Starting phenix.real_space_refine on Sat Jun 6 05:53:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y06_72386/06_2026/9y06_72386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y06_72386/06_2026/9y06_72386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y06_72386/06_2026/9y06_72386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y06_72386/06_2026/9y06_72386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y06_72386/06_2026/9y06_72386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y06_72386/06_2026/9y06_72386.map" } resolution = 2.74 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= -0.001 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 3 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: 6.80, per 1000 atoms: 0.26 Number of scatterers: 25692 At special positions: 0 Unit cell: (137, 145, 94, 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: 2.75 Conformation dependent library (CDL) restraints added in 1.3 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: 182 helices and 12 sheets defined 59.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 211 through 226 removed outlier: 5.177A 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 233 removed outlier: 3.516A 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: 3.816A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.564A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.936A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.675A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.710A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) 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 556 through 569 removed outlier: 4.313A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.688A 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 609 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.638A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.573A 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 742 removed outlier: 3.675A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 211 through 226 removed outlier: 5.096A 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: 3.511A 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: 3.815A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.907A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.642A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.153A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 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 439 through 445 Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.746A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) 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 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.857A 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 611 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.842A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.553A 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 742 removed outlier: 3.599A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 211 through 226 removed outlier: 5.155A 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 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.743A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.531A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.955A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.661A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 335 removed outlier: 3.550A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.032A 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 396 through 403 removed outlier: 3.619A pdb=" N ALA C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.594A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) 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 556 through 569 removed outlier: 4.332A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.737A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.787A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.626A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 211 through 226 removed outlier: 5.138A 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 233 removed outlier: 3.502A 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: 3.808A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.570A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.935A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.688A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.707A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) 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 556 through 569 removed outlier: 4.314A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.688A 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 609 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.638A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.580A 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 742 removed outlier: 3.663A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 211 through 226 removed outlier: 5.121A 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 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.823A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.893A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.634A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.063A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 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 425 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.756A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) 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 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.873A 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 611 Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.512A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.841A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.555A 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 742 removed outlier: 3.602A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 211 through 226 removed outlier: 5.179A 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 233 removed outlier: 3.503A 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 removed outlier: 3.728A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.523A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.960A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 removed outlier: 3.669A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 3.542A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.044A 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 397 through 403 Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.779A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) 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 556 through 569 removed outlier: 4.331A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.851A 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: 3.715A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.790A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.638A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.266A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.687A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.305A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.656A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.230A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.670A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.251A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.679A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.294A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.666A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.242A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.682A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 3.45 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: 8689 1.34 - 1.46: 2610 1.46 - 1.57: 14573 1.57 - 1.69: 36 1.69 - 1.81: 222 Bond restraints: 26130 Sorted by residual: bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.339 1.402 -0.062 3.40e-02 8.65e+02 3.37e+00 bond pdb=" C ASN E 460 " pdb=" N PRO E 461 " ideal model delta sigma weight residual 1.339 1.401 -0.062 3.40e-02 8.65e+02 3.33e+00 bond pdb=" C ASN A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.339 1.401 -0.062 3.40e-02 8.65e+02 3.28e+00 bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.339 1.400 -0.061 3.40e-02 8.65e+02 3.19e+00 bond pdb=" C ASN C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.339 1.398 -0.059 3.40e-02 8.65e+02 2.97e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 34089 1.53 - 3.05: 943 3.05 - 4.58: 231 4.58 - 6.10: 65 6.10 - 7.63: 12 Bond angle restraints: 35340 Sorted by residual: angle pdb=" C LEU C 243 " pdb=" N TYR C 244 " pdb=" CA TYR C 244 " ideal model delta sigma weight residual 122.29 116.78 5.51 1.65e+00 3.67e-01 1.12e+01 angle pdb=" C LEU E 243 " pdb=" N TYR E 244 " pdb=" CA TYR E 244 " ideal model delta sigma weight residual 122.29 117.30 4.99 1.65e+00 3.67e-01 9.13e+00 angle pdb=" C LEU F 243 " pdb=" N TYR F 244 " pdb=" CA TYR F 244 " ideal model delta sigma weight residual 122.62 118.14 4.48 1.56e+00 4.11e-01 8.24e+00 angle pdb=" N LEU E 328 " pdb=" CA LEU E 328 " pdb=" C LEU E 328 " ideal model delta sigma weight residual 113.12 109.72 3.40 1.25e+00 6.40e-01 7.40e+00 angle pdb=" N LEU B 328 " pdb=" CA LEU B 328 " pdb=" C LEU B 328 " ideal model delta sigma weight residual 113.12 109.75 3.37 1.25e+00 6.40e-01 7.25e+00 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 15086 21.67 - 43.34: 894 43.34 - 65.00: 81 65.00 - 86.67: 31 86.67 - 108.34: 6 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 -168.33 108.34 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 -165.85 105.86 1 2.00e+01 2.50e-03 3.06e+01 dihedral pdb=" C5' ADP C 902 " pdb=" O5' ADP C 902 " pdb=" PA ADP C 902 " pdb=" O2A ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 -165.76 105.76 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 16095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2841 0.043 - 0.086: 836 0.086 - 0.130: 279 0.130 - 0.173: 5 0.173 - 0.216: 11 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 B 460 " pdb=" N ASN B 460 " pdb=" C ASN B 460 " pdb=" CB ASN B 460 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+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 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3969 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO C 461 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " -0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO F 461 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 460 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 461 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " 0.031 5.00e-02 4.00e+02 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3814 2.76 - 3.29: 26214 3.29 - 3.83: 43679 3.83 - 4.36: 53342 4.36 - 4.90: 87550 Nonbonded interactions: 214599 Sorted by model distance: nonbonded pdb=" O ASN B 624 " pdb=" OH TYR B 755 " model vdw 2.222 3.040 nonbonded pdb=" O ASN E 624 " pdb=" OH TYR E 755 " model vdw 2.222 3.040 nonbonded pdb=" O ASN F 624 " pdb=" OH TYR F 755 " model vdw 2.242 3.040 nonbonded pdb=" O ASN C 624 " pdb=" OH TYR C 755 " model vdw 2.257 3.040 nonbonded pdb=" O ASN A 624 " pdb=" OH TYR A 755 " model vdw 2.276 3.040 ... (remaining 214594 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.740 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 0.062 26130 Z= 0.145 Angle : 0.672 7.628 35340 Z= 0.340 Chirality : 0.044 0.216 3972 Planarity : 0.005 0.056 4620 Dihedral : 13.250 108.338 10026 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.09 (0.15), residues: 3240 helix: 0.39 (0.13), residues: 1668 sheet: 0.01 (0.26), residues: 390 loop : -0.18 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 322 TYR 0.014 0.002 TYR B 755 PHE 0.013 0.001 PHE A 360 TRP 0.011 0.001 TRP C 476 HIS 0.005 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (26130) covalent geometry : angle 0.67244 / 0.34 (35340) hydrogen bonds : bond 0.14081 / 9.17 ( 1219) hydrogen bonds : angle 5.50222 / 3.99 ( 3444) *********************** 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 502 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 1.034 Fit side-chains REVERT: A 514 VAL cc_start: 0.9229 (t) cc_final: 0.8975 (p) REVERT: A 738 GLU cc_start: 0.8757 (tt0) cc_final: 0.8481 (tp30) REVERT: B 755 TYR cc_start: 0.7865 (m-80) cc_final: 0.7598 (m-80) REVERT: B 756 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8455 (mm-30) REVERT: C 349 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8665 (ttm110) REVERT: C 427 MET cc_start: -0.0544 (tpt) cc_final: -0.0809 (mmt) REVERT: C 738 GLU cc_start: 0.8736 (tt0) cc_final: 0.8161 (tp30) REVERT: C 756 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 470 GLU cc_start: 0.8500 (pt0) cc_final: 0.7810 (pm20) REVERT: D 514 VAL cc_start: 0.9234 (t) cc_final: 0.8986 (p) REVERT: D 663 LYS cc_start: 0.9193 (tptp) cc_final: 0.8471 (tptp) REVERT: D 738 GLU cc_start: 0.8730 (tt0) cc_final: 0.8462 (tp30) REVERT: D 756 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8433 (mm-30) REVERT: E 397 GLU cc_start: 0.8585 (tt0) cc_final: 0.8379 (tm-30) REVERT: E 663 LYS cc_start: 0.9151 (tptp) cc_final: 0.8708 (tptp) REVERT: E 756 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8538 (mm-30) REVERT: F 349 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8672 (ttm110) REVERT: F 427 MET cc_start: -0.0545 (tpt) cc_final: -0.0814 (mmt) REVERT: F 738 GLU cc_start: 0.8769 (tt0) cc_final: 0.8303 (tp30) REVERT: F 756 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8228 (mm-30) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.8800 time to fit residues: 495.2472 Evaluate side-chains 286 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 285 ASN D 616 ASN E 285 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088610 restraints weight = 44671.500| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.38 r_work: 0.3066 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26130 Z= 0.176 Angle : 0.704 8.997 35340 Z= 0.341 Chirality : 0.045 0.194 3972 Planarity : 0.005 0.053 4620 Dihedral : 7.671 105.813 3636 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.77 % Allowed : 7.65 % Favored : 90.58 % 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: 0.68 (0.13), residues: 1692 sheet: -0.08 (0.26), residues: 390 loop : 0.17 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 349 TYR 0.020 0.002 TYR E 203 PHE 0.011 0.001 PHE E 576 TRP 0.007 0.001 TRP D 476 HIS 0.004 0.001 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (26130) covalent geometry : angle 0.70391 / 0.34 (35340) hydrogen bonds : bond 0.04219 / 2.79 ( 1219) hydrogen bonds : angle 4.39615 / 3.17 ( 3444) *********************** 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 362 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 1.149 Fit side-chains REVERT: A 321 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: A 349 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8399 (mtm110) REVERT: A 402 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8240 (tp30) REVERT: A 738 GLU cc_start: 0.8867 (tt0) cc_final: 0.8508 (tp30) REVERT: B 321 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: B 349 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8438 (ttm110) REVERT: B 741 ARG cc_start: 0.8781 (mtp180) cc_final: 0.8459 (mpt180) REVERT: B 756 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8481 (mm-30) REVERT: C 317 HIS cc_start: 0.6943 (t-170) cc_final: 0.6708 (t-170) REVERT: C 349 ARG cc_start: 0.8970 (mtm-85) cc_final: 0.8535 (ttm110) REVERT: C 427 MET cc_start: -0.0254 (tpt) cc_final: -0.0510 (mmt) REVERT: C 449 MET cc_start: 0.8153 (tpt) cc_final: 0.7797 (tpp) REVERT: C 629 ILE cc_start: 0.8848 (tp) cc_final: 0.8596 (pp) REVERT: C 651 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8896 (ttpp) REVERT: C 738 GLU cc_start: 0.8870 (tt0) cc_final: 0.8304 (tp30) REVERT: C 741 ARG cc_start: 0.8772 (mtp180) cc_final: 0.8482 (mmt180) REVERT: C 756 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8339 (mm-30) REVERT: D 349 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8368 (mtm110) REVERT: D 470 GLU cc_start: 0.8512 (pt0) cc_final: 0.7747 (pm20) REVERT: D 663 LYS cc_start: 0.9233 (tptp) cc_final: 0.8535 (tptp) REVERT: D 738 GLU cc_start: 0.8850 (tt0) cc_final: 0.8488 (tp30) REVERT: D 756 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8483 (mm-30) REVERT: E 317 HIS cc_start: 0.7074 (t-170) cc_final: 0.6814 (t-170) REVERT: E 349 ARG cc_start: 0.8749 (ttm110) cc_final: 0.8444 (mtm110) REVERT: E 397 GLU cc_start: 0.8880 (tt0) cc_final: 0.8512 (tm-30) REVERT: E 663 LYS cc_start: 0.9212 (tptp) cc_final: 0.8803 (tptp) REVERT: E 756 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8567 (mm-30) REVERT: F 349 ARG cc_start: 0.8980 (mtm-85) cc_final: 0.8514 (ttm110) REVERT: F 427 MET cc_start: -0.0351 (tpt) cc_final: -0.0583 (mmt) REVERT: F 629 ILE cc_start: 0.8838 (tp) cc_final: 0.8631 (pp) REVERT: F 738 GLU cc_start: 0.8896 (tt0) cc_final: 0.8347 (tp30) REVERT: F 741 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.5992 (mmt180) outliers start: 48 outliers final: 23 residues processed: 347 average time/residue: 0.7567 time to fit residues: 299.8742 Evaluate side-chains 290 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 264 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 741 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 272 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 268 optimal weight: 0.0570 chunk 237 optimal weight: 0.7980 chunk 280 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 chunk 203 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 145 optimal weight: 0.0000 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090169 restraints weight = 44405.023| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.37 r_work: 0.3048 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26130 Z= 0.131 Angle : 0.649 6.664 35340 Z= 0.311 Chirality : 0.043 0.182 3972 Planarity : 0.005 0.058 4620 Dihedral : 7.457 100.334 3636 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.40 % Allowed : 10.72 % Favored : 87.88 % 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: 0.89 (0.13), residues: 1692 sheet: -0.17 (0.26), residues: 372 loop : 0.26 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 349 TYR 0.024 0.002 TYR B 244 PHE 0.015 0.001 PHE E 230 TRP 0.005 0.001 TRP C 476 HIS 0.003 0.000 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (26130) covalent geometry : angle 0.64931 / 0.31 (35340) hydrogen bonds : bond 0.03586 / 2.38 ( 1219) hydrogen bonds : angle 4.17903 / 3.01 ( 3444) *********************** 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 345 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7566 (t-170) cc_final: 0.7161 (t-170) REVERT: A 349 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8107 (mtm-85) REVERT: A 402 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8255 (tp30) REVERT: A 514 VAL cc_start: 0.9179 (t) cc_final: 0.8904 (p) REVERT: A 738 GLU cc_start: 0.8833 (tt0) cc_final: 0.8488 (tp30) REVERT: B 349 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8417 (ttm110) REVERT: B 470 GLU cc_start: 0.7977 (pm20) cc_final: 0.7758 (pm20) REVERT: B 741 ARG cc_start: 0.8792 (mtp180) cc_final: 0.8513 (mpt180) REVERT: B 756 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8427 (mm-30) REVERT: C 317 HIS cc_start: 0.7016 (t-170) cc_final: 0.6755 (t-90) REVERT: C 349 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8514 (ttm110) REVERT: C 366 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8608 (mt-10) REVERT: C 449 MET cc_start: 0.8121 (tpt) cc_final: 0.7906 (tpp) REVERT: C 629 ILE cc_start: 0.8890 (tp) cc_final: 0.8665 (pp) REVERT: C 738 GLU cc_start: 0.8863 (tt0) cc_final: 0.8314 (tp30) REVERT: C 741 ARG cc_start: 0.8785 (mtp180) cc_final: 0.8474 (mmt180) REVERT: C 756 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8327 (mm-30) REVERT: D 349 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8359 (mtm-85) REVERT: D 470 GLU cc_start: 0.8485 (pt0) cc_final: 0.7747 (pm20) REVERT: D 514 VAL cc_start: 0.9189 (t) cc_final: 0.8914 (p) REVERT: D 629 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8406 (tp) REVERT: D 663 LYS cc_start: 0.9216 (tptp) cc_final: 0.8525 (tptp) REVERT: D 738 GLU cc_start: 0.8847 (tt0) cc_final: 0.8482 (tp30) REVERT: D 756 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8500 (mm-30) REVERT: E 317 HIS cc_start: 0.7089 (t-170) cc_final: 0.6813 (t-90) REVERT: E 349 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8455 (mtm110) REVERT: E 397 GLU cc_start: 0.8884 (tt0) cc_final: 0.8556 (tm-30) REVERT: E 470 GLU cc_start: 0.8222 (pm20) cc_final: 0.7886 (pm20) REVERT: E 663 LYS cc_start: 0.9203 (tptp) cc_final: 0.8802 (tptp) REVERT: F 347 THR cc_start: 0.8953 (m) cc_final: 0.8744 (m) REVERT: F 349 ARG cc_start: 0.8926 (mtm-85) cc_final: 0.8515 (ttm110) REVERT: F 426 LYS cc_start: 0.6629 (tptm) cc_final: 0.6321 (tmtt) REVERT: F 629 ILE cc_start: 0.8912 (tp) cc_final: 0.8703 (pp) REVERT: F 738 GLU cc_start: 0.8861 (tt0) cc_final: 0.8325 (tp30) REVERT: F 744 ARG cc_start: 0.8495 (ppt170) cc_final: 0.7463 (ttt180) outliers start: 38 outliers final: 21 residues processed: 334 average time/residue: 0.6875 time to fit residues: 264.5825 Evaluate side-chains 292 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 315 optimal weight: 4.9990 chunk 120 optimal weight: 0.0470 chunk 243 optimal weight: 0.0050 chunk 10 optimal weight: 0.7980 chunk 195 optimal weight: 0.0030 chunk 139 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 616 ASN E 317 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.091093 restraints weight = 44765.757| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.37 r_work: 0.3102 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26130 Z= 0.124 Angle : 0.643 7.716 35340 Z= 0.304 Chirality : 0.043 0.176 3972 Planarity : 0.005 0.062 4620 Dihedral : 7.246 94.050 3636 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.22 % Allowed : 11.79 % Favored : 85.99 % 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: 1.03 (0.13), residues: 1692 sheet: -0.13 (0.26), residues: 366 loop : 0.27 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 349 TYR 0.022 0.002 TYR A 244 PHE 0.015 0.001 PHE C 230 TRP 0.005 0.001 TRP A 476 HIS 0.002 0.000 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (26130) covalent geometry : angle 0.64292 / 0.30 (35340) hydrogen bonds : bond 0.03327 / 2.22 ( 1219) hydrogen bonds : angle 4.05481 / 2.92 ( 3444) *********************** 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 358 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7589 (t-170) cc_final: 0.7148 (t-170) REVERT: A 349 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8084 (mtm-85) REVERT: A 402 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8208 (tp30) REVERT: A 514 VAL cc_start: 0.9164 (t) cc_final: 0.8887 (p) REVERT: A 738 GLU cc_start: 0.8856 (tt0) cc_final: 0.8499 (tp30) REVERT: B 321 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: B 349 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8431 (ttm110) REVERT: B 470 GLU cc_start: 0.8058 (pm20) cc_final: 0.7764 (pm20) REVERT: B 741 ARG cc_start: 0.8801 (mtp180) cc_final: 0.8503 (mmt180) REVERT: B 756 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C 317 HIS cc_start: 0.7122 (t-170) cc_final: 0.6860 (t-170) REVERT: C 349 ARG cc_start: 0.8899 (mtm-85) cc_final: 0.8492 (ttm110) REVERT: C 629 ILE cc_start: 0.8888 (tp) cc_final: 0.8681 (pp) REVERT: C 630 ASP cc_start: 0.8273 (p0) cc_final: 0.8017 (p0) REVERT: C 738 GLU cc_start: 0.8856 (tt0) cc_final: 0.8317 (tp30) REVERT: C 741 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8432 (mpt180) REVERT: C 744 ARG cc_start: 0.8445 (ppt170) cc_final: 0.7527 (ttt90) REVERT: C 756 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8341 (mm-30) REVERT: D 470 GLU cc_start: 0.8459 (pt0) cc_final: 0.7722 (pm20) REVERT: D 514 VAL cc_start: 0.9174 (t) cc_final: 0.8930 (p) REVERT: D 629 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8452 (tp) REVERT: D 663 LYS cc_start: 0.9236 (tptp) cc_final: 0.8570 (tptp) REVERT: D 738 GLU cc_start: 0.8851 (tt0) cc_final: 0.8445 (tp30) REVERT: D 756 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8503 (mm-30) REVERT: E 349 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8563 (ttm110) REVERT: E 397 GLU cc_start: 0.8891 (tt0) cc_final: 0.8547 (tm-30) REVERT: E 470 GLU cc_start: 0.8176 (pm20) cc_final: 0.7852 (pm20) REVERT: E 663 LYS cc_start: 0.9191 (tptp) cc_final: 0.8980 (tmtm) REVERT: F 349 ARG cc_start: 0.8919 (mtm-85) cc_final: 0.8517 (ttm110) REVERT: F 426 LYS cc_start: 0.6739 (tptm) cc_final: 0.6443 (ttpt) REVERT: F 630 ASP cc_start: 0.8216 (p0) cc_final: 0.7955 (p0) REVERT: F 738 GLU cc_start: 0.8858 (tt0) cc_final: 0.8324 (tp30) REVERT: F 744 ARG cc_start: 0.8412 (ppt170) cc_final: 0.7438 (ttt90) outliers start: 60 outliers final: 26 residues processed: 340 average time/residue: 0.6304 time to fit residues: 249.8187 Evaluate side-chains 297 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 118 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 290 optimal weight: 0.0370 chunk 294 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088373 restraints weight = 44761.262| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.36 r_work: 0.3068 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26130 Z= 0.144 Angle : 0.646 8.367 35340 Z= 0.307 Chirality : 0.043 0.170 3972 Planarity : 0.005 0.065 4620 Dihedral : 7.207 90.976 3636 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.29 % Allowed : 13.05 % Favored : 84.66 % 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: 1.09 (0.13), residues: 1698 sheet: -0.13 (0.26), residues: 372 loop : 0.35 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 349 TYR 0.022 0.002 TYR B 244 PHE 0.010 0.001 PHE C 230 TRP 0.007 0.001 TRP D 476 HIS 0.002 0.000 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (26130) covalent geometry : angle 0.64572 / 0.31 (35340) hydrogen bonds : bond 0.03371 / 2.25 ( 1219) hydrogen bonds : angle 4.01678 / 2.89 ( 3444) *********************** 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 351 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7591 (t-170) cc_final: 0.7104 (t-170) REVERT: A 349 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8123 (mtm-85) REVERT: A 389 LYS cc_start: 0.9124 (tptt) cc_final: 0.8853 (tptt) REVERT: A 402 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8203 (tp30) REVERT: A 514 VAL cc_start: 0.9210 (t) cc_final: 0.8932 (p) REVERT: A 738 GLU cc_start: 0.8860 (tt0) cc_final: 0.8475 (tp30) REVERT: B 321 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: B 470 GLU cc_start: 0.8144 (pm20) cc_final: 0.7812 (pm20) REVERT: C 317 HIS cc_start: 0.7159 (t-170) cc_final: 0.6846 (t-170) REVERT: C 349 ARG cc_start: 0.8866 (mtm-85) cc_final: 0.8446 (ttm110) REVERT: C 630 ASP cc_start: 0.8357 (p0) cc_final: 0.8094 (p0) REVERT: C 738 GLU cc_start: 0.8864 (tt0) cc_final: 0.8335 (tp30) REVERT: C 741 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8426 (mpt180) REVERT: C 744 ARG cc_start: 0.8406 (ppt170) cc_final: 0.7548 (ttt90) REVERT: C 756 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8323 (mm-30) REVERT: D 349 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8362 (mtm110) REVERT: D 423 ILE cc_start: 0.8067 (mt) cc_final: 0.7773 (mp) REVERT: D 470 GLU cc_start: 0.8514 (pt0) cc_final: 0.7764 (pm20) REVERT: D 514 VAL cc_start: 0.9215 (t) cc_final: 0.8944 (p) REVERT: D 663 LYS cc_start: 0.9244 (tptp) cc_final: 0.8582 (tptp) REVERT: D 738 GLU cc_start: 0.8831 (tt0) cc_final: 0.8450 (tp30) REVERT: D 756 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8508 (mm-30) REVERT: E 236 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6478 (tmtm) REVERT: E 317 HIS cc_start: 0.7329 (t-170) cc_final: 0.6833 (t-170) REVERT: E 349 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8560 (ttm110) REVERT: E 397 GLU cc_start: 0.8909 (tt0) cc_final: 0.8538 (tm-30) REVERT: E 470 GLU cc_start: 0.8237 (pm20) cc_final: 0.7914 (pm20) REVERT: F 349 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8497 (ttm110) REVERT: F 426 LYS cc_start: 0.6795 (tptm) cc_final: 0.6451 (tmtt) REVERT: F 738 GLU cc_start: 0.8883 (tt0) cc_final: 0.8359 (tp30) REVERT: F 744 ARG cc_start: 0.8456 (ppt170) cc_final: 0.7497 (ttt90) outliers start: 62 outliers final: 25 residues processed: 332 average time/residue: 0.6401 time to fit residues: 248.8178 Evaluate side-chains 298 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL 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: 5.9990 chunk 260 optimal weight: 1.9990 chunk 310 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.088377 restraints weight = 45018.879| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.38 r_work: 0.3057 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26130 Z= 0.143 Angle : 0.648 9.088 35340 Z= 0.306 Chirality : 0.043 0.168 3972 Planarity : 0.005 0.066 4620 Dihedral : 7.161 90.015 3636 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.44 % Allowed : 13.53 % Favored : 84.04 % 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: 0.97 (0.15), residues: 3240 helix: 1.14 (0.13), residues: 1710 sheet: -0.10 (0.26), residues: 372 loop : 0.36 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.024 0.002 TYR D 244 PHE 0.010 0.001 PHE C 230 TRP 0.006 0.001 TRP A 476 HIS 0.002 0.000 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (26130) covalent geometry : angle 0.64750 / 0.31 (35340) hydrogen bonds : bond 0.03326 / 2.22 ( 1219) hydrogen bonds : angle 3.97288 / 2.85 ( 3444) *********************** 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 355 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7605 (t-170) cc_final: 0.7076 (t-170) REVERT: A 349 ARG cc_start: 0.8613 (ttm110) cc_final: 0.8350 (ttm110) REVERT: A 389 LYS cc_start: 0.9105 (tptt) cc_final: 0.8858 (tptt) REVERT: A 402 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8233 (tp30) REVERT: A 514 VAL cc_start: 0.9212 (t) cc_final: 0.8925 (p) REVERT: B 321 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: B 470 GLU cc_start: 0.8146 (pm20) cc_final: 0.7789 (pm20) REVERT: B 756 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8454 (mm-30) REVERT: C 317 HIS cc_start: 0.7177 (t-170) cc_final: 0.6805 (t-170) REVERT: C 349 ARG cc_start: 0.8870 (mtm-85) cc_final: 0.8426 (ttm110) REVERT: C 738 GLU cc_start: 0.8884 (tt0) cc_final: 0.8346 (tp30) REVERT: C 741 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8440 (mmt180) REVERT: C 744 ARG cc_start: 0.8411 (ppt170) cc_final: 0.7533 (ttt90) REVERT: C 756 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8338 (mm-30) REVERT: D 349 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8314 (mtm-85) REVERT: D 389 LYS cc_start: 0.9130 (tptt) cc_final: 0.8853 (tptt) REVERT: D 423 ILE cc_start: 0.8152 (mt) cc_final: 0.7847 (mp) REVERT: D 470 GLU cc_start: 0.8523 (pt0) cc_final: 0.7765 (pm20) REVERT: D 514 VAL cc_start: 0.9205 (t) cc_final: 0.8919 (p) REVERT: D 663 LYS cc_start: 0.9252 (tptp) cc_final: 0.8587 (tptp) REVERT: D 756 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8528 (mm-30) REVERT: E 317 HIS cc_start: 0.7266 (t-170) cc_final: 0.6677 (t-170) REVERT: E 349 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8581 (ttm110) REVERT: E 397 GLU cc_start: 0.8922 (tt0) cc_final: 0.8544 (tm-30) REVERT: E 470 GLU cc_start: 0.8240 (pm20) cc_final: 0.7906 (pm20) REVERT: E 663 LYS cc_start: 0.9208 (tptp) cc_final: 0.9003 (tmtm) REVERT: F 349 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8460 (ttm110) REVERT: F 426 LYS cc_start: 0.6810 (tptm) cc_final: 0.6505 (tmtt) REVERT: F 738 GLU cc_start: 0.8902 (tt0) cc_final: 0.8393 (tp30) REVERT: F 744 ARG cc_start: 0.8449 (ppt170) cc_final: 0.7328 (ttt90) outliers start: 66 outliers final: 25 residues processed: 329 average time/residue: 0.6406 time to fit residues: 245.7689 Evaluate side-chains 300 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 238 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN E 317 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087201 restraints weight = 44970.642| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.36 r_work: 0.3048 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26130 Z= 0.150 Angle : 0.657 9.737 35340 Z= 0.311 Chirality : 0.043 0.163 3972 Planarity : 0.005 0.068 4620 Dihedral : 7.164 89.735 3636 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.11 % Allowed : 14.78 % Favored : 83.11 % 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: 1.01 (0.15), residues: 3240 helix: 1.17 (0.13), residues: 1710 sheet: 0.01 (0.26), residues: 366 loop : 0.35 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 349 TYR 0.022 0.002 TYR B 244 PHE 0.010 0.001 PHE E 576 TRP 0.007 0.001 TRP A 476 HIS 0.002 0.000 HIS E 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (26130) covalent geometry : angle 0.65690 / 0.31 (35340) hydrogen bonds : bond 0.03330 / 2.23 ( 1219) hydrogen bonds : angle 3.96935 / 2.85 ( 3444) *********************** 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 339 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7609 (t-170) cc_final: 0.7113 (t-170) REVERT: A 349 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8366 (ttm110) REVERT: A 389 LYS cc_start: 0.9100 (tptt) cc_final: 0.8840 (tptt) REVERT: A 402 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8211 (tp30) REVERT: A 423 ILE cc_start: 0.8193 (mt) cc_final: 0.7915 (mp) REVERT: A 514 VAL cc_start: 0.9201 (t) cc_final: 0.8911 (p) REVERT: A 663 LYS cc_start: 0.9334 (tppt) cc_final: 0.9109 (tmtm) REVERT: B 321 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: B 470 GLU cc_start: 0.8191 (pm20) cc_final: 0.7786 (pm20) REVERT: B 756 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8489 (mm-30) REVERT: C 317 HIS cc_start: 0.7215 (t-170) cc_final: 0.6852 (t-170) REVERT: C 349 ARG cc_start: 0.8844 (mtm-85) cc_final: 0.8605 (mtm-85) REVERT: C 738 GLU cc_start: 0.8892 (tt0) cc_final: 0.8369 (tp30) REVERT: C 741 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8450 (mmt180) REVERT: C 744 ARG cc_start: 0.8424 (ppt170) cc_final: 0.7574 (ttt90) REVERT: C 756 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8376 (mm-30) REVERT: D 349 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8271 (mtm-85) REVERT: D 389 LYS cc_start: 0.9140 (tptt) cc_final: 0.8897 (tptt) REVERT: D 423 ILE cc_start: 0.8168 (mt) cc_final: 0.7838 (mp) REVERT: D 470 GLU cc_start: 0.8527 (pt0) cc_final: 0.7762 (pm20) REVERT: D 514 VAL cc_start: 0.9217 (t) cc_final: 0.8928 (p) REVERT: D 663 LYS cc_start: 0.9258 (tptp) cc_final: 0.8599 (tptp) REVERT: D 756 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8511 (mm-30) REVERT: E 317 HIS cc_start: 0.7401 (t70) cc_final: 0.7061 (t-170) REVERT: E 349 ARG cc_start: 0.8825 (ttm110) cc_final: 0.8548 (ttm110) REVERT: E 397 GLU cc_start: 0.8911 (tt0) cc_final: 0.8557 (tm-30) REVERT: E 470 GLU cc_start: 0.8230 (pm20) cc_final: 0.7897 (pm20) REVERT: E 663 LYS cc_start: 0.9218 (tptp) cc_final: 0.9018 (tmtm) REVERT: F 349 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8472 (ttm110) REVERT: F 426 LYS cc_start: 0.7018 (tptm) cc_final: 0.6782 (tmtt) REVERT: F 738 GLU cc_start: 0.8910 (tt0) cc_final: 0.8402 (tp30) REVERT: F 744 ARG cc_start: 0.8544 (ppt170) cc_final: 0.7472 (ttt90) outliers start: 57 outliers final: 29 residues processed: 319 average time/residue: 0.6515 time to fit residues: 241.8759 Evaluate side-chains 299 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 88 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 306 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 232 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 624 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088329 restraints weight = 45027.253| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.37 r_work: 0.3060 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26130 Z= 0.132 Angle : 0.657 10.773 35340 Z= 0.309 Chirality : 0.043 0.162 3972 Planarity : 0.005 0.069 4620 Dihedral : 7.095 88.035 3636 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.96 % Allowed : 15.15 % Favored : 82.89 % 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: 1.19 (0.13), residues: 1716 sheet: -0.05 (0.26), residues: 366 loop : 0.36 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 349 TYR 0.022 0.002 TYR D 244 PHE 0.009 0.001 PHE E 576 TRP 0.006 0.001 TRP C 476 HIS 0.003 0.000 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (26130) covalent geometry : angle 0.65714 / 0.31 (35340) hydrogen bonds : bond 0.03223 / 2.16 ( 1219) hydrogen bonds : angle 3.91856 / 2.82 ( 3444) *********************** 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 337 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7576 (t-170) cc_final: 0.7049 (t-170) REVERT: A 349 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8326 (ttm110) REVERT: A 389 LYS cc_start: 0.9107 (tptt) cc_final: 0.8866 (tptt) REVERT: A 397 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 402 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8232 (tp30) REVERT: A 423 ILE cc_start: 0.8242 (mt) cc_final: 0.7953 (mp) REVERT: A 514 VAL cc_start: 0.9209 (t) cc_final: 0.8924 (p) REVERT: A 663 LYS cc_start: 0.9318 (tppt) cc_final: 0.9095 (tmtm) REVERT: B 321 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: B 470 GLU cc_start: 0.8224 (pm20) cc_final: 0.7892 (pm20) REVERT: B 663 LYS cc_start: 0.9163 (tmtm) cc_final: 0.8921 (tmtm) REVERT: B 756 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8503 (mm-30) REVERT: C 317 HIS cc_start: 0.7203 (t-170) cc_final: 0.6779 (t-170) REVERT: C 349 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8599 (mtm-85) REVERT: C 614 LYS cc_start: 0.8549 (tppt) cc_final: 0.8293 (tppt) REVERT: C 738 GLU cc_start: 0.8894 (tt0) cc_final: 0.8376 (tp30) REVERT: C 741 ARG cc_start: 0.8760 (mtp180) cc_final: 0.8449 (mmt180) REVERT: C 744 ARG cc_start: 0.8419 (ppt170) cc_final: 0.7563 (ttt90) REVERT: C 756 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8352 (mm-30) REVERT: D 349 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8342 (mtm110) REVERT: D 389 LYS cc_start: 0.9118 (tptt) cc_final: 0.8879 (tptt) REVERT: D 397 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 423 ILE cc_start: 0.8187 (mt) cc_final: 0.7852 (mp) REVERT: D 470 GLU cc_start: 0.8518 (pt0) cc_final: 0.7769 (pm20) REVERT: D 514 VAL cc_start: 0.9220 (t) cc_final: 0.8942 (p) REVERT: D 663 LYS cc_start: 0.9247 (tptp) cc_final: 0.8588 (tptp) REVERT: D 756 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8515 (mm-30) REVERT: E 317 HIS cc_start: 0.7375 (t70) cc_final: 0.7003 (t-170) REVERT: E 349 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8538 (ttm110) REVERT: E 397 GLU cc_start: 0.8922 (tt0) cc_final: 0.8553 (tm-30) REVERT: E 470 GLU cc_start: 0.8245 (pm20) cc_final: 0.7923 (pm20) REVERT: F 349 ARG cc_start: 0.8873 (mtm-85) cc_final: 0.8630 (mtm-85) REVERT: F 738 GLU cc_start: 0.8906 (tt0) cc_final: 0.8395 (tp30) REVERT: F 744 ARG cc_start: 0.8565 (ppt170) cc_final: 0.7556 (ttt90) outliers start: 53 outliers final: 29 residues processed: 317 average time/residue: 0.6866 time to fit residues: 251.2628 Evaluate side-chains 293 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 0.0470 chunk 249 optimal weight: 0.9980 chunk 311 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 624 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.119184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087327 restraints weight = 44969.372| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.37 r_work: 0.3062 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26130 Z= 0.144 Angle : 0.671 11.411 35340 Z= 0.315 Chirality : 0.043 0.180 3972 Planarity : 0.005 0.070 4620 Dihedral : 7.092 87.623 3636 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.81 % Allowed : 16.04 % Favored : 82.15 % 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: 1.05 (0.15), residues: 3240 helix: 1.20 (0.13), residues: 1716 sheet: -0.04 (0.27), residues: 366 loop : 0.38 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 349 TYR 0.023 0.002 TYR B 244 PHE 0.010 0.001 PHE E 576 TRP 0.007 0.001 TRP C 476 HIS 0.002 0.000 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (26130) covalent geometry : angle 0.67098 / 0.32 (35340) hydrogen bonds : bond 0.03258 / 2.18 ( 1219) hydrogen bonds : angle 3.91618 / 2.82 ( 3444) *********************** 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 322 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7581 (t-170) cc_final: 0.7046 (t-170) REVERT: A 349 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8362 (ttm110) REVERT: A 389 LYS cc_start: 0.9103 (tptt) cc_final: 0.8869 (tptt) REVERT: A 397 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 402 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8239 (tp30) REVERT: A 423 ILE cc_start: 0.8229 (mt) cc_final: 0.7946 (mp) REVERT: A 514 VAL cc_start: 0.9206 (t) cc_final: 0.8903 (p) REVERT: A 663 LYS cc_start: 0.9317 (tppt) cc_final: 0.9087 (tmtm) REVERT: B 470 GLU cc_start: 0.8227 (pm20) cc_final: 0.7887 (pm20) REVERT: B 663 LYS cc_start: 0.9190 (tmtm) cc_final: 0.8943 (tmtm) REVERT: B 756 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8500 (mm-30) REVERT: C 317 HIS cc_start: 0.7205 (t-170) cc_final: 0.6745 (t-170) REVERT: C 349 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8578 (mtm-85) REVERT: C 609 ASP cc_start: 0.8067 (p0) cc_final: 0.7849 (p0) REVERT: C 738 GLU cc_start: 0.8899 (tt0) cc_final: 0.8376 (tp30) REVERT: C 741 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8451 (mmt180) REVERT: C 744 ARG cc_start: 0.8462 (ppt170) cc_final: 0.7552 (ttt90) REVERT: C 756 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8354 (mm-30) REVERT: D 349 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8278 (mtm-85) REVERT: D 389 LYS cc_start: 0.9115 (tptt) cc_final: 0.8887 (tptt) REVERT: D 397 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7754 (tm-30) REVERT: D 423 ILE cc_start: 0.8165 (mt) cc_final: 0.7844 (mp) REVERT: D 470 GLU cc_start: 0.8539 (pt0) cc_final: 0.7764 (pm20) REVERT: D 514 VAL cc_start: 0.9241 (t) cc_final: 0.8951 (p) REVERT: D 663 LYS cc_start: 0.9246 (tptp) cc_final: 0.8580 (tptp) REVERT: D 756 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8552 (mm-30) REVERT: E 317 HIS cc_start: 0.7480 (t70) cc_final: 0.7142 (t-170) REVERT: E 349 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8531 (ttm110) REVERT: E 397 GLU cc_start: 0.8936 (tt0) cc_final: 0.8534 (tm-30) REVERT: E 470 GLU cc_start: 0.8246 (pm20) cc_final: 0.7895 (pm20) REVERT: F 349 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8624 (mtm-85) REVERT: F 738 GLU cc_start: 0.8920 (tt0) cc_final: 0.8426 (tp30) REVERT: F 744 ARG cc_start: 0.8551 (ppt170) cc_final: 0.7432 (ttt90) outliers start: 49 outliers final: 30 residues processed: 306 average time/residue: 0.6804 time to fit residues: 241.2356 Evaluate side-chains 295 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 322 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 624 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086364 restraints weight = 44885.457| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.35 r_work: 0.3026 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.004 0.051 26130 Z= 0.178 Angle : 0.697 12.052 35340 Z= 0.329 Chirality : 0.044 0.194 3972 Planarity : 0.005 0.069 4620 Dihedral : 7.219 90.107 3636 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.52 % Allowed : 16.44 % Favored : 82.04 % 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: 1.06 (0.15), residues: 3240 helix: 1.15 (0.13), residues: 1722 sheet: 0.01 (0.27), residues: 366 loop : 0.48 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 349 TYR 0.024 0.002 TYR D 244 PHE 0.010 0.001 PHE E 576 TRP 0.009 0.001 TRP A 476 HIS 0.002 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (26130) covalent geometry : angle 0.69666 / 0.33 (35340) hydrogen bonds : bond 0.03473 / 2.33 ( 1219) hydrogen bonds : angle 3.99095 / 2.87 ( 3444) ********************** 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 308 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7517 (t-170) cc_final: 0.7049 (t-170) REVERT: A 349 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8433 (ttm110) REVERT: A 389 LYS cc_start: 0.9111 (tptt) cc_final: 0.8890 (tptt) REVERT: A 402 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8292 (tp30) REVERT: A 423 ILE cc_start: 0.8309 (mt) cc_final: 0.8030 (mp) REVERT: A 663 LYS cc_start: 0.9352 (tppt) cc_final: 0.9081 (mmtm) REVERT: B 470 GLU cc_start: 0.8209 (pm20) cc_final: 0.7859 (pm20) REVERT: B 663 LYS cc_start: 0.9196 (tmtm) cc_final: 0.8924 (tmtm) REVERT: B 756 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8626 (mm-30) REVERT: C 317 HIS cc_start: 0.7164 (t-170) cc_final: 0.6689 (t-170) REVERT: C 349 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8583 (mtm-85) REVERT: C 738 GLU cc_start: 0.8911 (tt0) cc_final: 0.8337 (tp30) REVERT: C 744 ARG cc_start: 0.8457 (ppt170) cc_final: 0.7522 (ttt90) REVERT: C 756 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8388 (mm-30) REVERT: D 349 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8254 (mtm-85) REVERT: D 389 LYS cc_start: 0.9151 (tptt) cc_final: 0.8945 (tptm) REVERT: D 423 ILE cc_start: 0.8240 (mt) cc_final: 0.7889 (mp) REVERT: D 470 GLU cc_start: 0.8560 (pt0) cc_final: 0.7770 (pm20) REVERT: D 663 LYS cc_start: 0.9253 (tptp) cc_final: 0.8581 (tptp) REVERT: D 756 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 317 HIS cc_start: 0.7504 (t70) cc_final: 0.7170 (t-170) REVERT: E 349 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8530 (ttm110) REVERT: E 397 GLU cc_start: 0.8969 (tt0) cc_final: 0.8565 (tm-30) REVERT: E 470 GLU cc_start: 0.8218 (pm20) cc_final: 0.7879 (pm20) REVERT: F 349 ARG cc_start: 0.8881 (mtm-85) cc_final: 0.8635 (mtm-85) REVERT: F 738 GLU cc_start: 0.8946 (tt0) cc_final: 0.8440 (tp30) REVERT: F 744 ARG cc_start: 0.8565 (ppt170) cc_final: 0.7490 (ttt180) outliers start: 41 outliers final: 28 residues processed: 293 average time/residue: 0.6818 time to fit residues: 230.9745 Evaluate side-chains 287 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 271 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 262 optimal weight: 0.7980 chunk 191 optimal weight: 0.0570 chunk 283 optimal weight: 0.5980 chunk 317 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 624 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.118880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087141 restraints weight = 44950.204| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.36 r_work: 0.3056 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26130 Z= 0.138 Angle : 0.683 11.893 35340 Z= 0.322 Chirality : 0.043 0.180 3972 Planarity : 0.005 0.068 4620 Dihedral : 7.160 89.354 3636 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.29 % Allowed : 16.81 % Favored : 81.89 % 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: 1.18 (0.13), residues: 1722 sheet: -0.08 (0.27), residues: 366 loop : 0.40 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 349 TYR 0.023 0.002 TYR B 244 PHE 0.008 0.001 PHE E 576 TRP 0.007 0.001 TRP C 476 HIS 0.002 0.000 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (26130) covalent geometry : angle 0.68348 / 0.32 (35340) hydrogen bonds : bond 0.03277 / 2.19 ( 1219) hydrogen bonds : angle 3.95585 / 2.85 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8565.31 seconds wall clock time: 146 minutes 51.43 seconds (8811.43 seconds total)