Starting phenix.real_space_refine on Thu Mar 5 18:56:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5z_20659/03_2026/6u5z_20659.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5z_20659/03_2026/6u5z_20659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5z_20659/03_2026/6u5z_20659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5z_20659/03_2026/6u5z_20659.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5z_20659/03_2026/6u5z_20659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5z_20659/03_2026/6u5z_20659.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 15462 2.51 5 N 4380 2.21 5 O 4638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24606 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "B" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "C" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "D" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "E" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "F" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Time building chain proxies: 5.42, per 1000 atoms: 0.22 Number of scatterers: 24606 At special positions: 0 Unit cell: (143.312, 133.136, 166.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4638 8.00 N 4380 7.00 C 15462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 691 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 691 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 691 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 691 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 691 " distance=2.04 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 691 " distance=2.04 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 30 sheets defined 48.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE A 452 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 680 through 694 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG A 742 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 745 " --> pdb=" O ARG A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.734A pdb=" N GLU B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 Processing helix chain 'B' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 413 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE B 452 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.061A pdb=" N ASP B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 694 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG B 742 " --> pdb=" O GLU B 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE B 752 " --> pdb=" O PRO B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 321 Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 374 Processing helix chain 'C' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 436 through 445 Processing helix chain 'C' and resid 448 through 452 removed outlier: 3.533A pdb=" N PHE C 452 " --> pdb=" O ASN C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 561 Processing helix chain 'C' and resid 575 through 580 Processing helix chain 'C' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU C 650 " --> pdb=" O ARG C 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 Processing helix chain 'C' and resid 680 through 694 Processing helix chain 'C' and resid 718 through 729 Processing helix chain 'C' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG C 742 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 745 " --> pdb=" O ARG C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 287 through 301 removed outlier: 3.558A pdb=" N VAL D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG D 333 " --> pdb=" O ARG D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 374 Processing helix chain 'D' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 413 Processing helix chain 'D' and resid 436 through 445 Processing helix chain 'D' and resid 448 through 452 removed outlier: 3.533A pdb=" N PHE D 452 " --> pdb=" O ASN D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.761A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 561 Processing helix chain 'D' and resid 575 through 580 Processing helix chain 'D' and resid 631 through 653 removed outlier: 5.275A pdb=" N GLU D 650 " --> pdb=" O ARG D 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 680 through 694 Processing helix chain 'D' and resid 718 through 729 Processing helix chain 'D' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG D 742 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE D 752 " --> pdb=" O PRO D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL D 766 " --> pdb=" O ARG D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 374 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.262A pdb=" N ILE E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 436 through 445 Processing helix chain 'E' and resid 448 through 452 removed outlier: 3.531A pdb=" N PHE E 452 " --> pdb=" O ASN E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.061A pdb=" N ASP E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 561 Processing helix chain 'E' and resid 575 through 580 Processing helix chain 'E' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS E 651 " --> pdb=" O ALA E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 661 Processing helix chain 'E' and resid 680 through 694 Processing helix chain 'E' and resid 718 through 729 Processing helix chain 'E' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG E 742 " --> pdb=" O GLU E 739 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 745 " --> pdb=" O ARG E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE E 752 " --> pdb=" O PRO E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.734A pdb=" N GLU F 252 " --> pdb=" O PRO F 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.970A pdb=" N ARG F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 374 Processing helix chain 'F' and resid 387 through 392 removed outlier: 4.262A pdb=" N ILE F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 413 Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'F' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE F 452 " --> pdb=" O ASN F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 514 Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.761A pdb=" N ILE F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 561 Processing helix chain 'F' and resid 575 through 580 Processing helix chain 'F' and resid 631 through 653 removed outlier: 5.275A pdb=" N GLU F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS F 651 " --> pdb=" O ALA F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 694 Processing helix chain 'F' and resid 718 through 729 Processing helix chain 'F' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG F 742 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 745 " --> pdb=" O ARG F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE F 752 " --> pdb=" O PRO F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 771 removed outlier: 3.592A pdb=" N VAL F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP A 423 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 380 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR A 625 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA A 702 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 734 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 760 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 736 " --> pdb=" O VAL A 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU A 706 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 377 through 381 removed outlier: 7.362A pdb=" N VAL B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 380 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 523 removed outlier: 6.611A pdb=" N THR B 522 " --> pdb=" O ILE B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR B 625 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.650A pdb=" N ALA B 702 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 734 " --> pdb=" O HIS B 758 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 760 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 736 " --> pdb=" O VAL B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU B 706 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL C 378 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP C 423 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET C 380 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 521 through 523 Processing sheet with id=AB4, first strand: chain 'C' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR C 625 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA C 702 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 734 " --> pdb=" O HIS C 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 760 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 736 " --> pdb=" O VAL C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU C 706 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL D 378 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP D 423 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET D 380 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 521 through 523 Processing sheet with id=AB9, first strand: chain 'D' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR D 625 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA D 702 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 734 " --> pdb=" O HIS D 758 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL D 760 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE D 736 " --> pdb=" O VAL D 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU D 706 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP E 423 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET E 380 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 521 through 523 Processing sheet with id=AC5, first strand: chain 'E' and resid 597 through 602 removed outlier: 6.558A pdb=" N THR E 625 " --> pdb=" O VAL E 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 701 through 703 removed outlier: 6.650A pdb=" N ALA E 702 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 734 " --> pdb=" O HIS E 758 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL E 760 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 736 " --> pdb=" O VAL E 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU E 706 " --> pdb=" O LEU E 714 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 377 through 381 removed outlier: 7.362A pdb=" N VAL F 378 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP F 423 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET F 380 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 521 through 523 Processing sheet with id=AD1, first strand: chain 'F' and resid 597 through 602 removed outlier: 6.558A pdb=" N THR F 625 " --> pdb=" O VAL F 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA F 702 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL F 734 " --> pdb=" O HIS F 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL F 760 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE F 736 " --> pdb=" O VAL F 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU F 706 " --> pdb=" O LEU F 714 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3036 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8376 1.35 - 1.47: 4717 1.47 - 1.59: 11651 1.59 - 1.71: 0 1.71 - 1.83: 222 Bond restraints: 24966 Sorted by residual: bond pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.17e+00 bond pdb=" N ASP D 585 " pdb=" CA ASP D 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N ASP B 585 " pdb=" CA ASP B 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N ASP F 585 " pdb=" CA ASP F 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N LYS B 416 " pdb=" CA LYS B 416 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.86e+00 ... (remaining 24961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 32280 1.16 - 2.32: 1120 2.32 - 3.47: 205 3.47 - 4.63: 34 4.63 - 5.79: 45 Bond angle restraints: 33684 Sorted by residual: angle pdb=" C GLY D 326 " pdb=" N LEU D 327 " pdb=" CA LEU D 327 " ideal model delta sigma weight residual 121.54 126.22 -4.68 1.91e+00 2.74e-01 6.01e+00 angle pdb=" C GLY C 326 " pdb=" N LEU C 327 " pdb=" CA LEU C 327 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.96e+00 angle pdb=" C GLY B 326 " pdb=" N LEU B 327 " pdb=" CA LEU B 327 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.90e+00 angle pdb=" C GLY F 326 " pdb=" N LEU F 327 " pdb=" CA LEU F 327 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 angle pdb=" C GLY E 326 " pdb=" N LEU E 327 " pdb=" CA LEU E 327 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 ... (remaining 33679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.43: 14647 13.43 - 26.86: 650 26.86 - 40.29: 207 40.29 - 53.72: 54 53.72 - 67.15: 24 Dihedral angle restraints: 15582 sinusoidal: 6486 harmonic: 9096 Sorted by residual: dihedral pdb=" CA ASP F 454 " pdb=" CB ASP F 454 " pdb=" CG ASP F 454 " pdb=" OD1 ASP F 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.95 56.95 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP D 454 " pdb=" CB ASP D 454 " pdb=" CG ASP D 454 " pdb=" OD1 ASP D 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP A 454 " pdb=" CB ASP A 454 " pdb=" CG ASP A 454 " pdb=" OD1 ASP A 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 15579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2258 0.029 - 0.057: 1028 0.057 - 0.086: 348 0.086 - 0.114: 187 0.114 - 0.143: 37 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CA ILE F 747 " pdb=" N ILE F 747 " pdb=" C ILE F 747 " pdb=" CB ILE F 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE D 747 " pdb=" N ILE D 747 " pdb=" C ILE D 747 " pdb=" CB ILE D 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 747 " pdb=" N ILE E 747 " pdb=" C ILE E 747 " pdb=" CB ILE E 747 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3855 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 263 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO F 264 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 264 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 264 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 263 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO E 264 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 264 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 264 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 263 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 264 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.023 5.00e-02 4.00e+02 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1473 2.73 - 3.28: 25104 3.28 - 3.82: 38760 3.82 - 4.36: 48541 4.36 - 4.90: 80775 Nonbonded interactions: 194653 Sorted by model distance: nonbonded pdb=" OG SER C 453 " pdb=" OD1 ASP C 460 " model vdw 2.194 3.040 nonbonded pdb=" OG SER E 453 " pdb=" OD1 ASP E 460 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 453 " pdb=" OD1 ASP A 460 " model vdw 2.194 3.040 nonbonded pdb=" OG SER D 453 " pdb=" OD1 ASP D 460 " model vdw 2.195 3.040 nonbonded pdb=" OG SER F 453 " pdb=" OD1 ASP F 460 " model vdw 2.195 3.040 ... (remaining 194648 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: 0.04 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 group one per residue 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.080 Find NCS groups from input model: 0.160 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 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 : 0.002 0.034 24972 Z= 0.118 Angle : 0.541 5.790 33696 Z= 0.319 Chirality : 0.041 0.143 3858 Planarity : 0.004 0.042 4380 Dihedral : 9.077 67.151 9720 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.58 (0.13), residues: 3162 helix: -0.07 (0.14), residues: 1242 sheet: -1.03 (0.19), residues: 474 loop : -1.91 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 375 TYR 0.006 0.001 TYR C 377 PHE 0.003 0.001 PHE F 420 TRP 0.011 0.001 TRP D 303 HIS 0.001 0.000 HIS E 324 Details of bonding type rmsd covalent geometry : bond 0.00199 (24966) covalent geometry : angle 0.53972 (33684) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.90490 ( 12) hydrogen bonds : bond 0.14310 ( 1048) hydrogen bonds : angle 6.05972 ( 3036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.1416 (mtm) cc_final: 0.1196 (ttt) REVERT: A 312 ASP cc_start: 0.1662 (t0) cc_final: 0.0953 (m-30) REVERT: A 546 ARG cc_start: 0.4885 (mtm-85) cc_final: 0.4526 (tpt170) REVERT: A 573 ASP cc_start: 0.6622 (m-30) cc_final: 0.6171 (t0) REVERT: A 611 LEU cc_start: 0.5635 (mt) cc_final: 0.5261 (tp) REVERT: A 703 MET cc_start: 0.3628 (ptp) cc_final: 0.3381 (ptp) REVERT: A 704 THR cc_start: 0.3181 (t) cc_final: 0.2594 (t) REVERT: B 284 MET cc_start: -0.0143 (ttt) cc_final: -0.0763 (tpp) REVERT: B 410 MET cc_start: 0.4054 (mmm) cc_final: 0.2852 (tmm) REVERT: B 475 MET cc_start: 0.4453 (mtt) cc_final: 0.3851 (tpp) REVERT: C 432 MET cc_start: 0.4808 (ttm) cc_final: 0.4494 (ttt) REVERT: C 570 ILE cc_start: 0.6421 (mt) cc_final: 0.6143 (mt) REVERT: C 584 PHE cc_start: 0.5832 (m-80) cc_final: 0.4639 (m-10) REVERT: C 588 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7167 (mtt90) REVERT: C 651 LYS cc_start: 0.5636 (mttt) cc_final: 0.5399 (tptm) REVERT: C 659 TYR cc_start: 0.5708 (p90) cc_final: 0.5257 (p90) REVERT: D 735 LEU cc_start: 0.6078 (mt) cc_final: 0.4873 (mm) REVERT: E 284 MET cc_start: 0.4784 (ttt) cc_final: 0.4273 (ttt) REVERT: E 321 ASP cc_start: 0.7207 (m-30) cc_final: 0.6826 (m-30) REVERT: E 614 GLU cc_start: 0.5303 (mt-10) cc_final: 0.4867 (mt-10) REVERT: E 743 ASP cc_start: 0.4407 (m-30) cc_final: 0.4143 (t0) REVERT: F 432 MET cc_start: 0.3679 (ttm) cc_final: 0.3218 (mmt) REVERT: F 481 LEU cc_start: 0.2479 (mt) cc_final: 0.2143 (mt) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1844 time to fit residues: 145.6745 Evaluate side-chains 272 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 505 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN B 667 HIS C 251 ASN C 455 HIS C 593 ASN C 667 HIS C 712 GLN C 727 HIS D 455 HIS E 251 ASN E 758 HIS F 251 ASN F 455 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.285946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.255523 restraints weight = 32462.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.256452 restraints weight = 65802.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.254327 restraints weight = 36879.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.253204 restraints weight = 34475.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.253277 restraints weight = 30550.817| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24972 Z= 0.240 Angle : 0.794 9.890 33696 Z= 0.405 Chirality : 0.050 0.405 3858 Planarity : 0.006 0.058 4380 Dihedral : 4.002 18.750 3456 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.68 % Allowed : 10.52 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3162 helix: 0.64 (0.14), residues: 1236 sheet: -0.74 (0.20), residues: 534 loop : -1.51 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 537 TYR 0.037 0.002 TYR B 337 PHE 0.019 0.002 PHE B 420 TRP 0.018 0.002 TRP E 303 HIS 0.010 0.002 HIS D 727 Details of bonding type rmsd covalent geometry : bond 0.00565 (24966) covalent geometry : angle 0.79158 (33684) SS BOND : bond 0.01279 ( 6) SS BOND : angle 3.53487 ( 12) hydrogen bonds : bond 0.04569 ( 1048) hydrogen bonds : angle 5.02665 ( 3036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 350 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.1774 (mmt) cc_final: 0.0249 (ptp) REVERT: A 623 LYS cc_start: 0.5873 (mttt) cc_final: 0.5640 (mttm) REVERT: A 648 ARG cc_start: 0.4672 (mpt90) cc_final: 0.4271 (mmt180) REVERT: A 720 LYS cc_start: 0.4291 (OUTLIER) cc_final: 0.3707 (mtpp) REVERT: B 405 LYS cc_start: 0.5172 (mttt) cc_final: 0.4702 (mmtt) REVERT: C 474 SER cc_start: 0.7797 (t) cc_final: 0.7445 (p) REVERT: C 553 ARG cc_start: 0.7123 (mtt-85) cc_final: 0.6898 (mtp-110) REVERT: C 588 ARG cc_start: 0.7711 (mmt90) cc_final: 0.7319 (mtt90) REVERT: D 609 ASP cc_start: 0.7850 (p0) cc_final: 0.7505 (p0) REVERT: E 280 MET cc_start: 0.1737 (pmm) cc_final: 0.1341 (mmm) REVERT: E 610 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6885 (mp) outliers start: 71 outliers final: 25 residues processed: 396 average time/residue: 0.1760 time to fit residues: 105.8259 Evaluate side-chains 285 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 758 HIS Chi-restraints excluded: chain F residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 302 optimal weight: 4.9990 chunk 50 optimal weight: 0.0030 chunk 36 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 597 GLN B 251 ASN C 593 ASN D 341 GLN D 591 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.286291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.256147 restraints weight = 32460.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.258461 restraints weight = 64064.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.258537 restraints weight = 40239.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.258579 restraints weight = 28348.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.259860 restraints weight = 22429.328| |-----------------------------------------------------------------------------| r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24972 Z= 0.117 Angle : 0.577 10.337 33696 Z= 0.290 Chirality : 0.043 0.234 3858 Planarity : 0.004 0.060 4380 Dihedral : 3.561 24.542 3456 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.53 % Allowed : 12.52 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3162 helix: 1.28 (0.14), residues: 1236 sheet: -0.39 (0.20), residues: 558 loop : -1.35 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 762 TYR 0.023 0.001 TYR E 535 PHE 0.014 0.001 PHE E 658 TRP 0.012 0.001 TRP B 297 HIS 0.007 0.001 HIS E 758 Details of bonding type rmsd covalent geometry : bond 0.00263 (24966) covalent geometry : angle 0.57485 (33684) SS BOND : bond 0.00832 ( 6) SS BOND : angle 2.60854 ( 12) hydrogen bonds : bond 0.03443 ( 1048) hydrogen bonds : angle 4.56925 ( 3036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 291 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.1712 (mmt) cc_final: 0.0370 (ptp) REVERT: A 648 ARG cc_start: 0.4428 (mpt90) cc_final: 0.4188 (mmt180) REVERT: B 296 ASP cc_start: 0.2012 (OUTLIER) cc_final: 0.1652 (t0) REVERT: B 405 LYS cc_start: 0.4959 (mttt) cc_final: 0.4430 (mmtt) REVERT: B 475 MET cc_start: 0.6035 (tpp) cc_final: 0.5834 (tpp) REVERT: C 474 SER cc_start: 0.7831 (t) cc_final: 0.7556 (p) REVERT: C 588 ARG cc_start: 0.7667 (mmt90) cc_final: 0.7361 (mtt90) REVERT: C 593 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7630 (p0) REVERT: D 609 ASP cc_start: 0.7943 (p0) cc_final: 0.7661 (p0) REVERT: E 379 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5748 (ttm170) REVERT: E 402 MET cc_start: 0.0881 (tpp) cc_final: 0.0550 (tpp) REVERT: E 551 LEU cc_start: 0.3731 (mm) cc_final: 0.3406 (mm) REVERT: E 610 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6766 (mp) REVERT: F 410 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.2416 (ptm) outliers start: 67 outliers final: 36 residues processed: 336 average time/residue: 0.1542 time to fit residues: 83.1594 Evaluate side-chains 289 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain F residue 410 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 237 optimal weight: 0.6980 chunk 275 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 308 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 576 HIS C 591 ASN C 727 HIS D 558 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.285790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.256537 restraints weight = 32037.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.254966 restraints weight = 58051.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.247510 restraints weight = 37596.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.248647 restraints weight = 40610.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.248223 restraints weight = 32254.442| |-----------------------------------------------------------------------------| r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24972 Z= 0.106 Angle : 0.568 10.875 33696 Z= 0.281 Chirality : 0.042 0.197 3858 Planarity : 0.004 0.056 4380 Dihedral : 3.536 26.907 3456 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.71 % Allowed : 13.05 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3162 helix: 1.51 (0.15), residues: 1242 sheet: -0.04 (0.21), residues: 546 loop : -1.20 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 762 TYR 0.013 0.001 TYR B 337 PHE 0.013 0.001 PHE E 658 TRP 0.015 0.001 TRP B 297 HIS 0.009 0.001 HIS C 576 Details of bonding type rmsd covalent geometry : bond 0.00237 (24966) covalent geometry : angle 0.56574 (33684) SS BOND : bond 0.01049 ( 6) SS BOND : angle 2.71838 ( 12) hydrogen bonds : bond 0.03181 ( 1048) hydrogen bonds : angle 4.45390 ( 3036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.0792 (ttp) cc_final: 0.0392 (ttt) REVERT: A 402 MET cc_start: 0.1479 (mmt) cc_final: 0.0210 (ptp) REVERT: A 648 ARG cc_start: 0.4752 (mpt90) cc_final: 0.4377 (mmt180) REVERT: B 296 ASP cc_start: 0.2138 (OUTLIER) cc_final: 0.1798 (t0) REVERT: B 405 LYS cc_start: 0.5182 (mttt) cc_final: 0.4591 (mmtt) REVERT: B 475 MET cc_start: 0.6246 (tpp) cc_final: 0.6037 (tpt) REVERT: C 380 MET cc_start: 0.7230 (tmm) cc_final: 0.6718 (ptt) REVERT: C 405 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5795 (pttt) REVERT: C 474 SER cc_start: 0.7903 (t) cc_final: 0.7675 (p) REVERT: C 475 MET cc_start: 0.7313 (tpp) cc_final: 0.7012 (tpp) REVERT: C 588 ARG cc_start: 0.7687 (mmt90) cc_final: 0.7410 (mtt90) REVERT: D 744 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7523 (mp) REVERT: E 379 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.6019 (ttm110) REVERT: E 610 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6735 (mp) REVERT: E 634 MET cc_start: 0.5637 (mmm) cc_final: 0.5048 (tpt) REVERT: F 295 ILE cc_start: 0.2709 (OUTLIER) cc_final: 0.2366 (tp) REVERT: F 410 MET cc_start: 0.2360 (OUTLIER) cc_final: 0.2065 (ptm) outliers start: 72 outliers final: 40 residues processed: 314 average time/residue: 0.1613 time to fit residues: 80.5058 Evaluate side-chains 286 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain D residue 633 VAL Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 603 TRP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 167 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 199 optimal weight: 0.4980 chunk 253 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN D 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.285288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.255134 restraints weight = 31985.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.258023 restraints weight = 60948.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.257863 restraints weight = 38060.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.257800 restraints weight = 28208.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.260139 restraints weight = 21286.775| |-----------------------------------------------------------------------------| r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24972 Z= 0.113 Angle : 0.562 9.548 33696 Z= 0.279 Chirality : 0.042 0.198 3858 Planarity : 0.004 0.055 4380 Dihedral : 3.590 28.507 3456 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.83 % Allowed : 13.76 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3162 helix: 1.69 (0.15), residues: 1236 sheet: 0.12 (0.22), residues: 546 loop : -1.18 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 594 TYR 0.027 0.001 TYR C 377 PHE 0.011 0.001 PHE E 658 TRP 0.019 0.001 TRP E 303 HIS 0.003 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00260 (24966) covalent geometry : angle 0.55999 (33684) SS BOND : bond 0.00849 ( 6) SS BOND : angle 2.59163 ( 12) hydrogen bonds : bond 0.03090 ( 1048) hydrogen bonds : angle 4.34322 ( 3036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 270 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.1166 (ttp) cc_final: 0.0731 (ttt) REVERT: A 402 MET cc_start: 0.1912 (mmt) cc_final: 0.0470 (ptp) REVERT: A 648 ARG cc_start: 0.4865 (mpt90) cc_final: 0.4573 (mmt180) REVERT: B 296 ASP cc_start: 0.2286 (OUTLIER) cc_final: 0.1980 (t0) REVERT: B 475 MET cc_start: 0.6432 (tpp) cc_final: 0.6190 (tpt) REVERT: B 692 LEU cc_start: 0.7633 (mp) cc_final: 0.7258 (mp) REVERT: C 380 MET cc_start: 0.6856 (tmm) cc_final: 0.6487 (ptm) REVERT: C 474 SER cc_start: 0.8127 (t) cc_final: 0.7732 (p) REVERT: C 475 MET cc_start: 0.7215 (tpp) cc_final: 0.6918 (tpp) REVERT: C 588 ARG cc_start: 0.7648 (mmt90) cc_final: 0.7161 (mtt90) REVERT: D 744 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7633 (mp) REVERT: E 610 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6708 (mp) REVERT: F 263 MET cc_start: 0.1758 (mmm) cc_final: 0.1546 (mmm) REVERT: F 410 MET cc_start: 0.2525 (ptm) cc_final: 0.2222 (ptm) REVERT: F 467 MET cc_start: -0.2834 (tpp) cc_final: -0.4445 (tpp) outliers start: 75 outliers final: 46 residues processed: 320 average time/residue: 0.1550 time to fit residues: 80.6159 Evaluate side-chains 291 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain F residue 603 TRP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 3 optimal weight: 0.0370 chunk 177 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 278 optimal weight: 0.0170 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.285309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.252021 restraints weight = 32144.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.250489 restraints weight = 46771.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.246968 restraints weight = 39642.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.246209 restraints weight = 37947.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.244875 restraints weight = 32594.299| |-----------------------------------------------------------------------------| r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24972 Z= 0.116 Angle : 0.568 11.195 33696 Z= 0.281 Chirality : 0.042 0.156 3858 Planarity : 0.004 0.066 4380 Dihedral : 3.656 31.009 3456 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.41 % Allowed : 14.93 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.32 (0.15), residues: 3162 helix: 1.69 (0.15), residues: 1260 sheet: 0.21 (0.22), residues: 534 loop : -1.23 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 583 TYR 0.024 0.001 TYR C 377 PHE 0.010 0.001 PHE E 658 TRP 0.022 0.001 TRP E 303 HIS 0.003 0.001 HIS D 727 Details of bonding type rmsd covalent geometry : bond 0.00272 (24966) covalent geometry : angle 0.56592 (33684) SS BOND : bond 0.00657 ( 6) SS BOND : angle 2.70905 ( 12) hydrogen bonds : bond 0.03063 ( 1048) hydrogen bonds : angle 4.32062 ( 3036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.1569 (ttp) cc_final: 0.1072 (ttt) REVERT: A 402 MET cc_start: 0.1895 (mmt) cc_final: 0.0458 (ptp) REVERT: A 547 GLU cc_start: 0.4723 (OUTLIER) cc_final: 0.4385 (mp0) REVERT: B 296 ASP cc_start: 0.2345 (OUTLIER) cc_final: 0.1943 (t0) REVERT: B 475 MET cc_start: 0.6617 (tpp) cc_final: 0.6293 (tpt) REVERT: B 736 ILE cc_start: 0.8135 (pt) cc_final: 0.7934 (pt) REVERT: C 280 MET cc_start: 0.0841 (mtt) cc_final: 0.0074 (ppp) REVERT: C 405 LYS cc_start: 0.6140 (OUTLIER) cc_final: 0.5883 (pttt) REVERT: C 474 SER cc_start: 0.8207 (t) cc_final: 0.7838 (p) REVERT: C 475 MET cc_start: 0.7422 (tpp) cc_final: 0.7097 (tpp) REVERT: C 588 ARG cc_start: 0.7580 (mmt90) cc_final: 0.7123 (mtt90) REVERT: E 257 LYS cc_start: 0.2622 (tppt) cc_final: 0.2338 (mtpt) REVERT: E 610 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6712 (mp) REVERT: F 263 MET cc_start: 0.1791 (mmm) cc_final: 0.1501 (mmm) REVERT: F 410 MET cc_start: 0.2384 (ptm) cc_final: 0.2152 (ptm) REVERT: F 467 MET cc_start: -0.2874 (tpp) cc_final: -0.4486 (tpp) outliers start: 64 outliers final: 50 residues processed: 311 average time/residue: 0.1548 time to fit residues: 77.7060 Evaluate side-chains 301 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 201 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 278 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 ASN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.280347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.252432 restraints weight = 31909.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.249599 restraints weight = 66578.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.243850 restraints weight = 38984.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.244264 restraints weight = 41946.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.244048 restraints weight = 30235.697| |-----------------------------------------------------------------------------| r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24972 Z= 0.117 Angle : 0.568 16.028 33696 Z= 0.279 Chirality : 0.042 0.148 3858 Planarity : 0.004 0.057 4380 Dihedral : 3.661 26.163 3456 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.60 % Allowed : 15.12 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3162 helix: 1.71 (0.15), residues: 1260 sheet: 0.25 (0.22), residues: 534 loop : -1.24 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 583 TYR 0.021 0.001 TYR C 377 PHE 0.013 0.001 PHE D 420 TRP 0.023 0.001 TRP E 303 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00276 (24966) covalent geometry : angle 0.56634 (33684) SS BOND : bond 0.00785 ( 6) SS BOND : angle 2.57992 ( 12) hydrogen bonds : bond 0.03093 ( 1048) hydrogen bonds : angle 4.29890 ( 3036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 260 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.1279 (ttp) cc_final: 0.0882 (ttt) REVERT: A 402 MET cc_start: 0.1651 (mmt) cc_final: 0.0410 (ptp) REVERT: A 432 MET cc_start: 0.2022 (mmm) cc_final: -0.0030 (mpp) REVERT: A 728 ARG cc_start: 0.5431 (ptp-170) cc_final: 0.4977 (mtm180) REVERT: B 280 MET cc_start: 0.1659 (ptm) cc_final: 0.1441 (ptt) REVERT: B 296 ASP cc_start: 0.2187 (OUTLIER) cc_final: 0.1874 (t0) REVERT: B 475 MET cc_start: 0.6674 (tpp) cc_final: 0.6352 (tpt) REVERT: B 736 ILE cc_start: 0.8106 (pt) cc_final: 0.7883 (pt) REVERT: C 405 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.6087 (pttt) REVERT: C 474 SER cc_start: 0.8369 (t) cc_final: 0.7936 (p) REVERT: C 475 MET cc_start: 0.7475 (tpp) cc_final: 0.7119 (tpp) REVERT: C 588 ARG cc_start: 0.7768 (mmt90) cc_final: 0.7299 (mtt90) REVERT: E 402 MET cc_start: -0.0146 (tpp) cc_final: -0.0895 (tpp) REVERT: E 610 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6681 (mp) REVERT: F 263 MET cc_start: 0.1561 (mmm) cc_final: 0.1178 (mmm) REVERT: F 410 MET cc_start: 0.2287 (ptm) cc_final: 0.2074 (ptm) outliers start: 69 outliers final: 48 residues processed: 305 average time/residue: 0.1534 time to fit residues: 75.6896 Evaluate side-chains 298 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain E residue 303 TRP Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 98 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 667 HIS D 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.279594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.248921 restraints weight = 31881.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.247539 restraints weight = 48107.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.245803 restraints weight = 38977.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.244362 restraints weight = 35780.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.241094 restraints weight = 38711.126| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24972 Z= 0.117 Angle : 0.577 13.637 33696 Z= 0.284 Chirality : 0.042 0.237 3858 Planarity : 0.004 0.057 4380 Dihedral : 3.714 30.745 3456 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.30 % Allowed : 15.54 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.24 (0.15), residues: 3162 helix: 1.58 (0.14), residues: 1302 sheet: 0.45 (0.24), residues: 498 loop : -1.41 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 396 TYR 0.021 0.001 TYR C 377 PHE 0.009 0.001 PHE E 658 TRP 0.021 0.001 TRP E 303 HIS 0.003 0.001 HIS D 727 Details of bonding type rmsd covalent geometry : bond 0.00276 (24966) covalent geometry : angle 0.57504 (33684) SS BOND : bond 0.00692 ( 6) SS BOND : angle 2.73256 ( 12) hydrogen bonds : bond 0.03074 ( 1048) hydrogen bonds : angle 4.31309 ( 3036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.1464 (ttp) cc_final: 0.1142 (ttt) REVERT: A 402 MET cc_start: 0.1878 (mmt) cc_final: 0.0591 (ptp) REVERT: A 432 MET cc_start: 0.2301 (mmm) cc_final: 0.0122 (mpp) REVERT: A 728 ARG cc_start: 0.5374 (ptp-170) cc_final: 0.4963 (ptm160) REVERT: B 280 MET cc_start: 0.1951 (ptm) cc_final: 0.1686 (ptt) REVERT: B 281 MET cc_start: 0.0509 (ptt) cc_final: 0.0124 (ptm) REVERT: B 296 ASP cc_start: 0.2314 (OUTLIER) cc_final: 0.1959 (t0) REVERT: B 475 MET cc_start: 0.6541 (tpp) cc_final: 0.6193 (tpt) REVERT: B 606 VAL cc_start: 0.6825 (m) cc_final: 0.6577 (t) REVERT: C 405 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.6045 (pttt) REVERT: C 474 SER cc_start: 0.8279 (t) cc_final: 0.7860 (p) REVERT: C 475 MET cc_start: 0.7462 (tpp) cc_final: 0.7120 (tpp) REVERT: C 588 ARG cc_start: 0.7516 (mmt90) cc_final: 0.7122 (mtt90) REVERT: E 402 MET cc_start: -0.0009 (tpp) cc_final: -0.0961 (tpp) REVERT: E 475 MET cc_start: 0.3600 (mtm) cc_final: 0.3343 (mtm) REVERT: E 610 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6710 (mp) REVERT: E 657 ASP cc_start: 0.5834 (t0) cc_final: 0.5577 (t0) REVERT: F 410 MET cc_start: 0.2522 (ptm) cc_final: 0.2296 (ptm) REVERT: F 467 MET cc_start: -0.2726 (tpp) cc_final: -0.4592 (tpp) outliers start: 61 outliers final: 51 residues processed: 305 average time/residue: 0.1532 time to fit residues: 75.1265 Evaluate side-chains 296 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN D 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.275024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.242842 restraints weight = 31897.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.240869 restraints weight = 47885.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.238751 restraints weight = 39474.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.237421 restraints weight = 36750.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.235209 restraints weight = 35887.017| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24972 Z= 0.153 Angle : 0.624 10.293 33696 Z= 0.314 Chirality : 0.044 0.223 3858 Planarity : 0.004 0.058 4380 Dihedral : 4.017 30.601 3456 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.15 % Allowed : 15.99 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.13 (0.15), residues: 3162 helix: 1.47 (0.14), residues: 1272 sheet: 0.35 (0.24), residues: 492 loop : -1.37 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 379 TYR 0.030 0.002 TYR C 456 PHE 0.012 0.001 PHE B 468 TRP 0.018 0.002 TRP E 303 HIS 0.005 0.001 HIS C 455 Details of bonding type rmsd covalent geometry : bond 0.00364 (24966) covalent geometry : angle 0.62188 (33684) SS BOND : bond 0.01006 ( 6) SS BOND : angle 3.01109 ( 12) hydrogen bonds : bond 0.03534 ( 1048) hydrogen bonds : angle 4.49728 ( 3036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 278 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.1751 (ttp) cc_final: 0.1437 (ttt) REVERT: A 346 LYS cc_start: 0.3848 (mttt) cc_final: 0.2666 (tptt) REVERT: A 402 MET cc_start: 0.1871 (mmt) cc_final: 0.0574 (ptp) REVERT: A 432 MET cc_start: 0.2691 (mmm) cc_final: 0.0352 (mpp) REVERT: A 634 MET cc_start: 0.4143 (mmt) cc_final: 0.3872 (mmt) REVERT: A 728 ARG cc_start: 0.5459 (ptp-170) cc_final: 0.4326 (ppt170) REVERT: B 281 MET cc_start: 0.0745 (ptt) cc_final: 0.0346 (ptm) REVERT: B 296 ASP cc_start: 0.2560 (OUTLIER) cc_final: 0.2228 (t0) REVERT: B 475 MET cc_start: 0.6575 (tpp) cc_final: 0.6215 (tpt) REVERT: C 303 TRP cc_start: 0.2822 (p90) cc_final: 0.2518 (p90) REVERT: C 348 LYS cc_start: 0.5924 (mmtt) cc_final: 0.5148 (pttt) REVERT: C 373 THR cc_start: 0.8369 (p) cc_final: 0.8154 (m) REVERT: C 588 ARG cc_start: 0.7456 (mmt90) cc_final: 0.7072 (mtt90) REVERT: E 281 MET cc_start: 0.0699 (ppp) cc_final: 0.0154 (ptm) REVERT: E 402 MET cc_start: 0.0354 (tpp) cc_final: -0.0531 (tpp) REVERT: E 475 MET cc_start: 0.3691 (mtm) cc_final: 0.3367 (mtm) REVERT: E 610 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6690 (mp) REVERT: E 657 ASP cc_start: 0.6128 (t0) cc_final: 0.5878 (t0) REVERT: E 722 LYS cc_start: 0.6853 (mttt) cc_final: 0.6407 (ttmt) REVERT: F 433 ARG cc_start: 0.0790 (ttt180) cc_final: -0.0059 (tpt170) REVERT: F 467 MET cc_start: -0.2822 (tpp) cc_final: -0.4647 (tpp) outliers start: 57 outliers final: 47 residues processed: 318 average time/residue: 0.1595 time to fit residues: 80.8028 Evaluate side-chains 308 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 303 TRP Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain E residue 303 TRP Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 202 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 302 optimal weight: 0.0270 chunk 240 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.277495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.246133 restraints weight = 31957.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.243396 restraints weight = 46873.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.240927 restraints weight = 37728.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.239559 restraints weight = 38531.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.237530 restraints weight = 35641.769| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24972 Z= 0.111 Angle : 0.588 10.927 33696 Z= 0.290 Chirality : 0.042 0.190 3858 Planarity : 0.004 0.052 4380 Dihedral : 3.864 29.138 3456 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.70 % Allowed : 16.93 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3162 helix: 1.39 (0.14), residues: 1338 sheet: 0.44 (0.24), residues: 492 loop : -1.52 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 379 TYR 0.032 0.001 TYR E 659 PHE 0.010 0.001 PHE E 658 TRP 0.016 0.001 TRP E 303 HIS 0.003 0.001 HIS D 727 Details of bonding type rmsd covalent geometry : bond 0.00257 (24966) covalent geometry : angle 0.58646 (33684) SS BOND : bond 0.00728 ( 6) SS BOND : angle 2.41321 ( 12) hydrogen bonds : bond 0.03033 ( 1048) hydrogen bonds : angle 4.34662 ( 3036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.2179 (ttp) cc_final: 0.1861 (ttt) REVERT: A 402 MET cc_start: 0.1932 (mmt) cc_final: 0.0618 (ptp) REVERT: A 432 MET cc_start: 0.2570 (mmm) cc_final: 0.0235 (mpp) REVERT: A 634 MET cc_start: 0.3959 (mmt) cc_final: 0.3709 (mmt) REVERT: A 728 ARG cc_start: 0.5348 (ptp-170) cc_final: 0.4277 (ppt170) REVERT: B 281 MET cc_start: 0.0571 (ptt) cc_final: 0.0248 (ptm) REVERT: B 296 ASP cc_start: 0.2564 (OUTLIER) cc_final: 0.2250 (t0) REVERT: B 475 MET cc_start: 0.6654 (tpp) cc_final: 0.6311 (tpt) REVERT: C 303 TRP cc_start: 0.2733 (p90) cc_final: 0.2444 (p90) REVERT: C 348 LYS cc_start: 0.6006 (mmtt) cc_final: 0.5227 (pttt) REVERT: C 588 ARG cc_start: 0.7467 (mmt90) cc_final: 0.7029 (mtt90) REVERT: D 380 MET cc_start: 0.5201 (mmm) cc_final: 0.4811 (mmm) REVERT: E 402 MET cc_start: 0.0225 (tpp) cc_final: -0.0564 (tpp) REVERT: E 475 MET cc_start: 0.3666 (mtm) cc_final: 0.3383 (mtm) REVERT: E 610 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6670 (mp) REVERT: E 722 LYS cc_start: 0.6900 (mttt) cc_final: 0.6438 (ttmt) REVERT: F 433 ARG cc_start: 0.0671 (ttt180) cc_final: -0.0155 (tpt170) REVERT: F 467 MET cc_start: -0.2986 (tpp) cc_final: -0.4701 (tpp) outliers start: 45 outliers final: 39 residues processed: 295 average time/residue: 0.1538 time to fit residues: 72.5520 Evaluate side-chains 282 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 HIS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain E residue 303 TRP Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 610 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain F residue 603 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 260 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 HIS D 591 ASN E 758 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.270886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.241113 restraints weight = 31835.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.236884 restraints weight = 43767.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.233045 restraints weight = 38192.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.232015 restraints weight = 42286.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.230551 restraints weight = 35787.377| |-----------------------------------------------------------------------------| r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24972 Z= 0.186 Angle : 0.706 11.593 33696 Z= 0.352 Chirality : 0.046 0.243 3858 Planarity : 0.005 0.056 4380 Dihedral : 4.377 31.576 3456 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.96 % Allowed : 16.89 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % 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: -0.17 (0.15), residues: 3162 helix: 1.20 (0.14), residues: 1266 sheet: 0.11 (0.26), residues: 432 loop : -1.38 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 396 TYR 0.022 0.002 TYR E 659 PHE 0.011 0.002 PHE B 468 TRP 0.025 0.002 TRP C 297 HIS 0.007 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00455 (24966) covalent geometry : angle 0.70328 (33684) SS BOND : bond 0.01271 ( 6) SS BOND : angle 3.25317 ( 12) hydrogen bonds : bond 0.03945 ( 1048) hydrogen bonds : angle 4.71443 ( 3036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3692.93 seconds wall clock time: 64 minutes 39.53 seconds (3879.53 seconds total)