Starting phenix.real_space_refine on Sun Jan 19 04:58:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlr_38456/01_2025/8xlr_38456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlr_38456/01_2025/8xlr_38456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xlr_38456/01_2025/8xlr_38456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlr_38456/01_2025/8xlr_38456.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlr_38456/01_2025/8xlr_38456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlr_38456/01_2025/8xlr_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.38, per 1000 atoms: 0.48 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: 3.14 Conformation dependent library (CDL) restraints added in 1.4 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: 1.23 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: 3.94 Time building geometry restraints manager: 3.40 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: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.540 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.360 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.790 ------------------------------------------------------------------------------- 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 : 1.496 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: 1.1821 time to fit residues: 141.5797 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 : 1.670 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.205210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156696 restraints weight = 13404.661| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.96 r_work: 0.3470 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 1.405 Fit side-chains REVERT: A 647 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 657 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6763 (mm) REVERT: B 391 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7261 (ttm) REVERT: B 647 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7878 (tt) REVERT: B 657 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6740 (mm) REVERT: B 797 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: B 874 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8397 (mp) outliers start: 38 outliers final: 11 residues processed: 122 average time/residue: 1.1056 time to fit residues: 150.0339 Evaluate side-chains 111 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 111 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.205015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153048 restraints weight = 13579.393| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.96 r_work: 0.3335 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1023 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= 0.194 Angle : 0.508 6.925 18108 Z= 0.272 Chirality : 0.041 0.308 1934 Planarity : 0.005 0.068 2166 Dihedral : 10.805 79.200 2444 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.97 % Allowed : 19.81 % Favored : 77.23 % 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: 0.61 (0.21), residues: 1490 helix: 1.42 (0.17), residues: 866 sheet: 1.15 (0.67), residues: 56 loop : -1.29 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 389 HIS 0.006 0.001 HIS B 807 PHE 0.013 0.001 PHE B 415 TYR 0.016 0.001 TYR B 68 ARG 0.002 0.000 ARG B 321 *********************** 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 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.917 Fit side-chains REVERT: A 130 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6399 (tm-30) REVERT: A 391 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7084 (ttm) REVERT: A 647 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 657 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6180 (mm) REVERT: B 130 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6577 (tm-30) REVERT: B 391 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7414 (ttm) REVERT: B 647 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8023 (tt) REVERT: B 657 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6280 (mm) REVERT: B 874 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8146 (mp) outliers start: 40 outliers final: 22 residues processed: 120 average time/residue: 1.2189 time to fit residues: 162.5719 Evaluate side-chains 120 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 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 647 LEU Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- 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 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.199864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146947 restraints weight = 13442.766| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.90 r_work: 0.3258 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13602 Z= 0.332 Angle : 0.642 8.113 18108 Z= 0.342 Chirality : 0.046 0.376 1934 Planarity : 0.005 0.064 2166 Dihedral : 12.286 86.009 2444 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.01 % Allowed : 19.14 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.20), residues: 1490 helix: 1.32 (0.17), residues: 828 sheet: 1.31 (0.68), residues: 56 loop : -1.51 (0.21), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 389 HIS 0.012 0.002 HIS A 69 PHE 0.020 0.002 PHE A 710 TYR 0.013 0.002 TYR B 703 ARG 0.004 0.000 ARG A 321 *********************** 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 148 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 1.383 Fit side-chains REVERT: A 362 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: A 588 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6940 (tttp) REVERT: A 657 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6207 (mm) REVERT: A 913 GLN cc_start: 0.2652 (OUTLIER) cc_final: 0.2382 (mm-40) REVERT: B 130 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: B 362 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: B 588 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6946 (tttp) REVERT: B 657 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6221 (mm) REVERT: B 874 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8321 (mp) outliers start: 54 outliers final: 27 residues processed: 135 average time/residue: 1.1525 time to fit residues: 172.6430 Evaluate side-chains 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 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 794 MET Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 895 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 0.0050 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.205736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154752 restraints weight = 13629.269| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.93 r_work: 0.3344 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13602 Z= 0.148 Angle : 0.479 7.508 18108 Z= 0.254 Chirality : 0.040 0.314 1934 Planarity : 0.004 0.059 2166 Dihedral : 11.076 80.635 2444 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 19.51 % Favored : 77.23 % 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: 0.66 (0.21), residues: 1490 helix: 1.50 (0.17), residues: 866 sheet: 1.29 (0.67), residues: 56 loop : -1.36 (0.22), residues: 568 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 0.014 0.001 PHE B 415 TYR 0.010 0.001 TYR B 68 ARG 0.001 0.000 ARG B 910 *********************** 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 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6435 (tm-30) REVERT: A 362 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: A 588 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7002 (tttp) REVERT: A 657 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.6132 (mm) REVERT: A 702 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: A 797 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6829 (mm-40) REVERT: A 895 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.5806 (tm-30) REVERT: B 130 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: B 362 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: B 588 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7021 (tttp) REVERT: B 657 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6197 (mm) REVERT: B 702 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: B 874 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8066 (mp) REVERT: B 895 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5847 (tm-30) outliers start: 44 outliers final: 18 residues processed: 130 average time/residue: 1.1833 time to fit residues: 170.3293 Evaluate side-chains 122 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU 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 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 362 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 73 optimal weight: 0.0020 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.209303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169536 restraints weight = 13865.988| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.88 r_work: 0.3538 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1340 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= 0.138 Angle : 0.459 6.753 18108 Z= 0.242 Chirality : 0.039 0.288 1934 Planarity : 0.004 0.057 2166 Dihedral : 10.023 69.142 2444 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.56 % Allowed : 19.58 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.21), residues: 1490 helix: 1.75 (0.17), residues: 870 sheet: 0.74 (0.68), residues: 60 loop : -1.27 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.004 0.001 HIS B 807 PHE 0.012 0.001 PHE B 415 TYR 0.009 0.001 TYR B 68 ARG 0.003 0.000 ARG B 910 *********************** 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 146 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: A 130 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 362 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: A 391 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7162 (ttm) REVERT: A 588 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7465 (tttp) REVERT: A 657 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6782 (mm) REVERT: A 702 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: A 797 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6728 (mm-40) REVERT: A 874 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 895 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: B 64 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: B 69 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7853 (t-170) REVERT: B 362 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: B 588 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7470 (tttp) REVERT: B 657 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6788 (mm) REVERT: B 702 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: B 874 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 895 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6616 (tm-30) outliers start: 48 outliers final: 13 residues processed: 138 average time/residue: 1.1962 time to fit residues: 183.3018 Evaluate side-chains 120 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 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 874 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.207152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146460 restraints weight = 13714.974| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.03 r_work: 0.3375 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1394 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= 0.137 Angle : 0.462 8.364 18108 Z= 0.241 Chirality : 0.039 0.289 1934 Planarity : 0.004 0.055 2166 Dihedral : 9.417 67.140 2444 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.82 % Allowed : 20.47 % 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: 1.00 (0.21), residues: 1490 helix: 1.82 (0.17), residues: 870 sheet: 0.72 (0.67), residues: 60 loop : -1.24 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 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 B 842 *********************** 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 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 130 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: A 362 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: A 391 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7150 (ttm) REVERT: A 588 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7220 (tttp) REVERT: A 657 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6224 (mm) REVERT: A 702 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: A 797 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6692 (mm-40) REVERT: A 874 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 895 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5980 (tm-30) REVERT: B 64 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: B 69 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7896 (m-70) REVERT: B 362 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: B 588 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7215 (tttp) REVERT: B 657 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6155 (mm) REVERT: B 702 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 874 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 895 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6038 (tm-30) outliers start: 38 outliers final: 13 residues processed: 124 average time/residue: 1.2545 time to fit residues: 171.4999 Evaluate side-chains 120 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 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 874 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 0.5980 chunk 148 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148067 restraints weight = 13675.617| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.02 r_work: 0.3391 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1459 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= 0.125 Angle : 0.448 7.506 18108 Z= 0.233 Chirality : 0.039 0.279 1934 Planarity : 0.004 0.054 2166 Dihedral : 8.769 68.831 2444 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.97 % Allowed : 20.33 % 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: 1.13 (0.21), residues: 1490 helix: 1.92 (0.18), residues: 872 sheet: 0.67 (0.66), residues: 60 loop : -1.20 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.003 0.000 HIS B 807 PHE 0.011 0.001 PHE B 589 TYR 0.008 0.001 TYR B 68 ARG 0.001 0.000 ARG B 842 *********************** 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: 40 poor density : 95 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: A 130 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: A 362 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: A 588 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7199 (tttp) REVERT: A 657 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6169 (mm) REVERT: A 702 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: A 874 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 895 GLN cc_start: 0.6673 (tp-100) cc_final: 0.5964 (tm-30) REVERT: B 64 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: B 130 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6579 (tm-30) REVERT: B 362 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: B 588 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7209 (tttp) REVERT: B 657 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6173 (mm) REVERT: B 702 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: B 874 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (mp) outliers start: 40 outliers final: 15 residues processed: 128 average time/residue: 1.1761 time to fit residues: 166.2925 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 : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 362 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 113 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.209227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170686 restraints weight = 13625.619| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.53 r_work: 0.3589 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13602 Z= 0.145 Angle : 0.465 7.569 18108 Z= 0.244 Chirality : 0.040 0.287 1934 Planarity : 0.004 0.053 2166 Dihedral : 8.802 67.560 2444 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.60 % Allowed : 20.62 % 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: 1.08 (0.21), residues: 1490 helix: 1.88 (0.17), residues: 870 sheet: 0.70 (0.66), residues: 60 loop : -1.21 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 B 321 *********************** 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 128 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: A 362 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 588 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7534 (tttp) REVERT: A 657 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6765 (mm) REVERT: A 702 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 874 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 895 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: B 64 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 362 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: B 588 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7525 (tttp) REVERT: B 657 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6740 (mm) REVERT: B 702 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 874 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 895 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6782 (tm-30) outliers start: 35 outliers final: 18 residues processed: 123 average time/residue: 1.2185 time to fit residues: 165.6954 Evaluate side-chains 125 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 362 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 660 MET Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.204742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168824 restraints weight = 13563.099| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.64 r_work: 0.3500 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1705 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= 0.273 Angle : 0.595 10.551 18108 Z= 0.312 Chirality : 0.044 0.342 1934 Planarity : 0.005 0.054 2166 Dihedral : 10.404 68.026 2444 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 0.70 (0.21), residues: 1490 helix: 1.58 (0.17), residues: 856 sheet: 0.80 (0.68), residues: 60 loop : -1.33 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 389 HIS 0.013 0.002 HIS B 69 PHE 0.017 0.002 PHE B 582 TYR 0.013 0.002 TYR B 838 ARG 0.003 0.000 ARG B 321 ********************** 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 132 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: A 588 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7464 (tttp) REVERT: A 657 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6885 (mm) REVERT: A 702 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: A 874 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8528 (mp) REVERT: A 895 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: B 362 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: B 588 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7432 (tttp) REVERT: B 657 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6873 (mm) REVERT: B 874 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8517 (mp) REVERT: B 895 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6763 (tm-30) outliers start: 38 outliers final: 21 residues processed: 126 average time/residue: 1.2004 time to fit residues: 166.9665 Evaluate side-chains 126 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 362 GLU 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 660 MET Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 362 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 0.0020 chunk 146 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148131 restraints weight = 13705.646| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.03 r_work: 0.3377 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1564 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= 0.128 Angle : 0.457 9.261 18108 Z= 0.238 Chirality : 0.039 0.286 1934 Planarity : 0.004 0.053 2166 Dihedral : 8.865 64.672 2444 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.08 % Allowed : 21.14 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.17), residues: 872 sheet: 0.68 (0.66), residues: 60 loop : -1.22 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 389 HIS 0.005 0.001 HIS B 69 PHE 0.012 0.001 PHE B 589 TYR 0.009 0.001 TYR B 68 ARG 0.001 0.000 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7403.77 seconds wall clock time: 134 minutes 21.96 seconds (8061.96 seconds total)