Starting phenix.real_space_refine on Sun Jun 15 14:06:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwe_35055/06_2025/8hwe_35055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwe_35055/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwe_35055/06_2025/8hwe_35055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwe_35055/06_2025/8hwe_35055.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwe_35055/06_2025/8hwe_35055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwe_35055/06_2025/8hwe_35055.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.117 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.49, per 1000 atoms: 0.61 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: 4.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.97 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: 5.90 Time building geometry restraints manager: 5.29 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 41.480 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (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 TRP 0.052 0.001 TRP A 675 HIS 0.011 0.001 HIS E 629 PHE 0.036 0.001 PHE A 524 TYR 0.027 0.001 TYR F 670 ARG 0.004 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.19164 ( 553) hydrogen bonds : angle 7.58895 ( 1548) covalent geometry : bond 0.00301 (17594) covalent geometry : angle 0.60991 (23782) *********************** 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 : 2.226 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: 0.3005 time to fit residues: 114.1445 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 : 2.047 ------------------------------------------------------------------------------- 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 174 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 GLN F 328 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.204679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165452 restraints weight = 20734.448| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.02 r_work: 0.3625 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17594 Z= 0.119 Angle : 0.553 8.060 23782 Z= 0.281 Chirality : 0.042 0.227 2654 Planarity : 0.004 0.080 3003 Dihedral : 9.432 86.880 2469 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.96 % Allowed : 24.43 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2080 helix: 0.18 (0.19), residues: 769 sheet: -1.32 (0.29), residues: 352 loop : -1.75 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 675 HIS 0.009 0.001 HIS E 629 PHE 0.020 0.001 PHE A 524 TYR 0.014 0.001 TYR D 482 ARG 0.004 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 553) hydrogen bonds : angle 5.52545 ( 1548) covalent geometry : bond 0.00282 (17594) covalent geometry : angle 0.55297 (23782) *********************** 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 298 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 1.964 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7919 (t70) REVERT: D 533 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7888 (t) REVERT: D 649 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7900 (mppt) REVERT: C 335 ASP cc_start: 0.7854 (t70) cc_final: 0.7182 (m-30) REVERT: C 411 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7605 (p0) REVERT: F 499 THR cc_start: 0.5291 (OUTLIER) cc_final: 0.5072 (p) REVERT: F 554 PHE cc_start: 0.5364 (p90) cc_final: 0.4722 (p90) REVERT: F 678 LYS cc_start: 0.7922 (mttt) cc_final: 0.7583 (mmtm) REVERT: A 474 GLU cc_start: 0.6833 (tp30) cc_final: 0.6508 (tp30) REVERT: A 546 ASN cc_start: 0.7963 (t0) cc_final: 0.7738 (t0) REVERT: A 649 LYS cc_start: 0.8471 (tppt) cc_final: 0.7872 (tppp) REVERT: B 617 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7687 (mt) outliers start: 57 outliers final: 26 residues processed: 286 average time/residue: 0.2787 time to fit residues: 121.0916 Evaluate side-chains 261 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 371 ILE 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 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 411 ASP 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 F residue 404 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 VAL 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 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 380 SER Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 202 optimal weight: 0.2980 chunk 90 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.205166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165788 restraints weight = 20759.352| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.02 r_work: 0.3631 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1131 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= 0.107 Angle : 0.526 8.927 23782 Z= 0.265 Chirality : 0.042 0.216 2654 Planarity : 0.004 0.068 3003 Dihedral : 8.609 87.747 2467 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.53 % Allowed : 23.23 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 2080 helix: 0.33 (0.19), residues: 778 sheet: -1.30 (0.29), residues: 352 loop : -1.60 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 675 HIS 0.010 0.001 HIS E 629 PHE 0.014 0.001 PHE A 524 TYR 0.014 0.001 TYR F 670 ARG 0.003 0.000 ARG E 570 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 553) hydrogen bonds : angle 5.02117 ( 1548) covalent geometry : bond 0.00251 (17594) covalent geometry : angle 0.52644 (23782) *********************** 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 314 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 246 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 ASP cc_start: 0.7722 (m-30) cc_final: 0.7455 (m-30) REVERT: D 447 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.7982 (t70) REVERT: D 533 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7891 (t) REVERT: C 335 ASP cc_start: 0.7778 (t70) cc_final: 0.7149 (m-30) REVERT: C 411 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7421 (p0) REVERT: F 554 PHE cc_start: 0.5609 (p90) cc_final: 0.5112 (p90) REVERT: F 684 MET cc_start: 0.5724 (mtm) cc_final: 0.5483 (mtm) REVERT: A 546 ASN cc_start: 0.7985 (t0) cc_final: 0.7677 (t0) REVERT: E 558 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6116 (mp) REVERT: E 576 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8197 (mttm) REVERT: B 625 ARG cc_start: 0.7368 (mtm180) cc_final: 0.7103 (mtm-85) outliers start: 68 outliers final: 40 residues processed: 296 average time/residue: 0.2773 time to fit residues: 126.5297 Evaluate side-chains 280 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 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 683 ILE Chi-restraints excluded: chain C residue 324 ASN 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 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 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 511 THR 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 525 VAL 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 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 E residue 576 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 624 VAL 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 97 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS 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 = 0.4191 r_free = 0.4191 target = 0.196343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156336 restraints weight = 20824.259| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.31 r_work: 0.3474 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 17594 Z= 0.354 Angle : 0.758 9.340 23782 Z= 0.379 Chirality : 0.050 0.203 2654 Planarity : 0.005 0.065 3003 Dihedral : 9.363 89.554 2467 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.89 % Allowed : 23.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.18), residues: 2080 helix: -0.56 (0.18), residues: 788 sheet: -1.52 (0.28), residues: 380 loop : -1.92 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 350 HIS 0.009 0.002 HIS E 629 PHE 0.022 0.002 PHE D 444 TYR 0.027 0.002 TYR D 482 ARG 0.008 0.001 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 553) hydrogen bonds : angle 5.63962 ( 1548) covalent geometry : bond 0.00864 (17594) covalent geometry : angle 0.75818 (23782) *********************** 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 327 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 233 time to evaluate : 1.923 Fit side-chains REVERT: D 360 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7049 (pt0) REVERT: D 447 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8157 (t70) REVERT: D 533 THR cc_start: 0.8254 (t) cc_final: 0.7939 (t) REVERT: D 649 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8100 (mptt) REVERT: D 686 LEU cc_start: 0.8702 (mp) cc_final: 0.8407 (mt) REVERT: C 501 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: F 678 LYS cc_start: 0.7693 (mttt) cc_final: 0.7251 (mmtm) REVERT: A 649 LYS cc_start: 0.8614 (tppt) cc_final: 0.8405 (tppt) REVERT: E 450 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7863 (mtpp) REVERT: E 554 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7529 (t80) REVERT: E 576 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8250 (mttm) REVERT: E 593 ASN cc_start: 0.7373 (p0) cc_final: 0.7028 (p0) REVERT: B 411 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8469 (p0) REVERT: B 486 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8223 (mp) outliers start: 94 outliers final: 58 residues processed: 308 average time/residue: 0.2827 time to fit residues: 131.9406 Evaluate side-chains 282 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 491 CYS 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 371 ILE Chi-restraints excluded: chain C residue 384 LEU 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 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 439 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER 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 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 498 LEU 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 B residue 346 ASP 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 411 ASP Chi-restraints excluded: chain B residue 486 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 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 = 0.4198 r_free = 0.4198 target = 0.197640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156693 restraints weight = 21089.217| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.31 r_work: 0.3481 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17594 Z= 0.123 Angle : 0.567 13.653 23782 Z= 0.284 Chirality : 0.042 0.157 2654 Planarity : 0.004 0.062 3003 Dihedral : 8.588 87.009 2467 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.53 % Allowed : 24.64 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.18), residues: 2080 helix: -0.01 (0.19), residues: 781 sheet: -1.46 (0.29), residues: 361 loop : -1.76 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 675 HIS 0.008 0.001 HIS E 629 PHE 0.015 0.001 PHE A 554 TYR 0.015 0.001 TYR D 482 ARG 0.005 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 553) hydrogen bonds : angle 4.98824 ( 1548) covalent geometry : bond 0.00299 (17594) covalent geometry : angle 0.56712 (23782) *********************** 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 299 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 2.153 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.7969 (t70) REVERT: D 533 THR cc_start: 0.8050 (t) cc_final: 0.7824 (t) REVERT: D 649 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8043 (mptt) REVERT: C 335 ASP cc_start: 0.7896 (t70) cc_final: 0.7069 (m-30) REVERT: C 411 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7743 (p0) REVERT: F 678 LYS cc_start: 0.7750 (mttt) cc_final: 0.7311 (mmtm) REVERT: A 371 ILE cc_start: 0.8993 (tt) cc_final: 0.8703 (tt) REVERT: A 372 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7205 (ttp80) REVERT: E 554 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7314 (t80) REVERT: E 558 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6073 (mp) REVERT: E 576 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8354 (mtpp) REVERT: E 593 ASN cc_start: 0.7368 (p0) cc_final: 0.7088 (p0) REVERT: B 411 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8400 (p0) outliers start: 68 outliers final: 45 residues processed: 287 average time/residue: 0.3004 time to fit residues: 132.2788 Evaluate side-chains 274 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 401 VAL 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 558 LEU 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 440 VAL Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 351 ILE 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 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 488 SER Chi-restraints excluded: chain E residue 498 LEU 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 554 PHE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 576 LYS 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 411 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 624 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 116 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** A 546 ASN 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 = 0.4154 r_free = 0.4154 target = 0.193371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153113 restraints weight = 20770.469| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.51 r_work: 0.3407 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17594 Z= 0.205 Angle : 0.630 14.030 23782 Z= 0.314 Chirality : 0.045 0.157 2654 Planarity : 0.004 0.060 3003 Dihedral : 8.548 89.659 2465 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.47 % Allowed : 24.32 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2080 helix: -0.16 (0.19), residues: 787 sheet: -1.58 (0.28), residues: 370 loop : -1.78 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 350 HIS 0.010 0.001 HIS E 629 PHE 0.018 0.002 PHE E 501 TYR 0.021 0.001 TYR D 482 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 553) hydrogen bonds : angle 5.11660 ( 1548) covalent geometry : bond 0.00504 (17594) covalent geometry : angle 0.63006 (23782) *********************** 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 314 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 228 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8057 (t70) REVERT: D 533 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7809 (t) REVERT: D 649 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8084 (mptt) REVERT: C 335 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: C 411 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7785 (p0) REVERT: F 523 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6929 (pp) REVERT: F 554 PHE cc_start: 0.5649 (p90) cc_final: 0.5107 (p90) REVERT: F 678 LYS cc_start: 0.7718 (mttt) cc_final: 0.7314 (mmtm) REVERT: A 371 ILE cc_start: 0.9002 (tt) cc_final: 0.8722 (tt) REVERT: A 372 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7437 (ttp80) REVERT: E 554 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7334 (t80) REVERT: E 593 ASN cc_start: 0.7467 (p0) cc_final: 0.7187 (p0) REVERT: B 365 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8078 (p) outliers start: 86 outliers final: 59 residues processed: 297 average time/residue: 0.2748 time to fit residues: 125.5460 Evaluate side-chains 292 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 335 ASP 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 401 VAL 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 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 439 THR Chi-restraints excluded: chain F residue 440 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 351 ILE 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 523 LEU 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 488 SER Chi-restraints excluded: chain E residue 498 LEU 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 554 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 195 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.198208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156350 restraints weight = 20712.442| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.40 r_work: 0.3480 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1721 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= 0.116 Angle : 0.565 12.718 23782 Z= 0.281 Chirality : 0.042 0.156 2654 Planarity : 0.004 0.061 3003 Dihedral : 8.212 88.830 2465 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.11 % Allowed : 24.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 2080 helix: 0.19 (0.19), residues: 781 sheet: -1.48 (0.29), residues: 361 loop : -1.71 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 675 HIS 0.010 0.001 HIS E 629 PHE 0.014 0.001 PHE E 501 TYR 0.014 0.001 TYR D 482 ARG 0.003 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 553) hydrogen bonds : angle 4.81480 ( 1548) covalent geometry : bond 0.00282 (17594) covalent geometry : angle 0.56465 (23782) *********************** 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 309 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 230 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 359 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8126 (p) REVERT: D 447 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.7989 (t70) REVERT: D 533 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7783 (t) REVERT: D 649 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8039 (mptt) REVERT: C 335 ASP cc_start: 0.7897 (t70) cc_final: 0.7188 (m-30) REVERT: C 411 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7669 (p0) REVERT: F 523 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6559 (pp) REVERT: F 554 PHE cc_start: 0.5419 (p90) cc_final: 0.5151 (p90) REVERT: F 678 LYS cc_start: 0.7632 (mttt) cc_final: 0.7191 (mmtm) REVERT: A 371 ILE cc_start: 0.8981 (tt) cc_final: 0.8698 (tt) REVERT: A 372 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7282 (ttp80) REVERT: E 554 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7182 (t80) REVERT: E 558 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6173 (mp) REVERT: E 576 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8591 (mtpt) REVERT: E 593 ASN cc_start: 0.7438 (p0) cc_final: 0.7178 (p0) REVERT: B 416 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8211 (tttt) outliers start: 79 outliers final: 55 residues processed: 295 average time/residue: 0.2911 time to fit residues: 131.5306 Evaluate side-chains 287 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 GLU 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 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 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 351 ILE Chi-restraints excluded: chain C residue 367 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 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 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 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 523 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 GLU 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 488 SER Chi-restraints excluded: chain E residue 498 LEU 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 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 380 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 486 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 548 HIS ** 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 = 0.4196 r_free = 0.4196 target = 0.197759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155472 restraints weight = 20869.019| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.41 r_work: 0.3493 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1806 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= 0.128 Angle : 0.571 12.272 23782 Z= 0.285 Chirality : 0.042 0.164 2654 Planarity : 0.004 0.061 3003 Dihedral : 8.163 89.846 2465 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.85 % Allowed : 25.10 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 2080 helix: 0.30 (0.19), residues: 775 sheet: -1.56 (0.27), residues: 395 loop : -1.66 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 675 HIS 0.011 0.001 HIS E 629 PHE 0.022 0.001 PHE A 554 TYR 0.016 0.001 TYR D 482 ARG 0.002 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 553) hydrogen bonds : angle 4.77951 ( 1548) covalent geometry : bond 0.00311 (17594) covalent geometry : angle 0.57058 (23782) *********************** 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 304 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: D 359 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.8018 (p) REVERT: D 447 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8008 (t70) REVERT: D 533 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7794 (t) REVERT: D 649 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8029 (mptt) REVERT: C 335 ASP cc_start: 0.7855 (t70) cc_final: 0.7143 (m-30) REVERT: C 411 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7557 (p0) REVERT: F 523 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6764 (pp) REVERT: F 678 LYS cc_start: 0.7701 (mttt) cc_final: 0.7267 (mmtm) REVERT: A 371 ILE cc_start: 0.8962 (tt) cc_final: 0.8672 (tt) REVERT: A 554 PHE cc_start: 0.6830 (m-80) cc_final: 0.6524 (m-80) REVERT: E 554 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7068 (t80) REVERT: E 558 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6195 (mp) REVERT: E 593 ASN cc_start: 0.7431 (p0) cc_final: 0.7166 (p0) REVERT: E 612 ARG cc_start: 0.8277 (ptt-90) cc_final: 0.8073 (ptt90) REVERT: B 411 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8375 (p0) REVERT: B 416 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8259 (tttt) outliers start: 74 outliers final: 58 residues processed: 290 average time/residue: 0.2823 time to fit residues: 125.4813 Evaluate side-chains 293 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 371 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 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 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 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 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 437 THR 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 351 ILE Chi-restraints excluded: chain A residue 370 SER 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 523 LEU 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 488 SER Chi-restraints excluded: chain E residue 498 LEU 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 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 380 SER Chi-restraints excluded: chain B residue 401 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 45 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 124 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.197443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155376 restraints weight = 20990.978| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.45 r_work: 0.3460 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17594 Z= 0.138 Angle : 0.583 12.049 23782 Z= 0.291 Chirality : 0.043 0.167 2654 Planarity : 0.004 0.063 3003 Dihedral : 8.144 89.143 2465 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.26 % Allowed : 25.10 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 2080 helix: 0.31 (0.19), residues: 769 sheet: -1.55 (0.27), residues: 395 loop : -1.65 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.011 0.001 HIS E 629 PHE 0.019 0.001 PHE A 554 TYR 0.017 0.001 TYR D 482 ARG 0.003 0.000 ARG E 514 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 553) hydrogen bonds : angle 4.79235 ( 1548) covalent geometry : bond 0.00339 (17594) covalent geometry : angle 0.58305 (23782) *********************** 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 317 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 235 time to evaluate : 2.217 Fit side-chains revert: symmetry clash REVERT: D 359 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7888 (p) REVERT: D 447 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8049 (t70) REVERT: D 533 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7808 (t) REVERT: D 649 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8029 (mptt) REVERT: C 335 ASP cc_start: 0.7914 (t70) cc_final: 0.7248 (m-30) REVERT: C 411 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7605 (p0) REVERT: F 523 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6273 (pp) REVERT: F 678 LYS cc_start: 0.7741 (mttt) cc_final: 0.7312 (mmtm) REVERT: A 371 ILE cc_start: 0.9001 (tt) cc_final: 0.8725 (tt) REVERT: A 372 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7151 (ttp80) REVERT: A 554 PHE cc_start: 0.6978 (m-80) cc_final: 0.6607 (m-80) REVERT: E 450 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7940 (mtpp) REVERT: E 554 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6980 (t80) REVERT: E 558 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6191 (mp) REVERT: E 570 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7226 (mtp-110) REVERT: E 576 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8409 (mttm) REVERT: E 593 ASN cc_start: 0.7481 (p0) cc_final: 0.7228 (p0) REVERT: E 612 ARG cc_start: 0.8332 (ptt-90) cc_final: 0.8125 (ptt90) REVERT: B 334 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 389 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.6770 (mtm110) REVERT: B 416 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8304 (tttt) outliers start: 82 outliers final: 59 residues processed: 300 average time/residue: 0.3158 time to fit residues: 141.1415 Evaluate side-chains 300 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER 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 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 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 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 437 THR 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 664 TYR 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 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 527 THR 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 450 LYS Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU 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 554 PHE Chi-restraints excluded: chain E residue 558 LEU 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 389 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 86 optimal weight: 0.0370 chunk 170 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.189014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142661 restraints weight = 20635.868| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.63 r_work: 0.3375 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1940 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= 0.114 Angle : 0.565 11.571 23782 Z= 0.282 Chirality : 0.042 0.155 2654 Planarity : 0.004 0.063 3003 Dihedral : 8.020 89.644 2465 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.64 % Allowed : 25.68 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 2080 helix: 0.46 (0.19), residues: 769 sheet: -1.49 (0.27), residues: 395 loop : -1.62 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 675 HIS 0.011 0.001 HIS E 629 PHE 0.019 0.001 PHE A 524 TYR 0.024 0.001 TYR F 676 ARG 0.002 0.000 ARG E 514 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 553) hydrogen bonds : angle 4.68295 ( 1548) covalent geometry : bond 0.00273 (17594) covalent geometry : angle 0.56476 (23782) ********************** 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 309 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 239 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7766 (t70) REVERT: D 533 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7541 (t) REVERT: D 649 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7901 (mptt) REVERT: C 335 ASP cc_start: 0.7906 (t70) cc_final: 0.7188 (m-30) REVERT: C 411 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7435 (p0) REVERT: F 523 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6326 (pp) REVERT: F 666 PHE cc_start: 0.5384 (m-80) cc_final: 0.5011 (m-80) REVERT: F 678 LYS cc_start: 0.7899 (mttt) cc_final: 0.7504 (mmtm) REVERT: A 371 ILE cc_start: 0.8721 (tt) cc_final: 0.8413 (tt) REVERT: A 372 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6988 (ttp80) REVERT: E 448 ASP cc_start: 0.7675 (t0) cc_final: 0.7455 (p0) REVERT: E 450 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7928 (mtpp) REVERT: E 554 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6593 (t80) REVERT: E 558 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6152 (mp) REVERT: E 570 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.7024 (mtp-110) REVERT: E 576 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8313 (mtpp) REVERT: E 593 ASN cc_start: 0.7498 (p0) cc_final: 0.7290 (p0) REVERT: E 612 ARG cc_start: 0.8321 (ptt-90) cc_final: 0.8084 (ptt90) REVERT: B 334 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8298 (mm) REVERT: B 389 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.6657 (mtm110) REVERT: B 411 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8492 (p0) REVERT: B 416 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8076 (tttt) outliers start: 70 outliers final: 56 residues processed: 294 average time/residue: 0.3103 time to fit residues: 139.2528 Evaluate side-chains 295 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 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 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 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 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 437 THR 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 664 TYR 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 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 526 GLU 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 450 LYS Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU 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 554 PHE Chi-restraints excluded: chain E residue 558 LEU 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 389 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 486 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.188294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135620 restraints weight = 20649.478| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.69 r_work: 0.3350 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17594 Z= 0.130 Angle : 0.574 11.635 23782 Z= 0.288 Chirality : 0.042 0.159 2654 Planarity : 0.004 0.063 3003 Dihedral : 8.025 88.849 2465 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.90 % Allowed : 25.57 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2080 helix: 0.44 (0.19), residues: 769 sheet: -1.49 (0.27), residues: 395 loop : -1.60 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 355 HIS 0.012 0.001 HIS E 629 PHE 0.029 0.001 PHE A 524 TYR 0.024 0.001 TYR F 676 ARG 0.007 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 553) hydrogen bonds : angle 4.71078 ( 1548) covalent geometry : bond 0.00318 (17594) covalent geometry : angle 0.57446 (23782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8645.93 seconds wall clock time: 152 minutes 26.38 seconds (9146.38 seconds total)