Starting phenix.real_space_refine on Sun Aug 24 05:54:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwe_35055/08_2025/8hwe_35055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwe_35055/08_2025/8hwe_35055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hwe_35055/08_2025/8hwe_35055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwe_35055/08_2025/8hwe_35055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwe_35055/08_2025/8hwe_35055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwe_35055/08_2025/8hwe_35055.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.117 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 91 5.16 5 C 10938 2.51 5 N 2930 2.21 5 O 3266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17247 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3054 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3054 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2230 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 5 Chain: "A" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2666 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 4 Chain: "E" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3002 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 1 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3054 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.93, per 1000 atoms: 0.23 Number of scatterers: 17247 At special positions: 0 Unit cell: (106.653, 127.121, 130.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 17 15.00 Mg 5 11.99 O 3266 8.00 N 2930 7.00 C 10938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 796.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 27 sheets defined 43.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.691A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.522A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.783A pdb=" N LEU D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 384 removed outlier: 4.861A pdb=" N SER D 381 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU D 382 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 384 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.828A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 removed outlier: 3.501A pdb=" N PHE D 451 " --> pdb=" O ASP D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.504A pdb=" N THR D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 532 removed outlier: 3.909A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.715A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.599A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.831A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 635 Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.601A pdb=" N GLU D 640 " --> pdb=" O ARG D 636 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 636 through 641' Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.895A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.650A pdb=" N LYS D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 679 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 692 removed outlier: 3.757A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.722A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 4.029A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 4.647A pdb=" N SER C 381 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU C 382 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 384 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.673A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.773A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 451 " --> pdb=" O ASP C 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 451' Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.512A pdb=" N ARG C 479 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 541 through 547 removed outlier: 3.855A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 578 removed outlier: 3.790A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.730A pdb=" N ARG C 619 " --> pdb=" O ASN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.909A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.237A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.809A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 679 " --> pdb=" O TRP C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 692 removed outlier: 3.625A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 693 through 701 removed outlier: 4.275A pdb=" N LYS C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.891A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.536A pdb=" N LEU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 removed outlier: 3.792A pdb=" N LEU F 375 " --> pdb=" O ARG F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 385 through 388 Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.505A pdb=" N GLU F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.502A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE F 451 " --> pdb=" O ASP F 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 447 through 451' Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.841A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 522 through 524 No H-bonds generated for 'chain 'F' and resid 522 through 524' Processing helix chain 'F' and resid 573 through 577 Processing helix chain 'F' and resid 615 through 619 removed outlier: 3.730A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 615 through 619' Processing helix chain 'F' and resid 665 through 680 removed outlier: 3.746A pdb=" N LYS F 678 " --> pdb=" O LYS F 674 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR F 679 " --> pdb=" O TRP F 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.809A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.885A pdb=" N LEU A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.869A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.524A pdb=" N SER A 381 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 384 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.676A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.690A pdb=" N LYS A 450 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.633A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 635 Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.551A pdb=" N GLU A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 641' Processing helix chain 'A' and resid 656 through 661 removed outlier: 4.039A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 661' Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.700A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 removed outlier: 3.709A pdb=" N LEU E 375 " --> pdb=" O ARG E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 387 No H-bonds generated for 'chain 'E' and resid 385 through 387' Processing helix chain 'E' and resid 388 through 398 removed outlier: 3.882A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.710A pdb=" N LYS E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.852A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 476 through 489 removed outlier: 3.775A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 541 through 547 Processing helix chain 'E' and resid 570 through 578 Processing helix chain 'E' and resid 614 through 619 removed outlier: 3.712A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 636 Processing helix chain 'E' and resid 656 through 661 removed outlier: 3.969A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 661' Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.572A pdb=" N PHE E 668 " --> pdb=" O TYR E 664 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS E 678 " --> pdb=" O LYS E 674 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR E 679 " --> pdb=" O TRP E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 692 removed outlier: 3.798A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 692' Processing helix chain 'E' and resid 693 through 700 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.806A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.670A pdb=" N LEU B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.691A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 390 through 398 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.807A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.521A pdb=" N PHE B 451 " --> pdb=" O ASP B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.522A pdb=" N ARG B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 541 through 547 Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.804A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.865A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.667A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 Processing sheet with id=AA1, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'D' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'D' and resid 525 through 527 removed outlier: 6.613A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'D' and resid 629 through 631 removed outlier: 6.589A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AA8, first strand: chain 'C' and resid 525 through 527 removed outlier: 5.924A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 581 through 582 Processing sheet with id=AB1, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.167A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.582A pdb=" N ILE F 351 " --> pdb=" O SER F 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AB4, first strand: chain 'F' and resid 552 through 555 Processing sheet with id=AB5, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB6, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AB7, first strand: chain 'A' and resid 525 through 526 removed outlier: 5.991A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.376A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AC2, first strand: chain 'E' and resid 525 through 526 removed outlier: 7.277A pdb=" N THR E 499 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AC5, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.629A pdb=" N MET B 426 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 525 through 527 removed outlier: 6.430A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC9, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.049A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 553 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5469 1.34 - 1.46: 2861 1.46 - 1.58: 9104 1.58 - 1.70: 27 1.70 - 1.82: 133 Bond restraints: 17594 Sorted by residual: bond pdb=" N GLU A 361 " pdb=" CA GLU A 361 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.39e+00 bond pdb=" N GLU B 691 " pdb=" CA GLU B 691 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.43e+00 bond pdb=" N THR B 689 " pdb=" CA THR B 689 " ideal model delta sigma weight residual 1.464 1.488 -0.025 9.80e-03 1.04e+04 6.27e+00 bond pdb=" N GLU C 360 " pdb=" CA GLU C 360 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.37e-02 5.33e+03 5.63e+00 ... (remaining 17589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 23452 2.24 - 4.47: 288 4.47 - 6.71: 35 6.71 - 8.95: 5 8.95 - 11.18: 2 Bond angle restraints: 23782 Sorted by residual: angle pdb=" N ILE A 371 " pdb=" CA ILE A 371 " pdb=" C ILE A 371 " ideal model delta sigma weight residual 112.98 106.83 6.15 1.25e+00 6.40e-01 2.42e+01 angle pdb=" N ILE E 371 " pdb=" CA ILE E 371 " pdb=" C ILE E 371 " ideal model delta sigma weight residual 112.98 107.35 5.63 1.25e+00 6.40e-01 2.03e+01 angle pdb=" N ILE D 371 " pdb=" CA ILE D 371 " pdb=" C ILE D 371 " ideal model delta sigma weight residual 112.98 107.67 5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" CA PRO E 540 " pdb=" N PRO E 540 " pdb=" CD PRO E 540 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" N GLU A 360 " pdb=" CA GLU A 360 " pdb=" C GLU A 360 " ideal model delta sigma weight residual 114.16 108.17 5.99 1.48e+00 4.57e-01 1.64e+01 ... (remaining 23777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9093 17.98 - 35.96: 1341 35.96 - 53.94: 308 53.94 - 71.91: 61 71.91 - 89.89: 25 Dihedral angle restraints: 10828 sinusoidal: 4630 harmonic: 6198 Sorted by residual: dihedral pdb=" CA SER B 359 " pdb=" C SER B 359 " pdb=" N GLU B 360 " pdb=" CA GLU B 360 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA E 598 " pdb=" C ALA E 598 " pdb=" N THR E 599 " pdb=" CA THR E 599 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ALA B 598 " pdb=" C ALA B 598 " pdb=" N THR B 599 " pdb=" CA THR B 599 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1853 0.039 - 0.079: 596 0.079 - 0.118: 186 0.118 - 0.158: 17 0.158 - 0.197: 2 Chirality restraints: 2654 Sorted by residual: chirality pdb=" CB THR A 689 " pdb=" CA THR A 689 " pdb=" OG1 THR A 689 " pdb=" CG2 THR A 689 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB THR C 533 " pdb=" CA THR C 533 " pdb=" OG1 THR C 533 " pdb=" CG2 THR C 533 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE A 602 " pdb=" N ILE A 602 " pdb=" C ILE A 602 " pdb=" CB ILE A 602 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 2651 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 361 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO D 362 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 675 " 0.024 2.00e-02 2.50e+03 1.92e-02 9.17e+00 pdb=" CG TRP A 675 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 675 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 675 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 675 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 675 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 675 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 675 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 675 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 675 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 524 " 0.001 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE A 524 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 524 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE A 524 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 524 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE A 524 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 524 " 0.001 2.00e-02 2.50e+03 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 152 2.54 - 3.13: 12957 3.13 - 3.72: 26444 3.72 - 4.31: 36806 4.31 - 4.90: 62425 Nonbonded interactions: 138784 Sorted by model distance: nonbonded pdb=" O2B ATP D1001 " pdb="MG MG D1002 " model vdw 1.956 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 1.992 2.170 nonbonded pdb=" O2B ATP B1001 " pdb="MG MG B1002 " model vdw 2.029 2.170 nonbonded pdb=" OG SER C 510 " pdb="MG MG C1002 " model vdw 2.046 2.170 nonbonded pdb=" OG SER E 510 " pdb="MG MG E1002 " model vdw 2.064 2.170 ... (remaining 138779 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' selection = (chain 'B' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) selection = (chain 'C' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) selection = (chain 'D' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) selection = (chain 'E' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.930 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.003 0.104 17594 Z= 0.142 Angle : 0.610 11.182 23782 Z= 0.326 Chirality : 0.042 0.197 2654 Planarity : 0.004 0.110 3003 Dihedral : 17.841 89.894 6800 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.62 % Allowed : 27.39 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.19), residues: 2080 helix: 0.08 (0.20), residues: 738 sheet: -1.36 (0.28), residues: 356 loop : -1.70 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.027 0.001 TYR F 670 PHE 0.036 0.001 PHE A 524 TRP 0.052 0.001 TRP A 675 HIS 0.011 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00301 (17594) covalent geometry : angle 0.60991 (23782) hydrogen bonds : bond 0.19164 ( 553) hydrogen bonds : angle 7.58895 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: F 554 PHE cc_start: 0.6005 (p90) cc_final: 0.5775 (p90) outliers start: 12 outliers final: 3 residues processed: 250 average time/residue: 0.1234 time to fit residues: 47.2209 Evaluate side-chains 239 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain B residue 346 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 328 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.199182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157785 restraints weight = 20815.776| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.27 r_work: 0.3528 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17594 Z= 0.227 Angle : 0.646 8.186 23782 Z= 0.326 Chirality : 0.046 0.222 2654 Planarity : 0.005 0.081 3003 Dihedral : 9.640 86.159 2469 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.94 % Allowed : 23.49 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.18), residues: 2080 helix: -0.28 (0.19), residues: 784 sheet: -1.44 (0.29), residues: 352 loop : -1.84 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 570 TYR 0.021 0.002 TYR D 482 PHE 0.024 0.002 PHE A 524 TRP 0.039 0.002 TRP A 675 HIS 0.009 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00556 (17594) covalent geometry : angle 0.64631 (23782) hydrogen bonds : bond 0.04438 ( 553) hydrogen bonds : angle 5.73098 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 236 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8051 (t70) REVERT: C 411 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7737 (p0) REVERT: C 501 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: F 523 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6951 (pp) REVERT: F 554 PHE cc_start: 0.5754 (p90) cc_final: 0.5270 (p90) REVERT: F 678 LYS cc_start: 0.7802 (mttt) cc_final: 0.7458 (mmtm) REVERT: A 474 GLU cc_start: 0.6888 (tp30) cc_final: 0.6584 (tp30) REVERT: A 483 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5849 (tt0) REVERT: A 675 TRP cc_start: 0.8024 (m-10) cc_final: 0.7760 (m-10) REVERT: E 576 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8297 (mttt) outliers start: 95 outliers final: 52 residues processed: 312 average time/residue: 0.1235 time to fit residues: 59.1250 Evaluate side-chains 281 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 501 PHE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 204 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.203839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164057 restraints weight = 20817.972| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.06 r_work: 0.3632 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17594 Z= 0.108 Angle : 0.540 9.248 23782 Z= 0.273 Chirality : 0.042 0.158 2654 Planarity : 0.004 0.072 3003 Dihedral : 8.638 85.855 2465 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.17 % Allowed : 24.90 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.18), residues: 2080 helix: 0.10 (0.19), residues: 781 sheet: -1.40 (0.29), residues: 352 loop : -1.67 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 570 TYR 0.016 0.001 TYR E 482 PHE 0.012 0.001 PHE A 554 TRP 0.019 0.001 TRP A 675 HIS 0.010 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00258 (17594) covalent geometry : angle 0.53962 (23782) hydrogen bonds : bond 0.03306 ( 553) hydrogen bonds : angle 5.10586 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 346 ASP cc_start: 0.8062 (m-30) cc_final: 0.7733 (m-30) REVERT: D 447 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8022 (t70) REVERT: D 533 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.8005 (t) REVERT: D 649 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8011 (mptt) REVERT: C 335 ASP cc_start: 0.7988 (t70) cc_final: 0.7211 (m-30) REVERT: C 411 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7744 (p0) REVERT: F 523 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6906 (pp) REVERT: F 554 PHE cc_start: 0.5758 (p90) cc_final: 0.5310 (p90) REVERT: F 678 LYS cc_start: 0.7750 (mttt) cc_final: 0.7388 (mmtm) REVERT: F 684 MET cc_start: 0.5865 (mtm) cc_final: 0.5663 (mtm) REVERT: A 335 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7396 (t0) REVERT: A 514 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7313 (mtm-85) REVERT: E 558 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6066 (mp) REVERT: E 576 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8222 (mttm) outliers start: 61 outliers final: 32 residues processed: 290 average time/residue: 0.1338 time to fit residues: 59.1866 Evaluate side-chains 264 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 120 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 176 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 150 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 overall best weight: 0.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 ASN A 352 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.204878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.165270 restraints weight = 20962.801| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.08 r_work: 0.3638 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17594 Z= 0.106 Angle : 0.528 9.846 23782 Z= 0.266 Chirality : 0.042 0.239 2654 Planarity : 0.004 0.061 3003 Dihedral : 8.219 85.860 2465 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.48 % Allowed : 24.38 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.19), residues: 2080 helix: 0.37 (0.19), residues: 776 sheet: -1.33 (0.29), residues: 364 loop : -1.64 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 570 TYR 0.024 0.001 TYR F 670 PHE 0.020 0.001 PHE A 554 TRP 0.005 0.001 TRP D 355 HIS 0.010 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00253 (17594) covalent geometry : angle 0.52769 (23782) hydrogen bonds : bond 0.03006 ( 553) hydrogen bonds : angle 4.84065 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8047 (t70) REVERT: D 649 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8015 (mptt) REVERT: C 334 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7835 (mm) REVERT: C 335 ASP cc_start: 0.8059 (t70) cc_final: 0.7286 (m-30) REVERT: C 411 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7583 (p0) REVERT: F 523 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6729 (pp) REVERT: F 678 LYS cc_start: 0.7813 (mttt) cc_final: 0.7356 (mmtm) REVERT: F 684 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5581 (mtm) REVERT: A 335 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7409 (t0) REVERT: A 514 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7317 (mtm-85) REVERT: E 372 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8121 (ttp80) REVERT: E 450 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7730 (mtpp) REVERT: E 514 ARG cc_start: 0.8140 (mtm180) cc_final: 0.7939 (mtm-85) REVERT: E 576 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8520 (mtpt) REVERT: B 411 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8348 (p0) outliers start: 67 outliers final: 39 residues processed: 294 average time/residue: 0.1128 time to fit residues: 50.7629 Evaluate side-chains 274 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.203769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162605 restraints weight = 20878.291| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.16 r_work: 0.3578 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17594 Z= 0.120 Angle : 0.545 12.865 23782 Z= 0.271 Chirality : 0.042 0.186 2654 Planarity : 0.004 0.057 3003 Dihedral : 8.171 87.722 2465 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.85 % Allowed : 24.38 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.19), residues: 2080 helix: 0.41 (0.19), residues: 776 sheet: -1.33 (0.29), residues: 364 loop : -1.60 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 570 TYR 0.016 0.001 TYR C 482 PHE 0.012 0.001 PHE F 501 TRP 0.006 0.001 TRP D 355 HIS 0.010 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00292 (17594) covalent geometry : angle 0.54485 (23782) hydrogen bonds : bond 0.03080 ( 553) hydrogen bonds : angle 4.81370 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 time to evaluate : 0.686 Fit side-chains REVERT: D 343 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7223 (pm20) REVERT: D 447 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8001 (t70) REVERT: D 649 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7963 (mptt) REVERT: C 334 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7810 (mm) REVERT: C 335 ASP cc_start: 0.7856 (t70) cc_final: 0.7136 (m-30) REVERT: C 411 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7488 (p0) REVERT: F 523 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6364 (pp) REVERT: F 678 LYS cc_start: 0.7923 (mttt) cc_final: 0.7451 (mmtm) REVERT: A 335 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7234 (t0) REVERT: A 514 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: E 372 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8053 (ttp80) REVERT: E 554 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: E 558 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6107 (mp) REVERT: E 576 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8177 (mttt) REVERT: E 593 ASN cc_start: 0.7211 (p0) cc_final: 0.6837 (p0) outliers start: 74 outliers final: 47 residues processed: 294 average time/residue: 0.1129 time to fit residues: 51.0656 Evaluate side-chains 275 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 37 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 176 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 0.0170 chunk 69 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.201681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162693 restraints weight = 20774.680| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.03 r_work: 0.3559 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17594 Z= 0.163 Angle : 0.581 12.251 23782 Z= 0.290 Chirality : 0.043 0.156 2654 Planarity : 0.004 0.059 3003 Dihedral : 8.222 89.362 2465 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.57 % Allowed : 23.70 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.19), residues: 2080 helix: 0.25 (0.19), residues: 779 sheet: -1.36 (0.29), residues: 365 loop : -1.61 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.019 0.001 TYR D 482 PHE 0.016 0.001 PHE F 524 TRP 0.009 0.002 TRP E 675 HIS 0.010 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00399 (17594) covalent geometry : angle 0.58108 (23782) hydrogen bonds : bond 0.03431 ( 553) hydrogen bonds : angle 4.89994 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 227 time to evaluate : 0.590 Fit side-chains REVERT: D 343 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7374 (pm20) REVERT: D 447 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8057 (t70) REVERT: D 649 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8079 (mptt) REVERT: C 411 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7577 (p0) REVERT: F 523 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6391 (pp) REVERT: F 678 LYS cc_start: 0.7815 (mttt) cc_final: 0.7337 (mmtm) REVERT: A 335 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7222 (t0) REVERT: A 372 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7487 (ttp80) REVERT: A 514 ARG cc_start: 0.7370 (mtm-85) cc_final: 0.7138 (mtm-85) REVERT: E 372 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8013 (ttp-110) REVERT: E 481 LEU cc_start: 0.8311 (tp) cc_final: 0.8014 (tp) REVERT: E 554 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: E 558 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5707 (mp) REVERT: E 576 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8288 (mttt) REVERT: E 593 ASN cc_start: 0.7317 (p0) cc_final: 0.6991 (p0) REVERT: B 365 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 411 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8307 (p0) REVERT: B 663 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7741 (mtp-110) outliers start: 88 outliers final: 56 residues processed: 302 average time/residue: 0.1123 time to fit residues: 51.8859 Evaluate side-chains 287 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.200805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161776 restraints weight = 20855.638| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.03 r_work: 0.3548 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17594 Z= 0.176 Angle : 0.600 11.900 23782 Z= 0.298 Chirality : 0.044 0.156 2654 Planarity : 0.004 0.061 3003 Dihedral : 8.282 89.218 2465 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.42 % Allowed : 23.80 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.18), residues: 2080 helix: 0.16 (0.19), residues: 778 sheet: -1.42 (0.29), residues: 365 loop : -1.62 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 387 TYR 0.019 0.001 TYR D 482 PHE 0.013 0.001 PHE D 444 TRP 0.009 0.002 TRP E 675 HIS 0.010 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00433 (17594) covalent geometry : angle 0.60014 (23782) hydrogen bonds : bond 0.03499 ( 553) hydrogen bonds : angle 4.93296 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 234 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: D 343 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7382 (pm20) REVERT: D 360 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: D 447 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8066 (t70) REVERT: D 533 THR cc_start: 0.8063 (t) cc_final: 0.7752 (t) REVERT: D 649 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8076 (mptt) REVERT: C 411 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7713 (p0) REVERT: F 432 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7028 (p0) REVERT: F 523 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6366 (pp) REVERT: F 678 LYS cc_start: 0.7557 (mttt) cc_final: 0.7164 (mmtm) REVERT: A 335 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7291 (t0) REVERT: A 372 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7271 (ttp80) REVERT: A 514 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.7131 (mtm-85) REVERT: E 481 LEU cc_start: 0.8307 (tp) cc_final: 0.8005 (tp) REVERT: E 554 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: E 576 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8321 (mttt) REVERT: E 593 ASN cc_start: 0.7383 (p0) cc_final: 0.7095 (p0) REVERT: B 365 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8045 (p) REVERT: B 537 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7262 (p0) REVERT: B 663 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7809 (mtp-110) outliers start: 85 outliers final: 58 residues processed: 303 average time/residue: 0.1156 time to fit residues: 53.6967 Evaluate side-chains 295 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 226 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 152 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.200569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159345 restraints weight = 20747.075| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.18 r_work: 0.3558 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17594 Z= 0.167 Angle : 0.601 15.939 23782 Z= 0.299 Chirality : 0.043 0.166 2654 Planarity : 0.004 0.061 3003 Dihedral : 8.264 89.244 2465 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.26 % Allowed : 24.38 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.18), residues: 2080 helix: 0.15 (0.19), residues: 772 sheet: -1.46 (0.29), residues: 365 loop : -1.65 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.018 0.001 TYR D 482 PHE 0.029 0.001 PHE A 554 TRP 0.009 0.001 TRP E 675 HIS 0.011 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00411 (17594) covalent geometry : angle 0.60137 (23782) hydrogen bonds : bond 0.03445 ( 553) hydrogen bonds : angle 4.90148 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 0.512 Fit side-chains REVERT: D 343 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7552 (pm20) REVERT: D 360 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: D 447 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8035 (t70) REVERT: D 533 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7959 (t) REVERT: D 649 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8102 (mptt) REVERT: C 411 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7895 (p0) REVERT: F 432 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7186 (p0) REVERT: F 523 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6505 (pp) REVERT: F 554 PHE cc_start: 0.5584 (p90) cc_final: 0.5104 (p90) REVERT: F 678 LYS cc_start: 0.7624 (mttt) cc_final: 0.7281 (mmtm) REVERT: A 335 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7534 (t0) REVERT: A 372 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7371 (ttp80) REVERT: A 514 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7321 (mtm-85) REVERT: E 481 LEU cc_start: 0.8464 (tp) cc_final: 0.8152 (tp) REVERT: E 554 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: E 576 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: E 593 ASN cc_start: 0.7458 (p0) cc_final: 0.7206 (p0) REVERT: B 365 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8086 (p) REVERT: B 663 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7938 (mtp-110) outliers start: 82 outliers final: 64 residues processed: 296 average time/residue: 0.1128 time to fit residues: 51.2513 Evaluate side-chains 300 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 225 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 0.0000 chunk 162 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.199484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159702 restraints weight = 20852.872| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.19 r_work: 0.3549 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17594 Z= 0.187 Angle : 0.625 15.238 23782 Z= 0.311 Chirality : 0.044 0.237 2654 Planarity : 0.004 0.063 3003 Dihedral : 8.333 89.070 2465 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.16 % Allowed : 24.69 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.18), residues: 2080 helix: 0.06 (0.19), residues: 774 sheet: -1.55 (0.27), residues: 395 loop : -1.61 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.020 0.001 TYR D 482 PHE 0.027 0.001 PHE A 554 TRP 0.009 0.002 TRP E 675 HIS 0.011 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00461 (17594) covalent geometry : angle 0.62461 (23782) hydrogen bonds : bond 0.03592 ( 553) hydrogen bonds : angle 4.95468 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: D 343 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7401 (pm20) REVERT: D 360 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: D 447 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8036 (t70) REVERT: D 533 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7801 (t) REVERT: D 649 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8094 (mptt) REVERT: C 411 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7789 (p0) REVERT: F 432 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.7056 (p0) REVERT: F 523 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6271 (pp) REVERT: F 554 PHE cc_start: 0.5646 (p90) cc_final: 0.5185 (p90) REVERT: F 678 LYS cc_start: 0.7620 (mttt) cc_final: 0.7284 (mmtm) REVERT: A 335 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7306 (t0) REVERT: A 372 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7169 (ttp80) REVERT: E 554 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: E 570 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7366 (mtp-110) REVERT: E 576 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8400 (mttt) REVERT: E 593 ASN cc_start: 0.7458 (p0) cc_final: 0.7213 (p0) REVERT: B 365 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 663 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7791 (mtp-110) outliers start: 80 outliers final: 61 residues processed: 296 average time/residue: 0.1162 time to fit residues: 52.6157 Evaluate side-chains 295 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 501 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 74 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.200655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159913 restraints weight = 20672.948| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.20 r_work: 0.3569 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17594 Z= 0.153 Angle : 0.602 15.192 23782 Z= 0.300 Chirality : 0.043 0.183 2654 Planarity : 0.004 0.063 3003 Dihedral : 8.226 89.274 2465 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.11 % Allowed : 24.79 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.18), residues: 2080 helix: 0.17 (0.19), residues: 773 sheet: -1.55 (0.27), residues: 395 loop : -1.61 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 514 TYR 0.025 0.001 TYR F 676 PHE 0.019 0.001 PHE A 554 TRP 0.008 0.001 TRP E 675 HIS 0.011 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00376 (17594) covalent geometry : angle 0.60244 (23782) hydrogen bonds : bond 0.03331 ( 553) hydrogen bonds : angle 4.84570 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 233 time to evaluate : 0.663 Fit side-chains REVERT: D 343 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7403 (pm20) REVERT: D 359 SER cc_start: 0.8008 (m) cc_final: 0.6980 (p) REVERT: D 360 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: D 447 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8036 (t70) REVERT: D 533 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7767 (t) REVERT: D 649 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8069 (mptt) REVERT: C 411 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7745 (p0) REVERT: C 649 LYS cc_start: 0.8868 (tppp) cc_final: 0.8416 (mttm) REVERT: F 432 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.7051 (p0) REVERT: F 523 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6323 (pp) REVERT: F 554 PHE cc_start: 0.5634 (p90) cc_final: 0.4960 (p90) REVERT: F 678 LYS cc_start: 0.7681 (mttt) cc_final: 0.7323 (mmtm) REVERT: A 335 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7267 (t0) REVERT: A 372 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7158 (ttp80) REVERT: E 554 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: E 570 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7375 (mtp-110) REVERT: E 576 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8301 (mttt) REVERT: E 593 ASN cc_start: 0.7449 (p0) cc_final: 0.7219 (p0) REVERT: B 334 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8402 (mm) REVERT: B 365 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8016 (p) REVERT: B 663 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7762 (mtp-110) outliers start: 79 outliers final: 62 residues processed: 296 average time/residue: 0.1261 time to fit residues: 56.9938 Evaluate side-chains 300 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 226 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 6 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.202384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162001 restraints weight = 20770.979| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.12 r_work: 0.3570 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17594 Z= 0.124 Angle : 0.580 14.945 23782 Z= 0.289 Chirality : 0.042 0.170 2654 Planarity : 0.004 0.064 3003 Dihedral : 8.063 89.582 2465 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.85 % Allowed : 25.36 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.19), residues: 2080 helix: 0.38 (0.19), residues: 767 sheet: -1.47 (0.28), residues: 390 loop : -1.59 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.023 0.001 TYR F 676 PHE 0.025 0.001 PHE F 524 TRP 0.007 0.001 TRP E 675 HIS 0.011 0.001 HIS E 629 Details of bonding type rmsd covalent geometry : bond 0.00301 (17594) covalent geometry : angle 0.57951 (23782) hydrogen bonds : bond 0.03034 ( 553) hydrogen bonds : angle 4.70522 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.90 seconds wall clock time: 61 minutes 18.19 seconds (3678.19 seconds total)