Starting phenix.real_space_refine on Sat Jun 6 05:40:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y03_72383/06_2026/9y03_72383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y03_72383/06_2026/9y03_72383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y03_72383/06_2026/9y03_72383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y03_72383/06_2026/9y03_72383.map" model { file = "/net/cci-nas-00/data/ceres_data/9y03_72383/06_2026/9y03_72383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y03_72383/06_2026/9y03_72383.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 132 5.16 5 C 16104 2.51 5 N 4512 2.21 5 O 4920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25692 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "B" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "C" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "D" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "E" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "F" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4228 Classifications: {'peptide': 544} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.74, per 1000 atoms: 0.26 Number of scatterers: 25692 At special positions: 0 Unit cell: (145, 143, 95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 24 15.00 O 4920 8.00 N 4512 7.00 C 16104 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 12 sheets defined 60.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.627A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 5.099A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.564A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.522A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.819A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.641A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.845A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.521A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 removed outlier: 4.105A pdb=" N ASN A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.353A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.855A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.634A pdb=" N ILE A 633 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.608A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.523A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.551A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.789A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.648A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 5.051A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.561A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.558A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.826A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.611A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.825A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.579A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 445 removed outlier: 4.363A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.802A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.604A pdb=" N ILE B 633 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.541A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.606A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.608A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.946A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.585A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 5.044A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.611A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.511A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.871A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.648A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.993A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 438 through 445 removed outlier: 4.380A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.776A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.664A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.678A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.627A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.621A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 5.094A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.570A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 277 removed outlier: 3.523A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.568A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.638A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'D' and resid 327 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.884A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.531A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 438 through 445 removed outlier: 4.350A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.851A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.636A pdb=" N ILE D 633 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.602A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.535A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.563A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 3.797A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.677A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 226 removed outlier: 5.050A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.561A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.556A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.836A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.618A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.799A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.593A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 438 through 445 removed outlier: 4.373A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 554 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.804A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.627A pdb=" N ILE E 633 " --> pdb=" O ASP E 630 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.543A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.599A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.612A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 removed outlier: 3.953A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.578A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 226 removed outlier: 5.042A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.605A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.860A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.667A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 328 through 334 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.987A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 438 through 445 removed outlier: 4.371A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 457 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.776A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.659A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.681A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 705 Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.640A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 763 removed outlier: 3.628A pdb=" N GLN F 763 " --> pdb=" O ALA F 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.231A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.268A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.278A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.571A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.261A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.599A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.271A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.570A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3585 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: 4.78 Time building geometry restraints manager: 2.94 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: 8706 1.34 - 1.46: 4061 1.46 - 1.58: 13105 1.58 - 1.69: 36 1.69 - 1.81: 222 Bond restraints: 26130 Sorted by residual: bond pdb=" C ASN E 460 " pdb=" N PRO E 461 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.26e+00 bond pdb=" C ASN F 460 " pdb=" N PRO F 461 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.20e+00 bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.19e+00 bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.17e+00 bond pdb=" C ASN C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.16e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 34482 1.80 - 3.60: 645 3.60 - 5.40: 151 5.40 - 7.21: 49 7.21 - 9.01: 13 Bond angle restraints: 35340 Sorted by residual: angle pdb=" N LYS D 386 " pdb=" CA LYS D 386 " pdb=" C LYS D 386 " ideal model delta sigma weight residual 114.62 109.43 5.19 1.14e+00 7.69e-01 2.07e+01 angle pdb=" CA LYS D 386 " pdb=" C LYS D 386 " pdb=" N ASN D 387 " ideal model delta sigma weight residual 119.71 116.08 3.63 1.17e+00 7.31e-01 9.62e+00 angle pdb=" N ASN A 460 " pdb=" CA ASN A 460 " pdb=" C ASN A 460 " ideal model delta sigma weight residual 109.81 116.37 -6.56 2.21e+00 2.05e-01 8.81e+00 angle pdb=" N ASN C 460 " pdb=" CA ASN C 460 " pdb=" C ASN C 460 " ideal model delta sigma weight residual 109.81 116.36 -6.55 2.21e+00 2.05e-01 8.79e+00 angle pdb=" N ASN E 460 " pdb=" CA ASN E 460 " pdb=" C ASN E 460 " ideal model delta sigma weight residual 109.81 116.33 -6.52 2.21e+00 2.05e-01 8.70e+00 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 15059 21.09 - 42.19: 908 42.19 - 63.28: 86 63.28 - 84.38: 34 84.38 - 105.47: 11 Dihedral angle restraints: 16098 sinusoidal: 6738 harmonic: 9360 Sorted by residual: dihedral pdb=" C5' ADP B 901 " pdb=" O5' ADP B 901 " pdb=" PA ADP B 901 " pdb=" O2A ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 -165.47 105.47 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 -165.36 105.36 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -164.08 104.08 1 2.00e+01 2.50e-03 2.98e+01 ... (remaining 16095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2911 0.043 - 0.086: 765 0.086 - 0.130: 267 0.130 - 0.173: 20 0.173 - 0.216: 9 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA ASN D 460 " pdb=" N ASN D 460 " pdb=" C ASN D 460 " pdb=" CB ASN D 460 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASN C 460 " pdb=" N ASN C 460 " pdb=" C ASN C 460 " pdb=" CB ASN C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3969 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 237 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO D 238 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 238 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 238 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 635 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO E 636 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 636 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 636 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 635 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 636 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 636 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 636 " 0.023 5.00e-02 4.00e+02 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2227 2.74 - 3.28: 26926 3.28 - 3.82: 43596 3.82 - 4.36: 54854 4.36 - 4.90: 88181 Nonbonded interactions: 215784 Sorted by model distance: nonbonded pdb=" OE2 GLU B 578 " pdb=" NH1 ARG C 635 " model vdw 2.199 3.120 nonbonded pdb=" OE2 GLU E 578 " pdb=" NH1 ARG F 635 " model vdw 2.205 3.120 nonbonded pdb=" OE2 GLU A 578 " pdb=" NH1 ARG B 635 " model vdw 2.219 3.120 nonbonded pdb=" OE2 GLU D 578 " pdb=" NH1 ARG E 635 " model vdw 2.221 3.120 nonbonded pdb=" OD2 ASP E 393 " pdb=" OG1 THR E 448 " model vdw 2.253 3.040 ... (remaining 215779 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.440 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.980 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 0.067 26130 Z= 0.151 Angle : 0.663 9.008 35340 Z= 0.326 Chirality : 0.044 0.216 3972 Planarity : 0.005 0.058 4620 Dihedral : 13.424 105.473 10026 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3240 helix: 0.68 (0.13), residues: 1638 sheet: -0.06 (0.26), residues: 384 loop : -0.33 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 599 TYR 0.017 0.002 TYR F 244 PHE 0.013 0.001 PHE A 360 TRP 0.009 0.001 TRP B 476 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (26130) covalent geometry : angle 0.66295 / 0.33 (35340) hydrogen bonds : bond 0.22077 / 15.00 ( 1257) hydrogen bonds : angle 6.37138 / 4.66 ( 3585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.7736 (mmt90) cc_final: 0.7139 (ttt180) REVERT: A 397 GLU cc_start: 0.8502 (tp30) cc_final: 0.8104 (tp30) REVERT: A 420 LEU cc_start: 0.8442 (mt) cc_final: 0.8185 (mt) REVERT: A 488 GLU cc_start: 0.8338 (tt0) cc_final: 0.7911 (tp30) REVERT: A 560 ARG cc_start: 0.8730 (ttt180) cc_final: 0.8105 (ttt180) REVERT: A 663 LYS cc_start: 0.8990 (pttm) cc_final: 0.8625 (tptp) REVERT: A 689 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7823 (pt0) REVERT: A 744 ARG cc_start: 0.7989 (ptm-80) cc_final: 0.7030 (ttt90) REVERT: B 359 ARG cc_start: 0.7637 (mmt90) cc_final: 0.7141 (ttt180) REVERT: B 397 GLU cc_start: 0.8542 (tp30) cc_final: 0.8088 (pm20) REVERT: B 449 MET cc_start: 0.8529 (tpt) cc_final: 0.8286 (tpt) REVERT: B 560 ARG cc_start: 0.8770 (ttt180) cc_final: 0.8078 (ttt180) REVERT: B 640 ASP cc_start: 0.7913 (m-30) cc_final: 0.7712 (m-30) REVERT: C 203 TYR cc_start: 0.9120 (m-80) cc_final: 0.8817 (m-80) REVERT: C 359 ARG cc_start: 0.7723 (mmt90) cc_final: 0.7197 (ttt180) REVERT: C 445 LEU cc_start: 0.7891 (tt) cc_final: 0.7653 (tp) REVERT: C 560 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8092 (tpp-160) REVERT: C 663 LYS cc_start: 0.8779 (pttm) cc_final: 0.8545 (tptp) REVERT: C 689 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7933 (pt0) REVERT: C 744 ARG cc_start: 0.8281 (ptm-80) cc_final: 0.7395 (tpt-90) REVERT: D 359 ARG cc_start: 0.7553 (mmt90) cc_final: 0.6971 (ttt180) REVERT: D 420 LEU cc_start: 0.8472 (mt) cc_final: 0.8240 (mt) REVERT: D 450 ASP cc_start: 0.8872 (t0) cc_final: 0.8656 (t0) REVERT: D 488 GLU cc_start: 0.8358 (tt0) cc_final: 0.7956 (tp30) REVERT: D 560 ARG cc_start: 0.8676 (ttt180) cc_final: 0.8070 (ttt180) REVERT: D 663 LYS cc_start: 0.8962 (pttm) cc_final: 0.8591 (tptp) REVERT: D 689 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7816 (pt0) REVERT: D 744 ARG cc_start: 0.8023 (ptm-80) cc_final: 0.7067 (ttt90) REVERT: E 322 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7371 (mpt180) REVERT: E 359 ARG cc_start: 0.7660 (mmt90) cc_final: 0.7141 (ttt180) REVERT: E 445 LEU cc_start: 0.7781 (tt) cc_final: 0.7438 (tm) REVERT: E 449 MET cc_start: 0.8555 (tpt) cc_final: 0.8313 (tpt) REVERT: E 560 ARG cc_start: 0.8779 (ttt180) cc_final: 0.8079 (ttt180) REVERT: E 663 LYS cc_start: 0.8824 (pttm) cc_final: 0.8543 (tptp) REVERT: F 203 TYR cc_start: 0.9128 (m-80) cc_final: 0.8816 (m-80) REVERT: F 359 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7176 (ttt180) REVERT: F 445 LEU cc_start: 0.7928 (tt) cc_final: 0.7632 (tp) REVERT: F 449 MET cc_start: 0.8605 (tpt) cc_final: 0.8331 (tpp) REVERT: F 560 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8056 (tpp-160) REVERT: F 689 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7928 (pt0) REVERT: F 744 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.7369 (tpt-90) outliers start: 0 outliers final: 1 residues processed: 577 average time/residue: 0.9342 time to fit residues: 599.3928 Evaluate side-chains 373 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 484 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0370 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 351 ASN A 382 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS C 327 GLN C 404 HIS C 616 ASN C 763 GLN D 327 GLN D 351 ASN D 382 GLN D 404 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 348 ASN E 382 GLN E 404 HIS F 327 GLN F 382 GLN F 404 HIS F 616 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088628 restraints weight = 37918.792| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.87 r_work: 0.2950 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26130 Z= 0.167 Angle : 0.746 11.448 35340 Z= 0.362 Chirality : 0.046 0.216 3972 Planarity : 0.005 0.050 4620 Dihedral : 7.720 103.506 3638 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.67 % Rotamer: Outliers : 2.33 % Allowed : 10.20 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3240 helix: 0.72 (0.13), residues: 1716 sheet: -0.14 (0.26), residues: 390 loop : 0.10 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 349 TYR 0.027 0.002 TYR B 203 PHE 0.010 0.001 PHE D 360 TRP 0.009 0.001 TRP D 454 HIS 0.007 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (26130) covalent geometry : angle 0.74625 / 0.36 (35340) hydrogen bonds : bond 0.05211 / 3.47 ( 1257) hydrogen bonds : angle 4.61535 / 3.33 ( 3585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 421 time to evaluate : 1.141 Fit side-chains REVERT: A 278 LEU cc_start: 0.8544 (mp) cc_final: 0.8294 (mm) REVERT: A 359 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7059 (ttt180) REVERT: A 560 ARG cc_start: 0.8703 (ttt180) cc_final: 0.8072 (ttt180) REVERT: A 611 MET cc_start: 0.8110 (mtm) cc_final: 0.7751 (mtm) REVERT: A 663 LYS cc_start: 0.8990 (pttm) cc_final: 0.8658 (tptp) REVERT: A 689 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7840 (pt0) REVERT: A 741 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.7492 (mmt-90) REVERT: A 744 ARG cc_start: 0.7980 (ptm-80) cc_final: 0.6919 (ttt90) REVERT: B 359 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7100 (ttt180) REVERT: B 397 GLU cc_start: 0.8533 (tp30) cc_final: 0.8128 (pm20) REVERT: B 560 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8159 (ttt180) REVERT: C 203 TYR cc_start: 0.9025 (m-10) cc_final: 0.8651 (m-80) REVERT: C 327 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7923 (tp-100) REVERT: C 359 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6892 (ttt180) REVERT: C 534 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: C 560 ARG cc_start: 0.8824 (ttt180) cc_final: 0.7988 (tpp-160) REVERT: C 616 ASN cc_start: 0.8541 (t0) cc_final: 0.8124 (t0) REVERT: C 663 LYS cc_start: 0.8982 (pttm) cc_final: 0.8610 (tptp) REVERT: C 689 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7857 (pt0) REVERT: C 741 ARG cc_start: 0.7838 (mmp-170) cc_final: 0.7495 (mmt-90) REVERT: C 744 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.7272 (tpt170) REVERT: D 288 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8814 (mtmm) REVERT: D 321 GLU cc_start: 0.7735 (mp0) cc_final: 0.7186 (mp0) REVERT: D 359 ARG cc_start: 0.7758 (mmt90) cc_final: 0.6999 (ttt180) REVERT: D 445 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7171 (tt) REVERT: D 560 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8050 (ttt180) REVERT: D 663 LYS cc_start: 0.8998 (pttm) cc_final: 0.8657 (tptp) REVERT: D 689 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7802 (pt0) REVERT: D 741 ARG cc_start: 0.7712 (mmp-170) cc_final: 0.7452 (mmt-90) REVERT: D 744 ARG cc_start: 0.8021 (ptm-80) cc_final: 0.6959 (ttt90) REVERT: E 359 ARG cc_start: 0.7773 (mmt90) cc_final: 0.7184 (ttt180) REVERT: E 560 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8155 (ttt180) REVERT: E 616 ASN cc_start: 0.8574 (t0) cc_final: 0.8088 (t0) REVERT: E 663 LYS cc_start: 0.8930 (pttm) cc_final: 0.8643 (tptp) REVERT: F 203 TYR cc_start: 0.9025 (m-80) cc_final: 0.8648 (m-80) REVERT: F 327 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7883 (tp-100) REVERT: F 359 ARG cc_start: 0.7456 (mmt90) cc_final: 0.6902 (ttt180) REVERT: F 366 GLU cc_start: 0.8234 (tt0) cc_final: 0.7959 (tt0) REVERT: F 449 MET cc_start: 0.8605 (tpt) cc_final: 0.8288 (tpp) REVERT: F 534 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: F 560 ARG cc_start: 0.8843 (ttt180) cc_final: 0.7987 (tpp-160) REVERT: F 616 ASN cc_start: 0.8552 (t0) cc_final: 0.8154 (t0) REVERT: F 689 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7866 (pt0) REVERT: F 741 ARG cc_start: 0.7831 (mmp-170) cc_final: 0.7490 (mmt-90) REVERT: F 744 ARG cc_start: 0.8255 (ptm-80) cc_final: 0.7258 (tpt170) outliers start: 63 outliers final: 19 residues processed: 467 average time/residue: 0.9113 time to fit residues: 475.4489 Evaluate side-chains 380 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 356 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 534 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 382 GLN C 327 GLN C 404 HIS D 327 GLN E 340 HIS E 616 ASN F 327 GLN F 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.086817 restraints weight = 37943.051| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.90 r_work: 0.2926 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26130 Z= 0.179 Angle : 0.717 9.934 35340 Z= 0.345 Chirality : 0.046 0.202 3972 Planarity : 0.005 0.048 4620 Dihedral : 7.745 104.430 3636 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.96 % Allowed : 11.35 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3240 helix: 0.84 (0.12), residues: 1740 sheet: -0.07 (0.26), residues: 390 loop : 0.31 (0.21), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 349 TYR 0.016 0.002 TYR E 244 PHE 0.010 0.001 PHE D 360 TRP 0.005 0.001 TRP D 476 HIS 0.008 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (26130) covalent geometry : angle 0.71740 / 0.35 (35340) hydrogen bonds : bond 0.04629 / 3.07 ( 1257) hydrogen bonds : angle 4.41665 / 3.18 ( 3585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 375 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8470 (mtm-85) REVERT: A 359 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7159 (ttt180) REVERT: A 560 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8125 (ttt180) REVERT: A 611 MET cc_start: 0.8155 (mtm) cc_final: 0.7834 (mtm) REVERT: A 663 LYS cc_start: 0.8997 (pttm) cc_final: 0.8642 (tptp) REVERT: A 689 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7862 (pt0) REVERT: A 744 ARG cc_start: 0.8012 (ptm-80) cc_final: 0.6916 (ttt90) REVERT: B 288 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: B 359 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7296 (ttt180) REVERT: B 397 GLU cc_start: 0.8537 (tp30) cc_final: 0.8146 (pm20) REVERT: B 534 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: B 560 ARG cc_start: 0.8852 (ttt180) cc_final: 0.8148 (ttt180) REVERT: C 203 TYR cc_start: 0.9052 (m-10) cc_final: 0.8731 (m-80) REVERT: C 359 ARG cc_start: 0.7547 (mmt90) cc_final: 0.7060 (ttt180) REVERT: C 445 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7224 (mt) REVERT: C 534 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8427 (tp30) REVERT: C 560 ARG cc_start: 0.8798 (ttt180) cc_final: 0.8012 (tpp-160) REVERT: C 565 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8740 (ttmt) REVERT: C 663 LYS cc_start: 0.9003 (pttm) cc_final: 0.8603 (tptp) REVERT: C 689 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7903 (pt0) REVERT: C 744 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.7453 (tpp-160) REVERT: D 560 ARG cc_start: 0.8719 (ttt180) cc_final: 0.8081 (ttt180) REVERT: D 663 LYS cc_start: 0.8995 (pttm) cc_final: 0.8595 (tptp) REVERT: D 689 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7848 (pt0) REVERT: D 744 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.6936 (ttt90) REVERT: E 359 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7251 (ttt180) REVERT: E 397 GLU cc_start: 0.8240 (mp0) cc_final: 0.8038 (mp0) REVERT: E 534 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: E 560 ARG cc_start: 0.8830 (ttt180) cc_final: 0.8129 (ttt180) REVERT: E 565 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8572 (tttp) REVERT: E 663 LYS cc_start: 0.8916 (pttm) cc_final: 0.8618 (tptp) REVERT: F 203 TYR cc_start: 0.9066 (m-10) cc_final: 0.8708 (m-80) REVERT: F 359 ARG cc_start: 0.7532 (mmt90) cc_final: 0.6994 (ttt180) REVERT: F 445 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7368 (mt) REVERT: F 449 MET cc_start: 0.8558 (tpt) cc_final: 0.8273 (tpp) REVERT: F 534 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8426 (tp30) REVERT: F 560 ARG cc_start: 0.8812 (ttt180) cc_final: 0.7997 (tpp-160) REVERT: F 565 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: F 663 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8659 (tptp) REVERT: F 689 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7894 (pt0) REVERT: F 744 ARG cc_start: 0.8283 (ptm-80) cc_final: 0.7415 (tpt170) outliers start: 80 outliers final: 17 residues processed: 433 average time/residue: 0.8491 time to fit residues: 413.2821 Evaluate side-chains 374 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 345 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 663 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 315 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 243 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 chunk 195 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 chunk 37 optimal weight: 0.0010 chunk 1 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 HIS C 616 ASN E 340 HIS E 568 GLN F 226 HIS F 404 HIS F 616 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087530 restraints weight = 37267.906| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.94 r_work: 0.2929 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26130 Z= 0.135 Angle : 0.698 11.289 35340 Z= 0.332 Chirality : 0.044 0.188 3972 Planarity : 0.004 0.055 4620 Dihedral : 7.489 99.158 3636 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.40 % Allowed : 13.34 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3240 helix: 0.90 (0.12), residues: 1752 sheet: -0.01 (0.26), residues: 390 loop : 0.35 (0.21), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 349 TYR 0.015 0.002 TYR D 244 PHE 0.007 0.001 PHE B 506 TRP 0.004 0.001 TRP B 454 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (26130) covalent geometry : angle 0.69842 / 0.33 (35340) hydrogen bonds : bond 0.03933 / 2.61 ( 1257) hydrogen bonds : angle 4.22948 / 3.04 ( 3585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 373 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7015 (ttt180) REVERT: A 560 ARG cc_start: 0.8642 (ttt180) cc_final: 0.7919 (ttt180) REVERT: A 624 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8812 (p0) REVERT: A 663 LYS cc_start: 0.9029 (pttm) cc_final: 0.8569 (tptp) REVERT: A 689 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7818 (pt0) REVERT: A 744 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.6693 (ttt90) REVERT: B 288 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8639 (mtmm) REVERT: B 359 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7086 (ttt180) REVERT: B 397 GLU cc_start: 0.8556 (tp30) cc_final: 0.8076 (pm20) REVERT: B 534 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: B 560 ARG cc_start: 0.8635 (ttt180) cc_final: 0.7852 (ttt180) REVERT: B 616 ASN cc_start: 0.8580 (t0) cc_final: 0.8156 (t0) REVERT: B 630 ASP cc_start: 0.8171 (p0) cc_final: 0.7957 (p0) REVERT: C 203 TYR cc_start: 0.9019 (m-10) cc_final: 0.8631 (m-80) REVERT: C 359 ARG cc_start: 0.7357 (mmt90) cc_final: 0.6855 (ttt180) REVERT: C 442 MET cc_start: 0.6101 (mmp) cc_final: 0.5638 (mpm) REVERT: C 534 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: C 560 ARG cc_start: 0.8765 (ttt180) cc_final: 0.7853 (tpp-160) REVERT: C 616 ASN cc_start: 0.8640 (t0) cc_final: 0.8250 (t0) REVERT: C 630 ASP cc_start: 0.8252 (p0) cc_final: 0.8034 (p0) REVERT: C 663 LYS cc_start: 0.9062 (pttm) cc_final: 0.8581 (tptp) REVERT: C 689 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7725 (pt0) REVERT: C 744 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.7388 (tpt170) REVERT: D 222 LEU cc_start: 0.8846 (tp) cc_final: 0.8371 (tp) REVERT: D 359 ARG cc_start: 0.7732 (mmt90) cc_final: 0.6934 (ttt180) REVERT: D 560 ARG cc_start: 0.8611 (ttt180) cc_final: 0.7913 (ttt180) REVERT: D 663 LYS cc_start: 0.9038 (pttm) cc_final: 0.8575 (tptp) REVERT: D 689 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7802 (pt0) REVERT: D 744 ARG cc_start: 0.7890 (ptm-80) cc_final: 0.6735 (ttt90) REVERT: E 359 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7110 (ttt180) REVERT: E 534 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: E 560 ARG cc_start: 0.8615 (ttt180) cc_final: 0.7826 (ttt180) REVERT: E 565 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8364 (tttp) REVERT: E 568 GLN cc_start: 0.8670 (mm110) cc_final: 0.8427 (tp-100) REVERT: E 616 ASN cc_start: 0.8594 (t0) cc_final: 0.8133 (t0) REVERT: E 663 LYS cc_start: 0.8969 (pttm) cc_final: 0.8628 (tptp) REVERT: F 203 TYR cc_start: 0.9017 (m-10) cc_final: 0.8625 (m-80) REVERT: F 359 ARG cc_start: 0.7408 (mmt90) cc_final: 0.6880 (ttt180) REVERT: F 449 MET cc_start: 0.8471 (tpt) cc_final: 0.8199 (tpp) REVERT: F 534 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: F 560 ARG cc_start: 0.8745 (ttt180) cc_final: 0.7842 (tpp-160) REVERT: F 616 ASN cc_start: 0.8633 (t0) cc_final: 0.8250 (t0) REVERT: F 630 ASP cc_start: 0.8259 (p0) cc_final: 0.8046 (p0) REVERT: F 663 LYS cc_start: 0.8976 (pttp) cc_final: 0.8656 (tptp) REVERT: F 689 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7726 (pt0) REVERT: F 741 ARG cc_start: 0.7408 (tpm170) cc_final: 0.7142 (mmp-170) REVERT: F 744 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7282 (tpt170) outliers start: 65 outliers final: 16 residues processed: 421 average time/residue: 0.8404 time to fit residues: 398.3640 Evaluate side-chains 373 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 350 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 534 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 179 optimal weight: 0.4980 chunk 290 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 191 optimal weight: 0.0870 chunk 153 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN E 340 HIS F 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083846 restraints weight = 37699.446| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.99 r_work: 0.2819 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 26130 Z= 0.239 Angle : 0.740 11.027 35340 Z= 0.358 Chirality : 0.047 0.187 3972 Planarity : 0.005 0.058 4620 Dihedral : 7.937 107.635 3636 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.59 % Allowed : 15.00 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3240 helix: 0.87 (0.12), residues: 1752 sheet: 0.13 (0.27), residues: 390 loop : 0.42 (0.21), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 349 TYR 0.019 0.002 TYR B 244 PHE 0.012 0.002 PHE A 452 TRP 0.006 0.001 TRP D 476 HIS 0.008 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (26130) covalent geometry : angle 0.74049 / 0.36 (35340) hydrogen bonds : bond 0.04451 / 2.96 ( 1257) hydrogen bonds : angle 4.27347 / 3.08 ( 3585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 349 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ARG cc_start: 0.8679 (ttt180) cc_final: 0.7903 (ttt180) REVERT: A 611 MET cc_start: 0.8198 (mtm) cc_final: 0.7800 (mtm) REVERT: A 663 LYS cc_start: 0.9049 (pttm) cc_final: 0.8583 (tptp) REVERT: A 689 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7849 (pt0) REVERT: A 741 ARG cc_start: 0.6440 (mmt180) cc_final: 0.6025 (tpm170) REVERT: B 359 ARG cc_start: 0.7745 (mmt90) cc_final: 0.7145 (mtp-110) REVERT: B 397 GLU cc_start: 0.8566 (tp30) cc_final: 0.8089 (pm20) REVERT: B 534 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: B 560 ARG cc_start: 0.8737 (ttt180) cc_final: 0.7955 (ttt180) REVERT: C 203 TYR cc_start: 0.9090 (m-10) cc_final: 0.8633 (m-80) REVERT: C 359 ARG cc_start: 0.7515 (mmt90) cc_final: 0.6980 (ttt180) REVERT: C 397 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: C 534 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: C 560 ARG cc_start: 0.8752 (ttt180) cc_final: 0.7844 (tpp-160) REVERT: C 565 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8506 (ttmt) REVERT: C 630 ASP cc_start: 0.8312 (p0) cc_final: 0.8033 (p0) REVERT: C 663 LYS cc_start: 0.9061 (pttm) cc_final: 0.8498 (tptp) REVERT: C 689 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7718 (pt0) REVERT: C 744 ARG cc_start: 0.8259 (ptm-80) cc_final: 0.7200 (tpt170) REVERT: D 359 ARG cc_start: 0.7739 (mmt90) cc_final: 0.6940 (ttt180) REVERT: D 560 ARG cc_start: 0.8666 (ttt180) cc_final: 0.7903 (ttt180) REVERT: D 663 LYS cc_start: 0.9043 (pttm) cc_final: 0.8568 (tptp) REVERT: D 689 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7844 (pt0) REVERT: D 741 ARG cc_start: 0.6443 (mmt180) cc_final: 0.6028 (tpm170) REVERT: E 359 ARG cc_start: 0.7838 (mmt90) cc_final: 0.7267 (mtp-110) REVERT: E 534 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: E 560 ARG cc_start: 0.8700 (ttt180) cc_final: 0.7920 (ttt180) REVERT: E 616 ASN cc_start: 0.8432 (t0) cc_final: 0.8229 (t0) REVERT: E 663 LYS cc_start: 0.9059 (pttm) cc_final: 0.8614 (tptp) REVERT: F 203 TYR cc_start: 0.9085 (m-10) cc_final: 0.8611 (m-80) REVERT: F 359 ARG cc_start: 0.7500 (mmt90) cc_final: 0.6968 (ttt180) REVERT: F 397 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: F 449 MET cc_start: 0.8480 (tpt) cc_final: 0.8203 (tpp) REVERT: F 534 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: F 560 ARG cc_start: 0.8763 (ttt180) cc_final: 0.7862 (tpp-160) REVERT: F 565 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8508 (ttmt) REVERT: F 663 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8624 (tptp) REVERT: F 689 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7714 (pt0) REVERT: F 741 ARG cc_start: 0.7440 (tpm170) cc_final: 0.7154 (mmp-170) REVERT: F 744 ARG cc_start: 0.8216 (ptm-80) cc_final: 0.7102 (tpt170) outliers start: 70 outliers final: 23 residues processed: 397 average time/residue: 0.8903 time to fit residues: 395.4002 Evaluate side-chains 368 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 336 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 683 SER Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 663 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 234 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 310 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 616 ASN F 404 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086394 restraints weight = 37350.902| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.95 r_work: 0.2845 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26130 Z= 0.168 Angle : 0.724 11.937 35340 Z= 0.345 Chirality : 0.045 0.176 3972 Planarity : 0.005 0.066 4620 Dihedral : 7.787 105.197 3636 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.03 % Allowed : 16.48 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3240 helix: 0.90 (0.12), residues: 1770 sheet: 0.09 (0.27), residues: 390 loop : 0.39 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 349 TYR 0.020 0.002 TYR B 244 PHE 0.011 0.001 PHE A 452 TRP 0.004 0.001 TRP E 454 HIS 0.006 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (26130) covalent geometry : angle 0.72369 / 0.35 (35340) hydrogen bonds : bond 0.03989 / 2.64 ( 1257) hydrogen bonds : angle 4.20481 / 3.01 ( 3585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 348 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.7814 (mmt90) cc_final: 0.7037 (ttt180) REVERT: A 560 ARG cc_start: 0.8662 (ttt180) cc_final: 0.7914 (ttt180) REVERT: A 611 MET cc_start: 0.8187 (mtm) cc_final: 0.7786 (mtm) REVERT: A 663 LYS cc_start: 0.9039 (pttm) cc_final: 0.8562 (tptp) REVERT: A 689 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7850 (pt0) REVERT: A 741 ARG cc_start: 0.6390 (mmt180) cc_final: 0.6016 (tpm170) REVERT: B 244 TYR cc_start: 0.8582 (p90) cc_final: 0.8215 (p90) REVERT: B 359 ARG cc_start: 0.7752 (mmt90) cc_final: 0.7210 (mtp-110) REVERT: B 397 GLU cc_start: 0.8548 (tp30) cc_final: 0.8094 (pm20) REVERT: B 534 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8319 (tp30) REVERT: B 560 ARG cc_start: 0.8696 (ttt180) cc_final: 0.7884 (ttt180) REVERT: B 741 ARG cc_start: 0.7725 (mmp-170) cc_final: 0.7249 (mmt180) REVERT: C 203 TYR cc_start: 0.9037 (m-10) cc_final: 0.8611 (m-80) REVERT: C 359 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7000 (ttt180) REVERT: C 397 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: C 534 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: C 560 ARG cc_start: 0.8745 (ttt180) cc_final: 0.7801 (tpp-160) REVERT: C 630 ASP cc_start: 0.8255 (p0) cc_final: 0.8001 (p0) REVERT: C 633 ILE cc_start: 0.9002 (tp) cc_final: 0.8714 (tp) REVERT: C 663 LYS cc_start: 0.9066 (pttm) cc_final: 0.8501 (tptp) REVERT: C 689 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7717 (pt0) REVERT: C 744 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7355 (tpp-160) REVERT: D 359 ARG cc_start: 0.7741 (mmt90) cc_final: 0.6949 (ttt180) REVERT: D 560 ARG cc_start: 0.8650 (ttt180) cc_final: 0.7909 (ttt180) REVERT: D 663 LYS cc_start: 0.9047 (pttm) cc_final: 0.8567 (tptp) REVERT: D 689 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7839 (pt0) REVERT: D 741 ARG cc_start: 0.6383 (mmt180) cc_final: 0.6013 (tpm170) REVERT: E 359 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7312 (mtp-110) REVERT: E 534 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: E 560 ARG cc_start: 0.8667 (ttt180) cc_final: 0.7858 (ttt180) REVERT: E 663 LYS cc_start: 0.9034 (pttm) cc_final: 0.8614 (tptp) REVERT: E 741 ARG cc_start: 0.7756 (mmp-170) cc_final: 0.7287 (mmt180) REVERT: F 203 TYR cc_start: 0.9056 (m-10) cc_final: 0.8564 (m-80) REVERT: F 359 ARG cc_start: 0.7532 (mmt90) cc_final: 0.6995 (ttt180) REVERT: F 397 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8049 (pm20) REVERT: F 449 MET cc_start: 0.8460 (tpt) cc_final: 0.8182 (tpp) REVERT: F 534 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: F 560 ARG cc_start: 0.8734 (ttt180) cc_final: 0.7800 (tpp-160) REVERT: F 565 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8535 (ttmt) REVERT: F 630 ASP cc_start: 0.8320 (p0) cc_final: 0.8081 (p0) REVERT: F 663 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8599 (tptp) REVERT: F 689 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7713 (pt0) REVERT: F 741 ARG cc_start: 0.7467 (tpm170) cc_final: 0.7180 (mmp-170) REVERT: F 744 ARG cc_start: 0.8233 (ptm-80) cc_final: 0.7337 (tpp-160) REVERT: F 750 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8219 (p0) outliers start: 55 outliers final: 19 residues processed: 387 average time/residue: 0.8667 time to fit residues: 376.3744 Evaluate side-chains 361 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 663 LYS Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 238 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 398 GLN E 340 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083224 restraints weight = 37679.702| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.98 r_work: 0.2857 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 26130 Z= 0.204 Angle : 0.742 9.906 35340 Z= 0.355 Chirality : 0.046 0.244 3972 Planarity : 0.005 0.052 4620 Dihedral : 7.902 107.887 3636 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.51 % Allowed : 16.15 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3240 helix: 0.85 (0.12), residues: 1782 sheet: 0.05 (0.26), residues: 390 loop : 0.33 (0.22), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 349 TYR 0.023 0.002 TYR E 244 PHE 0.012 0.001 PHE A 452 TRP 0.005 0.001 TRP D 476 HIS 0.007 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (26130) covalent geometry : angle 0.74183 / 0.36 (35340) hydrogen bonds : bond 0.04115 / 2.73 ( 1257) hydrogen bonds : angle 4.20644 / 3.02 ( 3585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 341 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.7820 (mmt90) cc_final: 0.7035 (ttt180) REVERT: A 560 ARG cc_start: 0.8696 (ttt180) cc_final: 0.7980 (ttt180) REVERT: A 611 MET cc_start: 0.8193 (mtm) cc_final: 0.7859 (mtm) REVERT: A 663 LYS cc_start: 0.9042 (pttm) cc_final: 0.8579 (tptp) REVERT: A 689 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7827 (pt0) REVERT: A 741 ARG cc_start: 0.6363 (mmt180) cc_final: 0.5995 (tpm170) REVERT: B 359 ARG cc_start: 0.7824 (mmt90) cc_final: 0.7320 (mtp-110) REVERT: B 397 GLU cc_start: 0.8548 (tp30) cc_final: 0.8086 (pm20) REVERT: B 534 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: B 560 ARG cc_start: 0.8733 (ttt180) cc_final: 0.7997 (ttt180) REVERT: C 203 TYR cc_start: 0.9110 (m-10) cc_final: 0.8615 (m-80) REVERT: C 359 ARG cc_start: 0.7557 (mmt90) cc_final: 0.7101 (ttt180) REVERT: C 397 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: C 534 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: C 560 ARG cc_start: 0.8779 (ttt180) cc_final: 0.7898 (tpp-160) REVERT: C 565 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8540 (ttmt) REVERT: C 630 ASP cc_start: 0.8263 (p0) cc_final: 0.8025 (p0) REVERT: C 663 LYS cc_start: 0.9055 (pttm) cc_final: 0.8471 (tptp) REVERT: C 689 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7754 (pt0) REVERT: C 744 ARG cc_start: 0.8299 (ptm-80) cc_final: 0.7426 (tpp-160) REVERT: D 359 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7092 (ttt180) REVERT: D 560 ARG cc_start: 0.8697 (ttt180) cc_final: 0.7965 (ttt180) REVERT: D 663 LYS cc_start: 0.9051 (pttm) cc_final: 0.8586 (tptp) REVERT: D 689 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7821 (pt0) REVERT: D 741 ARG cc_start: 0.6372 (mmt180) cc_final: 0.5997 (tpm170) REVERT: E 359 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7431 (mtp-110) REVERT: E 397 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: E 442 MET cc_start: 0.6789 (mmm) cc_final: 0.6337 (mpm) REVERT: E 534 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: E 560 ARG cc_start: 0.8718 (ttt180) cc_final: 0.7965 (ttt180) REVERT: E 663 LYS cc_start: 0.9015 (pttm) cc_final: 0.8623 (tptp) REVERT: F 203 TYR cc_start: 0.9097 (m-10) cc_final: 0.8561 (m-80) REVERT: F 359 ARG cc_start: 0.7549 (mmt90) cc_final: 0.7072 (ttt180) REVERT: F 397 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: F 449 MET cc_start: 0.8468 (tpt) cc_final: 0.8216 (tpp) REVERT: F 534 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: F 560 ARG cc_start: 0.8781 (ttt180) cc_final: 0.7870 (tpp-160) REVERT: F 565 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8538 (ttmt) REVERT: F 630 ASP cc_start: 0.8290 (p0) cc_final: 0.8076 (p0) REVERT: F 663 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8499 (tptp) REVERT: F 689 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7747 (pt0) REVERT: F 744 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.7385 (tpp-160) REVERT: F 750 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8373 (p0) outliers start: 68 outliers final: 26 residues processed: 392 average time/residue: 0.8328 time to fit residues: 367.6322 Evaluate side-chains 358 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 663 LYS Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 88 optimal weight: 0.5980 chunk 254 optimal weight: 0.7980 chunk 154 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 306 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 232 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085765 restraints weight = 37575.336| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.95 r_work: 0.2869 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26130 Z= 0.146 Angle : 0.737 12.336 35340 Z= 0.349 Chirality : 0.044 0.242 3972 Planarity : 0.005 0.052 4620 Dihedral : 7.635 102.892 3636 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.11 % Allowed : 16.78 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 3240 helix: 0.99 (0.12), residues: 1782 sheet: 0.10 (0.26), residues: 390 loop : 0.37 (0.22), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 349 TYR 0.021 0.002 TYR E 244 PHE 0.011 0.001 PHE A 452 TRP 0.006 0.001 TRP D 454 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (26130) covalent geometry : angle 0.73670 / 0.35 (35340) hydrogen bonds : bond 0.03680 / 2.43 ( 1257) hydrogen bonds : angle 4.14495 / 2.96 ( 3585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8832 (tp) cc_final: 0.8394 (tp) REVERT: A 359 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7049 (ttt180) REVERT: A 560 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7860 (ttt180) REVERT: A 611 MET cc_start: 0.8099 (mtm) cc_final: 0.7748 (mtm) REVERT: A 614 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7702 (mmmt) REVERT: A 663 LYS cc_start: 0.9040 (pttm) cc_final: 0.8555 (tptp) REVERT: A 689 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7860 (pt0) REVERT: A 741 ARG cc_start: 0.6374 (mmt180) cc_final: 0.5972 (tpm170) REVERT: B 359 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7263 (mtp-110) REVERT: B 397 GLU cc_start: 0.8535 (tp30) cc_final: 0.8074 (pm20) REVERT: B 442 MET cc_start: 0.6528 (mmm) cc_final: 0.6037 (mpm) REVERT: B 534 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: B 560 ARG cc_start: 0.8689 (ttt180) cc_final: 0.7888 (ttt180) REVERT: C 203 TYR cc_start: 0.9054 (m-10) cc_final: 0.8696 (m-80) REVERT: C 359 ARG cc_start: 0.7490 (mmt90) cc_final: 0.7016 (ttt180) REVERT: C 397 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: C 442 MET cc_start: 0.6477 (mmm) cc_final: 0.6145 (mpm) REVERT: C 534 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8312 (tp30) REVERT: C 560 ARG cc_start: 0.8728 (ttt180) cc_final: 0.7802 (tpp-160) REVERT: C 630 ASP cc_start: 0.8309 (p0) cc_final: 0.8072 (p0) REVERT: C 663 LYS cc_start: 0.9046 (pttm) cc_final: 0.8451 (tptp) REVERT: C 689 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7700 (pt0) REVERT: C 744 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7399 (tpt170) REVERT: D 244 TYR cc_start: 0.8706 (p90) cc_final: 0.8489 (p90) REVERT: D 359 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7076 (ttt180) REVERT: D 397 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8255 (pm20) REVERT: D 442 MET cc_start: 0.6329 (mmm) cc_final: 0.6021 (mpm) REVERT: D 560 ARG cc_start: 0.8658 (ttt180) cc_final: 0.7880 (ttt180) REVERT: D 614 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7652 (mmmt) REVERT: D 663 LYS cc_start: 0.9049 (pttm) cc_final: 0.8565 (tptp) REVERT: D 689 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7799 (pt0) REVERT: D 741 ARG cc_start: 0.6374 (mmt180) cc_final: 0.5971 (tpm170) REVERT: E 359 ARG cc_start: 0.7794 (mmt90) cc_final: 0.7341 (mtp-110) REVERT: E 397 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7993 (pm20) REVERT: E 534 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: E 560 ARG cc_start: 0.8658 (ttt180) cc_final: 0.7868 (ttt180) REVERT: E 663 LYS cc_start: 0.8987 (pttm) cc_final: 0.8621 (tptp) REVERT: F 203 TYR cc_start: 0.9063 (m-10) cc_final: 0.8639 (m-80) REVERT: F 359 ARG cc_start: 0.7492 (mmt90) cc_final: 0.7013 (ttt180) REVERT: F 397 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: F 442 MET cc_start: 0.6408 (mmm) cc_final: 0.5994 (mpm) REVERT: F 449 MET cc_start: 0.8468 (tpt) cc_final: 0.8241 (tpp) REVERT: F 534 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: F 560 ARG cc_start: 0.8726 (ttt180) cc_final: 0.7805 (tpp-160) REVERT: F 616 ASN cc_start: 0.8711 (t0) cc_final: 0.8375 (t0) REVERT: F 630 ASP cc_start: 0.8350 (p0) cc_final: 0.8104 (p0) REVERT: F 663 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8448 (tptp) REVERT: F 689 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7701 (pt0) REVERT: F 741 ARG cc_start: 0.7521 (tpm170) cc_final: 0.7057 (mmp-170) REVERT: F 744 ARG cc_start: 0.8281 (ptm-80) cc_final: 0.7400 (tpt170) REVERT: F 750 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8367 (p0) outliers start: 57 outliers final: 20 residues processed: 384 average time/residue: 0.8269 time to fit residues: 357.2328 Evaluate side-chains 352 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 534 GLU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 663 LYS Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 311 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 41 optimal weight: 0.0010 chunk 300 optimal weight: 0.0770 chunk 269 optimal weight: 0.6980 chunk 223 optimal weight: 0.1980 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087311 restraints weight = 37627.460| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.99 r_work: 0.2907 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26130 Z= 0.131 Angle : 0.727 12.184 35340 Z= 0.342 Chirality : 0.043 0.231 3972 Planarity : 0.005 0.053 4620 Dihedral : 7.298 95.904 3636 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.63 % Allowed : 17.55 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.15), residues: 3240 helix: 1.12 (0.12), residues: 1782 sheet: 0.09 (0.26), residues: 390 loop : 0.40 (0.22), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 349 TYR 0.019 0.002 TYR B 244 PHE 0.008 0.001 PHE F 758 TRP 0.006 0.001 TRP A 454 HIS 0.004 0.000 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (26130) covalent geometry : angle 0.72660 / 0.34 (35340) hydrogen bonds : bond 0.03413 / 2.25 ( 1257) hydrogen bonds : angle 4.05940 / 2.89 ( 3585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 349 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.7736 (mmt90) cc_final: 0.7019 (ttt180) REVERT: A 442 MET cc_start: 0.6261 (mmm) cc_final: 0.6042 (mpm) REVERT: A 560 ARG cc_start: 0.8580 (ttt180) cc_final: 0.7800 (ttt180) REVERT: A 611 MET cc_start: 0.8067 (mtm) cc_final: 0.7684 (mtm) REVERT: A 663 LYS cc_start: 0.9040 (pttm) cc_final: 0.8569 (tptp) REVERT: B 210 ARG cc_start: 0.8306 (tmm160) cc_final: 0.8099 (tmm-80) REVERT: B 244 TYR cc_start: 0.8525 (p90) cc_final: 0.8105 (p90) REVERT: B 359 ARG cc_start: 0.7632 (mmt90) cc_final: 0.7221 (mtp-110) REVERT: B 397 GLU cc_start: 0.8519 (tp30) cc_final: 0.8060 (pm20) REVERT: B 442 MET cc_start: 0.6534 (mmm) cc_final: 0.5986 (mpm) REVERT: B 560 ARG cc_start: 0.8663 (ttt180) cc_final: 0.7846 (ttt180) REVERT: B 568 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8392 (mt0) REVERT: B 630 ASP cc_start: 0.8122 (p0) cc_final: 0.7867 (p0) REVERT: B 689 GLU cc_start: 0.8423 (tt0) cc_final: 0.7848 (pt0) REVERT: C 203 TYR cc_start: 0.9062 (m-10) cc_final: 0.8783 (m-80) REVERT: C 288 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8596 (mtmm) REVERT: C 359 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6989 (ttt180) REVERT: C 449 MET cc_start: 0.8436 (tpt) cc_final: 0.8164 (tpp) REVERT: C 560 ARG cc_start: 0.8737 (ttt180) cc_final: 0.7806 (tpp-160) REVERT: C 630 ASP cc_start: 0.8212 (p0) cc_final: 0.7997 (p0) REVERT: C 663 LYS cc_start: 0.9041 (pttm) cc_final: 0.8462 (tptp) REVERT: C 689 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7801 (pt0) REVERT: C 744 ARG cc_start: 0.8223 (ptm-80) cc_final: 0.7425 (tpt170) REVERT: D 359 ARG cc_start: 0.7770 (mmt90) cc_final: 0.7067 (ttt180) REVERT: D 397 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: D 560 ARG cc_start: 0.8596 (ttt180) cc_final: 0.7772 (ttt180) REVERT: D 663 LYS cc_start: 0.9064 (pttm) cc_final: 0.8585 (tptp) REVERT: D 678 MET cc_start: 0.9127 (mmp) cc_final: 0.8924 (mmm) REVERT: D 689 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7769 (pt0) REVERT: D 741 ARG cc_start: 0.6362 (mmt180) cc_final: 0.5955 (tpm170) REVERT: E 359 ARG cc_start: 0.7753 (mmt90) cc_final: 0.7375 (mtp-110) REVERT: E 397 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: E 560 ARG cc_start: 0.8691 (ttt180) cc_final: 0.7892 (ttt180) REVERT: E 630 ASP cc_start: 0.8131 (p0) cc_final: 0.7906 (p0) REVERT: E 663 LYS cc_start: 0.8985 (pttm) cc_final: 0.8625 (tptp) REVERT: E 689 GLU cc_start: 0.8434 (tt0) cc_final: 0.7848 (pt0) REVERT: F 203 TYR cc_start: 0.9032 (m-10) cc_final: 0.8684 (m-80) REVERT: F 359 ARG cc_start: 0.7435 (mmt90) cc_final: 0.6969 (ttt180) REVERT: F 397 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: F 449 MET cc_start: 0.8485 (tpt) cc_final: 0.8259 (tpp) REVERT: F 560 ARG cc_start: 0.8743 (ttt180) cc_final: 0.7803 (tpp-160) REVERT: F 580 ASP cc_start: 0.8975 (p0) cc_final: 0.8768 (p0) REVERT: F 630 ASP cc_start: 0.8221 (p0) cc_final: 0.8008 (p0) REVERT: F 663 LYS cc_start: 0.8995 (pttp) cc_final: 0.8454 (tptp) REVERT: F 689 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7800 (pt0) REVERT: F 741 ARG cc_start: 0.7548 (tpm170) cc_final: 0.7100 (mmp-170) REVERT: F 744 ARG cc_start: 0.8234 (ptm-80) cc_final: 0.7408 (tpt170) outliers start: 44 outliers final: 20 residues processed: 377 average time/residue: 0.8409 time to fit residues: 356.5114 Evaluate side-chains 356 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 9 optimal weight: 0.2980 chunk 83 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 174 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 187 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 322 optimal weight: 0.0020 chunk 66 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.2886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 HIS E 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089469 restraints weight = 37485.593| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.96 r_work: 0.2912 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26130 Z= 0.135 Angle : 0.746 10.902 35340 Z= 0.350 Chirality : 0.044 0.233 3972 Planarity : 0.005 0.060 4620 Dihedral : 7.162 91.666 3636 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.96 % Allowed : 18.70 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3240 helix: 1.22 (0.12), residues: 1752 sheet: 0.10 (0.26), residues: 390 loop : 0.31 (0.21), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 349 TYR 0.021 0.002 TYR C 244 PHE 0.006 0.001 PHE C 506 TRP 0.004 0.001 TRP A 454 HIS 0.004 0.000 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (26130) covalent geometry : angle 0.74642 / 0.35 (35340) hydrogen bonds : bond 0.03376 / 2.24 ( 1257) hydrogen bonds : angle 4.02178 / 2.87 ( 3585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 344 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8580 (mm) cc_final: 0.8187 (tp) REVERT: A 359 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7103 (ttt180) REVERT: A 397 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8345 (tm-30) REVERT: A 442 MET cc_start: 0.6311 (mmm) cc_final: 0.6048 (mpm) REVERT: A 560 ARG cc_start: 0.8578 (ttt180) cc_final: 0.7776 (ttt180) REVERT: A 611 MET cc_start: 0.7996 (mtm) cc_final: 0.7637 (mtm) REVERT: A 614 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7672 (mmmt) REVERT: A 663 LYS cc_start: 0.9048 (pttm) cc_final: 0.8574 (tptp) REVERT: B 210 ARG cc_start: 0.8324 (tmm160) cc_final: 0.8120 (tmm-80) REVERT: B 244 TYR cc_start: 0.8519 (p90) cc_final: 0.8175 (p90) REVERT: B 359 ARG cc_start: 0.7668 (mmt90) cc_final: 0.7268 (mtp-110) REVERT: B 397 GLU cc_start: 0.8522 (tp30) cc_final: 0.8078 (pm20) REVERT: B 560 ARG cc_start: 0.8652 (ttt180) cc_final: 0.7886 (ttt180) REVERT: B 568 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8398 (mt0) REVERT: B 630 ASP cc_start: 0.8160 (p0) cc_final: 0.7902 (p0) REVERT: B 689 GLU cc_start: 0.8439 (tt0) cc_final: 0.7895 (pt0) REVERT: C 203 TYR cc_start: 0.9064 (m-10) cc_final: 0.8784 (m-80) REVERT: C 288 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8601 (mtmm) REVERT: C 359 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6990 (ttt180) REVERT: C 442 MET cc_start: 0.6366 (mmm) cc_final: 0.5888 (mpm) REVERT: C 560 ARG cc_start: 0.8722 (ttt180) cc_final: 0.7813 (tpp-160) REVERT: C 630 ASP cc_start: 0.8226 (p0) cc_final: 0.7969 (p0) REVERT: C 663 LYS cc_start: 0.9035 (pttm) cc_final: 0.8466 (tptp) REVERT: C 689 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7821 (pt0) REVERT: C 744 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7436 (tpp-160) REVERT: D 359 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7085 (ttt180) REVERT: D 397 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: D 560 ARG cc_start: 0.8574 (ttt180) cc_final: 0.7773 (ttt180) REVERT: D 663 LYS cc_start: 0.9068 (pttm) cc_final: 0.8592 (tptp) REVERT: D 689 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7743 (pt0) REVERT: D 741 ARG cc_start: 0.6365 (mmt180) cc_final: 0.5951 (tpm170) REVERT: E 210 ARG cc_start: 0.8266 (tmm160) cc_final: 0.8064 (tmm-80) REVERT: E 359 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7365 (mtp-110) REVERT: E 397 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8038 (pm20) REVERT: E 442 MET cc_start: 0.6624 (mmm) cc_final: 0.6209 (mpm) REVERT: E 560 ARG cc_start: 0.8666 (ttt180) cc_final: 0.7867 (ttt180) REVERT: E 630 ASP cc_start: 0.8126 (p0) cc_final: 0.7884 (p0) REVERT: E 663 LYS cc_start: 0.8966 (pttm) cc_final: 0.8616 (tptp) REVERT: E 689 GLU cc_start: 0.8475 (tt0) cc_final: 0.7931 (pt0) REVERT: F 203 TYR cc_start: 0.9052 (m-10) cc_final: 0.8701 (m-80) REVERT: F 359 ARG cc_start: 0.7442 (mmt90) cc_final: 0.6999 (ttt180) REVERT: F 397 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8040 (pm20) REVERT: F 442 MET cc_start: 0.6398 (mmm) cc_final: 0.5854 (mpm) REVERT: F 449 MET cc_start: 0.8500 (tpt) cc_final: 0.8231 (tpp) REVERT: F 560 ARG cc_start: 0.8729 (ttt180) cc_final: 0.7811 (tpp-160) REVERT: F 580 ASP cc_start: 0.8952 (p0) cc_final: 0.8747 (p0) REVERT: F 630 ASP cc_start: 0.8222 (p0) cc_final: 0.7990 (p0) REVERT: F 663 LYS cc_start: 0.9019 (pttp) cc_final: 0.8463 (tptp) REVERT: F 689 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7811 (pt0) REVERT: F 741 ARG cc_start: 0.7585 (tpm170) cc_final: 0.7105 (mmp-170) REVERT: F 744 ARG cc_start: 0.8208 (ptm-80) cc_final: 0.7408 (tpp-160) outliers start: 26 outliers final: 23 residues processed: 361 average time/residue: 0.8583 time to fit residues: 347.3693 Evaluate side-chains 350 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 326 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 584 LYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 271 optimal weight: 0.9990 chunk 252 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 180 optimal weight: 0.0060 chunk 18 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 262 optimal weight: 0.1980 chunk 191 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 HIS E 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086859 restraints weight = 37566.698| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.96 r_work: 0.2907 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26130 Z= 0.138 Angle : 0.746 13.040 35340 Z= 0.349 Chirality : 0.044 0.225 3972 Planarity : 0.005 0.060 4620 Dihedral : 7.107 89.818 3636 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.15 % Allowed : 18.59 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3240 helix: 1.24 (0.12), residues: 1752 sheet: 0.13 (0.26), residues: 390 loop : 0.34 (0.21), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 349 TYR 0.030 0.002 TYR E 244 PHE 0.006 0.001 PHE B 506 TRP 0.004 0.001 TRP D 476 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (26130) covalent geometry : angle 0.74596 / 0.35 (35340) hydrogen bonds : bond 0.03454 / 2.30 ( 1257) hydrogen bonds : angle 4.00366 / 2.86 ( 3585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10585.03 seconds wall clock time: 180 minutes 44.75 seconds (10844.75 seconds total)