers final: 19 residues processed: 120 average time/residue: 1.2722 time to fit residues: 169.2928 Evaluate side-chains 126 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain 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 391 MET Chi-restraints excluded: chain B residue 564 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 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0050 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 0.0070 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13602 Z= 0.116 Angle : 0.437 8.657 18108 Z= 0.225 Chirality : 0.039 0.267 1934 Planarity : 0.004 0.053 2166 Dihedral : 8.197 64.628 2444 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.08 % Allowed : 21.51 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1490 helix: 1.97 (0.18), residues: 870 sheet: 0.60 (0.65), residues: 60 loop : -1.15 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.003 0.000 HIS A 807 PHE 0.012 0.001 PHE B 589 TYR 0.007 0.001 TYR B 68 ARG 0.001 0.000 ARG A 686 ********************** 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 127 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.685 Fit side-chains REVERT: A 64 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: A 588 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7121 (tttp) REVERT: A 657 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6685 (mm) REVERT: A 702 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: A 895 GLN cc_start: 0.6969 (tp-100) cc_final: 0.6685 (tm-30) REVERT: B 64 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: B 391 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7207 (ttm) REVERT: B 588 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7132 (tttp) REVERT: B 657 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6669 (mm) REVERT: B 702 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: B 874 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8098 (mp) REVERT: B 895 GLN cc_start: 0.7026 (tp-100) cc_final: 0.6745 (tm-30) outliers start: 28 outliers final: 11 residues processed: 122 average time/residue: 1.2779 time to fit residues: 173.1628 Evaluate side-chains 116 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 491 PHE 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 811 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.0050 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.202675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151621 restraints weight = 13506.658| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.94 r_work: 0.3349 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13602 Z= 0.252 Angle : 0.570 9.117 18108 Z= 0.300 Chirality : 0.043 0.330 1934 Planarity : 0.005 0.053 2166 Dihedral : 9.968 66.554 2444 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.60 % Allowed : 20.85 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1490 helix: 1.66 (0.17), residues: 856 sheet: 0.75 (0.67), residues: 60 loop : -1.31 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 389 HIS 0.007 0.001 HIS A 807 PHE 0.016 0.002 PHE B 582 TYR 0.012 0.002 TYR A 838 ARG 0.003 0.000 ARG B 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.11 seconds wall clock time: 67 minutes 26.39 seconds (4046.39 seconds total)