Starting phenix.real_space_refine on Fri Mar 6 15:50:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uw5_26823/03_2026/7uw5_26823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uw5_26823/03_2026/7uw5_26823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uw5_26823/03_2026/7uw5_26823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uw5_26823/03_2026/7uw5_26823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uw5_26823/03_2026/7uw5_26823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uw5_26823/03_2026/7uw5_26823.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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 70 5.16 5 C 20489 2.51 5 N 5943 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 32340 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4620 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 350} Link IDs: {'PTRANS': 14, 'TRANS': 708} Chain breaks: 8 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1233 Unresolved non-hydrogen angles: 1578 Unresolved non-hydrogen dihedrals: 985 Unresolved non-hydrogen chiralities: 142 Planarities with less than four sites: {'GLN:plan1': 35, 'GLU:plan': 24, 'ASN:plan1': 24, 'ARG:plan': 20, 'TRP:plan': 6, 'TYR:plan': 4, 'ASP:plan': 15, 'PHE:plan': 14, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 639 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 4.65, per 1000 atoms: 0.14 Number of scatterers: 32340 At special positions: 0 Unit cell: (173.9, 172.02, 190.82, 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 70 16.00 O 5838 8.00 N 5943 7.00 C 20489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9674 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 16 sheets defined 76.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 286 through 339 Processing helix chain 'A' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 405 through 464 Processing helix chain 'A' and resid 475 through 489 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 505 through 537 Proline residue: A 512 - end of helix removed outlier: 4.158A pdb=" N GLY A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 574 Proline residue: A 562 - end of helix removed outlier: 4.572A pdb=" N LEU A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 605 removed outlier: 3.731A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Proline residue: A 639 - end of helix removed outlier: 3.507A pdb=" N PHE A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 682 Proline residue: A 677 - end of helix Processing helix chain 'A' and resid 694 through 711 Proline residue: A 703 - end of helix removed outlier: 3.867A pdb=" N ALA A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 760 Processing helix chain 'A' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR A 790 " --> pdb=" O VAL A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 821 Processing helix chain 'A' and resid 842 through 862 Processing helix chain 'A' and resid 862 through 875 removed outlier: 3.930A pdb=" N LEU A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 906 Processing helix chain 'A' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 915 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 944 removed outlier: 3.642A pdb=" N ASN A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 1014 through 1029 removed outlier: 3.858A pdb=" N HIS A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1083 Processing helix chain 'B' and resid 287 through 339 Processing helix chain 'B' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU B 361 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 386 Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 405 through 464 Processing helix chain 'B' and resid 475 through 489 Proline residue: B 480 - end of helix Processing helix chain 'B' and resid 505 through 537 Proline residue: B 512 - end of helix removed outlier: 4.158A pdb=" N GLY B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP B 526 " --> pdb=" O TRP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 574 Proline residue: B 562 - end of helix removed outlier: 4.571A pdb=" N LEU B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 605 removed outlier: 3.731A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 636 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Proline residue: B 639 - end of helix removed outlier: 3.507A pdb=" N PHE B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 649 " --> pdb=" O VAL B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 682 Proline residue: B 677 - end of helix Processing helix chain 'B' and resid 694 through 711 Proline residue: B 703 - end of helix removed outlier: 3.867A pdb=" N ALA B 711 " --> pdb=" O MET B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 760 Processing helix chain 'B' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 821 Processing helix chain 'B' and resid 842 through 862 Processing helix chain 'B' and resid 862 through 875 removed outlier: 3.930A pdb=" N LEU B 866 " --> pdb=" O ASN B 862 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 906 Processing helix chain 'B' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU B 915 " --> pdb=" O LYS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 944 removed outlier: 3.641A pdb=" N ASN B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 988 Processing helix chain 'B' and resid 1014 through 1029 removed outlier: 3.858A pdb=" N HIS B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1083 Processing helix chain 'C' and resid 287 through 339 Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU C 361 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 388 through 398 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 405 through 464 Processing helix chain 'C' and resid 475 through 489 Proline residue: C 480 - end of helix Processing helix chain 'C' and resid 505 through 537 Proline residue: C 512 - end of helix removed outlier: 4.158A pdb=" N GLY C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP C 526 " --> pdb=" O TRP C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 574 Proline residue: C 562 - end of helix removed outlier: 4.571A pdb=" N LEU C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 605 removed outlier: 3.732A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER C 634 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 636 " --> pdb=" O ARG C 632 " (cutoff:3.500A) Proline residue: C 639 - end of helix removed outlier: 3.508A pdb=" N PHE C 642 " --> pdb=" O LEU C 638 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 682 Proline residue: C 677 - end of helix Processing helix chain 'C' and resid 694 through 711 Proline residue: C 703 - end of helix removed outlier: 3.867A pdb=" N ALA C 711 " --> pdb=" O MET C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 760 Processing helix chain 'C' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR C 790 " --> pdb=" O VAL C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 821 Processing helix chain 'C' and resid 842 through 862 Processing helix chain 'C' and resid 862 through 875 removed outlier: 3.930A pdb=" N LEU C 866 " --> pdb=" O ASN C 862 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER C 873 " --> pdb=" O VAL C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 906 Processing helix chain 'C' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP C 914 " --> pdb=" O ASP C 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 915 " --> pdb=" O LYS C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 944 removed outlier: 3.642A pdb=" N ASN C 933 " --> pdb=" O GLU C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 988 Processing helix chain 'C' and resid 1014 through 1029 removed outlier: 3.858A pdb=" N HIS C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1083 Processing helix chain 'D' and resid 287 through 339 Processing helix chain 'D' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU D 361 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 388 through 398 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 405 through 464 Processing helix chain 'D' and resid 475 through 489 Proline residue: D 480 - end of helix Processing helix chain 'D' and resid 505 through 537 Proline residue: D 512 - end of helix removed outlier: 4.158A pdb=" N GLY D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP D 526 " --> pdb=" O TRP D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 574 Proline residue: D 562 - end of helix removed outlier: 4.571A pdb=" N LEU D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 605 removed outlier: 3.731A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER D 634 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 636 " --> pdb=" O ARG D 632 " (cutoff:3.500A) Proline residue: D 639 - end of helix removed outlier: 3.508A pdb=" N PHE D 642 " --> pdb=" O LEU D 638 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 649 " --> pdb=" O VAL D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 682 Proline residue: D 677 - end of helix Processing helix chain 'D' and resid 694 through 711 Proline residue: D 703 - end of helix removed outlier: 3.867A pdb=" N ALA D 711 " --> pdb=" O MET D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 760 Processing helix chain 'D' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 821 Processing helix chain 'D' and resid 842 through 862 Processing helix chain 'D' and resid 862 through 875 removed outlier: 3.930A pdb=" N LEU D 866 " --> pdb=" O ASN D 862 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER D 873 " --> pdb=" O VAL D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 906 Processing helix chain 'D' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP D 914 " --> pdb=" O ASP D 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU D 915 " --> pdb=" O LYS D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 944 removed outlier: 3.641A pdb=" N ASN D 933 " --> pdb=" O GLU D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 988 Processing helix chain 'D' and resid 1014 through 1029 removed outlier: 3.858A pdb=" N HIS D1029 " --> pdb=" O ALA D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1065 through 1083 Processing helix chain 'E' and resid 287 through 339 Processing helix chain 'E' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU E 361 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 386 Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 405 through 464 Processing helix chain 'E' and resid 475 through 489 Proline residue: E 480 - end of helix Processing helix chain 'E' and resid 505 through 537 Proline residue: E 512 - end of helix removed outlier: 4.158A pdb=" N GLY E 525 " --> pdb=" O HIS E 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP E 526 " --> pdb=" O TRP E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 574 Proline residue: E 562 - end of helix removed outlier: 4.571A pdb=" N LEU E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 605 removed outlier: 3.732A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER E 634 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 635 " --> pdb=" O VAL E 631 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 636 " --> pdb=" O ARG E 632 " (cutoff:3.500A) Proline residue: E 639 - end of helix removed outlier: 3.508A pdb=" N PHE E 642 " --> pdb=" O LEU E 638 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 649 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 682 Proline residue: E 677 - end of helix Processing helix chain 'E' and resid 694 through 711 Proline residue: E 703 - end of helix removed outlier: 3.867A pdb=" N ALA E 711 " --> pdb=" O MET E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 760 Processing helix chain 'E' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR E 790 " --> pdb=" O VAL E 786 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 821 Processing helix chain 'E' and resid 842 through 862 Processing helix chain 'E' and resid 862 through 875 removed outlier: 3.931A pdb=" N LEU E 866 " --> pdb=" O ASN E 862 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER E 873 " --> pdb=" O VAL E 869 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 906 Processing helix chain 'E' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP E 914 " --> pdb=" O ASP E 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU E 915 " --> pdb=" O LYS E 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 944 removed outlier: 3.641A pdb=" N ASN E 933 " --> pdb=" O GLU E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 988 Processing helix chain 'E' and resid 1014 through 1029 removed outlier: 3.858A pdb=" N HIS E1029 " --> pdb=" O ALA E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1065 through 1083 Processing helix chain 'F' and resid 287 through 339 Processing helix chain 'F' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU F 361 " --> pdb=" O SER F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 386 Processing helix chain 'F' and resid 388 through 398 Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'F' and resid 405 through 464 Processing helix chain 'F' and resid 475 through 489 Proline residue: F 480 - end of helix Processing helix chain 'F' and resid 505 through 537 Proline residue: F 512 - end of helix removed outlier: 4.158A pdb=" N GLY F 525 " --> pdb=" O HIS F 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP F 526 " --> pdb=" O TRP F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 574 Proline residue: F 562 - end of helix removed outlier: 4.571A pdb=" N LEU F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 605 removed outlier: 3.731A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER F 634 " --> pdb=" O ILE F 630 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU F 635 " --> pdb=" O VAL F 631 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 636 " --> pdb=" O ARG F 632 " (cutoff:3.500A) Proline residue: F 639 - end of helix removed outlier: 3.507A pdb=" N PHE F 642 " --> pdb=" O LEU F 638 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 649 " --> pdb=" O VAL F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 682 Proline residue: F 677 - end of helix Processing helix chain 'F' and resid 694 through 711 Proline residue: F 703 - end of helix removed outlier: 3.867A pdb=" N ALA F 711 " --> pdb=" O MET F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 760 Processing helix chain 'F' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR F 790 " --> pdb=" O VAL F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 821 Processing helix chain 'F' and resid 842 through 862 Processing helix chain 'F' and resid 862 through 875 removed outlier: 3.930A pdb=" N LEU F 866 " --> pdb=" O ASN F 862 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 872 " --> pdb=" O GLU F 868 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER F 873 " --> pdb=" O VAL F 869 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 906 Processing helix chain 'F' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP F 914 " --> pdb=" O ASP F 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU F 915 " --> pdb=" O LYS F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 927 through 944 removed outlier: 3.642A pdb=" N ASN F 933 " --> pdb=" O GLU F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 983 through 988 Processing helix chain 'F' and resid 1014 through 1029 removed outlier: 3.857A pdb=" N HIS F1029 " --> pdb=" O ALA F1025 " (cutoff:3.500A) Processing helix chain 'F' and resid 1065 through 1083 Processing helix chain 'G' and resid 287 through 339 Processing helix chain 'G' and resid 342 through 356 removed outlier: 4.143A pdb=" N SER G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG G 347 " --> pdb=" O LEU G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.947A pdb=" N GLU G 361 " --> pdb=" O SER G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 386 Processing helix chain 'G' and resid 388 through 398 Processing helix chain 'G' and resid 400 through 404 Processing helix chain 'G' and resid 405 through 464 Processing helix chain 'G' and resid 475 through 489 Proline residue: G 480 - end of helix Processing helix chain 'G' and resid 505 through 537 Proline residue: G 512 - end of helix removed outlier: 4.158A pdb=" N GLY G 525 " --> pdb=" O HIS G 521 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP G 526 " --> pdb=" O TRP G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 574 Proline residue: G 562 - end of helix removed outlier: 4.571A pdb=" N LEU G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 605 removed outlier: 3.731A pdb=" N PHE G 588 " --> pdb=" O LEU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 649 removed outlier: 3.803A pdb=" N SER G 634 " --> pdb=" O ILE G 630 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU G 635 " --> pdb=" O VAL G 631 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 636 " --> pdb=" O ARG G 632 " (cutoff:3.500A) Proline residue: G 639 - end of helix removed outlier: 3.507A pdb=" N PHE G 642 " --> pdb=" O LEU G 638 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU G 649 " --> pdb=" O VAL G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 659 through 682 Proline residue: G 677 - end of helix Processing helix chain 'G' and resid 694 through 711 Proline residue: G 703 - end of helix removed outlier: 3.867A pdb=" N ALA G 711 " --> pdb=" O MET G 707 " (cutoff:3.500A) Processing helix chain 'G' and resid 717 through 760 Processing helix chain 'G' and resid 785 through 810 removed outlier: 3.572A pdb=" N THR G 790 " --> pdb=" O VAL G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 842 through 862 Processing helix chain 'G' and resid 862 through 875 removed outlier: 3.931A pdb=" N LEU G 866 " --> pdb=" O ASN G 862 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER G 873 " --> pdb=" O VAL G 869 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 906 Processing helix chain 'G' and resid 908 through 925 removed outlier: 5.857A pdb=" N TRP G 914 " --> pdb=" O ASP G 910 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU G 915 " --> pdb=" O LYS G 911 " (cutoff:3.500A) Processing helix chain 'G' and resid 927 through 944 removed outlier: 3.641A pdb=" N ASN G 933 " --> pdb=" O GLU G 929 " (cutoff:3.500A) Processing helix chain 'G' and resid 983 through 988 Processing helix chain 'G' and resid 1014 through 1029 removed outlier: 3.858A pdb=" N HIS G1029 " --> pdb=" O ALA G1025 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1083 Processing sheet with id=AA1, first strand: chain 'A' and resid 827 through 832 Processing sheet with id=AA2, first strand: chain 'A' and resid 951 through 953 removed outlier: 5.203A pdb=" N VAL A 961 " --> pdb=" O THR A 972 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR A 972 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 963 " --> pdb=" O THR A 970 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL G 961 " --> pdb=" O THR G 972 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR G 972 " --> pdb=" O VAL G 961 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 963 " --> pdb=" O THR G 970 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL F 961 " --> pdb=" O THR F 972 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR F 972 " --> pdb=" O VAL F 961 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 963 " --> pdb=" O THR F 970 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL E 961 " --> pdb=" O THR E 972 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR E 972 " --> pdb=" O VAL E 961 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 963 " --> pdb=" O THR E 970 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL D 961 " --> pdb=" O THR D 972 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR D 972 " --> pdb=" O VAL D 961 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 963 " --> pdb=" O THR D 970 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL C 961 " --> pdb=" O THR C 972 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR C 972 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 963 " --> pdb=" O THR C 970 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL B 961 " --> pdb=" O THR B 972 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR B 972 " --> pdb=" O VAL B 961 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 963 " --> pdb=" O THR B 970 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP A1051 " --> pdb=" O THR A1043 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1089 through 1096 removed outlier: 4.196A pdb=" N ASN B1089 " --> pdb=" O GLN A1090 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS A1096 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B1095 " --> pdb=" O HIS A1096 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN C1089 " --> pdb=" O GLN B1090 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS B1096 " --> pdb=" O VAL C1093 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C1095 " --> pdb=" O HIS B1096 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN D1089 " --> pdb=" O GLN C1090 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS C1096 " --> pdb=" O VAL D1093 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D1095 " --> pdb=" O HIS C1096 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN E1089 " --> pdb=" O GLN D1090 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS D1096 " --> pdb=" O VAL E1093 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU E1095 " --> pdb=" O HIS D1096 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN F1089 " --> pdb=" O GLN E1090 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS E1096 " --> pdb=" O VAL F1093 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU F1095 " --> pdb=" O HIS E1096 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN G1089 " --> pdb=" O GLN F1090 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS F1096 " --> pdb=" O VAL G1093 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU G1095 " --> pdb=" O HIS F1096 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A1089 " --> pdb=" O GLU G1092 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N HIS G1094 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A1091 " --> pdb=" O HIS G1094 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N HIS G1096 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A1093 " --> pdb=" O HIS G1096 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 827 through 832 Processing sheet with id=AA6, first strand: chain 'B' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP B1051 " --> pdb=" O THR B1043 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 827 through 832 Processing sheet with id=AA8, first strand: chain 'C' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP C1051 " --> pdb=" O THR C1043 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 827 through 832 Processing sheet with id=AB1, first strand: chain 'D' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP D1051 " --> pdb=" O THR D1043 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 827 through 832 Processing sheet with id=AB3, first strand: chain 'E' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP E1051 " --> pdb=" O THR E1043 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 827 through 832 Processing sheet with id=AB5, first strand: chain 'F' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP F1051 " --> pdb=" O THR F1043 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 827 through 832 Processing sheet with id=AB7, first strand: chain 'G' and resid 1001 through 1009 removed outlier: 6.862A pdb=" N ASP G1051 " --> pdb=" O THR G1043 " (cutoff:3.500A) 3189 hydrogen bonds defined for protein. 9378 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: 9.46 Time building geometry restraints manager: 4.06 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: 11205 1.35 - 1.46: 7699 1.46 - 1.58: 13730 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 32760 Sorted by residual: bond pdb=" CB PHE A 925 " pdb=" CG PHE A 925 " ideal model delta sigma weight residual 1.502 1.525 -0.023 2.30e-02 1.89e+03 9.63e-01 bond pdb=" CB PHE G 925 " pdb=" CG PHE G 925 " ideal model delta sigma weight residual 1.502 1.525 -0.023 2.30e-02 1.89e+03 9.58e-01 bond pdb=" CB PHE E 925 " pdb=" CG PHE E 925 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.47e-01 bond pdb=" CB PHE B 925 " pdb=" CG PHE B 925 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.47e-01 bond pdb=" CB PHE C 925 " pdb=" CG PHE C 925 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.37e-01 ... (remaining 32755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 44609 2.02 - 4.04: 268 4.04 - 6.05: 84 6.05 - 8.07: 35 8.07 - 10.09: 14 Bond angle restraints: 45010 Sorted by residual: angle pdb=" CA LEU A 923 " pdb=" CB LEU A 923 " pdb=" CG LEU A 923 " ideal model delta sigma weight residual 116.30 126.39 -10.09 3.50e+00 8.16e-02 8.31e+00 angle pdb=" CA LEU B 923 " pdb=" CB LEU B 923 " pdb=" CG LEU B 923 " ideal model delta sigma weight residual 116.30 126.39 -10.09 3.50e+00 8.16e-02 8.31e+00 angle pdb=" CA LEU G 923 " pdb=" CB LEU G 923 " pdb=" CG LEU G 923 " ideal model delta sigma weight residual 116.30 126.38 -10.08 3.50e+00 8.16e-02 8.29e+00 angle pdb=" CA LEU E 923 " pdb=" CB LEU E 923 " pdb=" CG LEU E 923 " ideal model delta sigma weight residual 116.30 126.37 -10.07 3.50e+00 8.16e-02 8.28e+00 angle pdb=" CA LEU F 923 " pdb=" CB LEU F 923 " pdb=" CG LEU F 923 " ideal model delta sigma weight residual 116.30 126.37 -10.07 3.50e+00 8.16e-02 8.28e+00 ... (remaining 45005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 17045 16.21 - 32.42: 1442 32.42 - 48.62: 490 48.62 - 64.83: 56 64.83 - 81.04: 7 Dihedral angle restraints: 19040 sinusoidal: 4319 harmonic: 14721 Sorted by residual: dihedral pdb=" CA LEU G1056 " pdb=" C LEU G1056 " pdb=" N TYR G1057 " pdb=" CA TYR G1057 " ideal model delta harmonic sigma weight residual -180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU D1056 " pdb=" C LEU D1056 " pdb=" N TYR D1057 " pdb=" CA TYR D1057 " ideal model delta harmonic sigma weight residual 180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU B1056 " pdb=" C LEU B1056 " pdb=" N TYR B1057 " pdb=" CA TYR B1057 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 19037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4169 0.034 - 0.068: 1174 0.068 - 0.102: 295 0.102 - 0.135: 105 0.135 - 0.169: 11 Chirality restraints: 5754 Sorted by residual: chirality pdb=" CG LEU G 923 " pdb=" CB LEU G 923 " pdb=" CD1 LEU G 923 " pdb=" CD2 LEU G 923 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CG LEU B 923 " pdb=" CB LEU B 923 " pdb=" CD1 LEU B 923 " pdb=" CD2 LEU B 923 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CG LEU A 923 " pdb=" CB LEU A 923 " pdb=" CD1 LEU A 923 " pdb=" CD2 LEU A 923 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 5751 not shown) Planarity restraints: 5817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 599 " -0.007 2.00e-02 2.50e+03 9.25e-03 1.50e+00 pdb=" CG PHE C 599 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 599 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 599 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 599 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 599 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 599 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 599 " -0.007 2.00e-02 2.50e+03 9.24e-03 1.49e+00 pdb=" CG PHE D 599 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 599 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 599 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 599 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 599 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 599 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 599 " -0.007 2.00e-02 2.50e+03 9.23e-03 1.49e+00 pdb=" CG PHE E 599 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE E 599 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 599 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 599 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 599 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 599 " -0.001 2.00e-02 2.50e+03 ... (remaining 5814 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4836 2.75 - 3.29: 29937 3.29 - 3.83: 58581 3.83 - 4.36: 47476 4.36 - 4.90: 93465 Nonbonded interactions: 234295 Sorted by model distance: nonbonded pdb=" OD1 ASP A 975 " pdb=" NH1 ARG G1002 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG B1002 " pdb=" OD1 ASP C 975 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG F1002 " pdb=" OD1 ASP G 975 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG D1002 " pdb=" OD1 ASP E 975 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG E1002 " pdb=" OD1 ASP F 975 " model vdw 2.218 3.120 ... (remaining 234290 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.800 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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 0.038 32760 Z= 0.100 Angle : 0.500 10.091 45010 Z= 0.244 Chirality : 0.037 0.169 5754 Planarity : 0.002 0.029 5817 Dihedral : 14.554 81.041 9366 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.35 % Allowed : 37.89 % Favored : 61.75 % 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: 4.16 (0.12), residues: 4935 helix: 3.86 (0.08), residues: 3731 sheet: -0.06 (0.31), residues: 245 loop : -1.47 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 976 TYR 0.007 0.001 TYR G1057 PHE 0.021 0.001 PHE C 599 TRP 0.019 0.001 TRP E 586 HIS 0.001 0.000 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00203 (32760) covalent geometry : angle 0.50002 (45010) hydrogen bonds : bond 0.07761 ( 3189) hydrogen bonds : angle 3.08915 ( 9378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 666 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 847 LEU cc_start: 0.6819 (pp) cc_final: 0.6619 (mm) REVERT: A 967 ARG cc_start: 0.7817 (tmm160) cc_final: 0.7617 (ttp80) REVERT: A 1048 SER cc_start: 0.8689 (t) cc_final: 0.8384 (m) REVERT: B 847 LEU cc_start: 0.6827 (pp) cc_final: 0.6535 (mm) REVERT: B 879 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7238 (tm-30) REVERT: B 967 ARG cc_start: 0.7870 (tmm160) cc_final: 0.7581 (tmm160) REVERT: C 599 PHE cc_start: 0.6804 (t80) cc_final: 0.6584 (t80) REVERT: C 847 LEU cc_start: 0.7011 (pp) cc_final: 0.6785 (mm) REVERT: C 896 VAL cc_start: 0.8065 (p) cc_final: 0.7832 (t) REVERT: C 947 ARG cc_start: 0.7182 (ptp-170) cc_final: 0.6972 (ptp90) REVERT: D 879 GLN cc_start: 0.7022 (tm-30) cc_final: 0.6687 (tm-30) REVERT: D 967 ARG cc_start: 0.7584 (tmm160) cc_final: 0.7331 (tmm160) REVERT: D 1014 ASP cc_start: 0.7281 (t0) cc_final: 0.6993 (t70) REVERT: E 752 ARG cc_start: 0.7157 (ttm170) cc_final: 0.6888 (ttm170) REVERT: E 1014 ASP cc_start: 0.7269 (t0) cc_final: 0.6985 (t0) REVERT: E 1062 ARG cc_start: 0.6163 (mtm110) cc_final: 0.5876 (mtm110) REVERT: F 590 LYS cc_start: 0.6494 (tppt) cc_final: 0.6239 (ttmm) REVERT: F 879 GLN cc_start: 0.7024 (tm-30) cc_final: 0.6679 (tm-30) REVERT: F 915 LEU cc_start: 0.7382 (mp) cc_final: 0.7152 (mp) REVERT: F 977 LYS cc_start: 0.8070 (mttt) cc_final: 0.7766 (mttm) REVERT: F 1048 SER cc_start: 0.8611 (t) cc_final: 0.8392 (m) REVERT: G 752 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6643 (ttm170) REVERT: G 847 LEU cc_start: 0.6914 (pp) cc_final: 0.6652 (mm) REVERT: G 861 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6667 (mtt180) REVERT: G 947 ARG cc_start: 0.6962 (ptp-170) cc_final: 0.6620 (mpp80) REVERT: G 950 ASP cc_start: 0.7681 (p0) cc_final: 0.7463 (p0) REVERT: G 977 LYS cc_start: 0.8180 (mttt) cc_final: 0.7960 (mttm) outliers start: 7 outliers final: 0 residues processed: 673 average time/residue: 0.1974 time to fit residues: 206.9200 Evaluate side-chains 649 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.5980 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 GLN B 933 ASN C 933 ASN D 740 GLN D 933 ASN E 933 ASN E1090 GLN F 933 ASN ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152390 restraints weight = 58777.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149226 restraints weight = 78237.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146888 restraints weight = 54325.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145929 restraints weight = 53741.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146519 restraints weight = 50554.576| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32760 Z= 0.237 Angle : 0.604 8.814 45010 Z= 0.312 Chirality : 0.041 0.167 5754 Planarity : 0.004 0.068 5817 Dihedral : 3.907 23.114 5215 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 8.82 % Allowed : 30.18 % Favored : 61.00 % 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: 3.69 (0.12), residues: 4935 helix: 3.40 (0.08), residues: 3717 sheet: 0.82 (0.28), residues: 343 loop : -1.55 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 976 TYR 0.012 0.002 TYR F 883 PHE 0.029 0.002 PHE D1042 TRP 0.026 0.002 TRP C 826 HIS 0.009 0.001 HIS E1052 Details of bonding type rmsd covalent geometry : bond 0.00525 (32760) covalent geometry : angle 0.60353 (45010) hydrogen bonds : bond 0.04337 ( 3189) hydrogen bonds : angle 3.39576 ( 9378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 677 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 879 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 938 LEU cc_start: 0.8498 (tp) cc_final: 0.8184 (tt) REVERT: A 1014 ASP cc_start: 0.7297 (t0) cc_final: 0.6919 (t0) REVERT: B 590 LYS cc_start: 0.7202 (tppt) cc_final: 0.6793 (ttmm) REVERT: B 795 MET cc_start: 0.7751 (mmp) cc_final: 0.7494 (mmm) REVERT: B 879 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 890 ASN cc_start: 0.7696 (t0) cc_final: 0.7414 (t0) REVERT: B 977 LYS cc_start: 0.8298 (mttt) cc_final: 0.8021 (mttm) REVERT: B 1002 ARG cc_start: 0.8313 (ptt-90) cc_final: 0.8032 (ptt90) REVERT: C 843 MET cc_start: 0.6418 (tpt) cc_final: 0.6115 (tpp) REVERT: C 847 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6897 (mm) REVERT: C 889 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 1063 ASP cc_start: 0.7122 (p0) cc_final: 0.6693 (p0) REVERT: D 588 PHE cc_start: 0.5886 (t80) cc_final: 0.5677 (t80) REVERT: D 641 HIS cc_start: 0.6557 (OUTLIER) cc_final: 0.6068 (m-70) REVERT: D 879 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7010 (tm-30) REVERT: D 977 LYS cc_start: 0.8263 (mttt) cc_final: 0.7939 (mtpp) REVERT: D 1002 ARG cc_start: 0.8354 (ptt-90) cc_final: 0.8077 (ptt90) REVERT: D 1014 ASP cc_start: 0.7219 (t0) cc_final: 0.6843 (t0) REVERT: D 1030 PRO cc_start: 0.8586 (Cg_endo) cc_final: 0.8330 (Cg_exo) REVERT: D 1048 SER cc_start: 0.8862 (t) cc_final: 0.8544 (m) REVERT: E 752 ARG cc_start: 0.7366 (ttm170) cc_final: 0.7134 (ttm170) REVERT: E 798 MET cc_start: 0.6446 (mmm) cc_final: 0.6164 (mmm) REVERT: E 938 LEU cc_start: 0.8475 (tp) cc_final: 0.8258 (tt) REVERT: E 1063 ASP cc_start: 0.6968 (p0) cc_final: 0.6641 (p0) REVERT: F 879 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7028 (tm-30) REVERT: F 977 LYS cc_start: 0.8463 (mttt) cc_final: 0.8168 (mttm) REVERT: F 1014 ASP cc_start: 0.7240 (t0) cc_final: 0.6932 (t0) REVERT: F 1059 ARG cc_start: 0.7082 (ptt180) cc_final: 0.6871 (ptt-90) REVERT: F 1063 ASP cc_start: 0.6676 (p0) cc_final: 0.6292 (p0) REVERT: G 588 PHE cc_start: 0.6281 (t80) cc_final: 0.5998 (t80) REVERT: G 791 LEU cc_start: 0.8064 (tt) cc_final: 0.7859 (tt) REVERT: G 879 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7143 (tm-30) REVERT: G 938 LEU cc_start: 0.8420 (tp) cc_final: 0.8111 (tt) REVERT: G 967 ARG cc_start: 0.7941 (tmm160) cc_final: 0.7686 (ttp80) REVERT: G 1083 ASP cc_start: 0.7233 (t0) cc_final: 0.7009 (t0) outliers start: 176 outliers final: 120 residues processed: 784 average time/residue: 0.1830 time to fit residues: 227.4281 Evaluate side-chains 781 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 658 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 TRP Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 ARG Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 986 PHE Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 909 TRP Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain E residue 625 HIS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 842 THR Chi-restraints excluded: chain E residue 843 MET Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 860 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 734 ILE Chi-restraints excluded: chain G residue 748 VAL Chi-restraints excluded: chain G residue 841 VAL Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 860 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 901 VAL Chi-restraints excluded: chain G residue 909 TRP Chi-restraints excluded: chain G residue 986 PHE Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1017 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 50.0000 chunk 260 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 398 optimal weight: 0.5980 chunk 380 optimal weight: 8.9990 chunk 405 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 GLN F 933 ASN ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.171115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153845 restraints weight = 59219.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153020 restraints weight = 63711.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151692 restraints weight = 45830.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151048 restraints weight = 42480.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151508 restraints weight = 39065.022| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32760 Z= 0.119 Angle : 0.465 7.743 45010 Z= 0.239 Chirality : 0.037 0.138 5754 Planarity : 0.003 0.065 5817 Dihedral : 3.519 20.463 5215 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.47 % Allowed : 34.04 % Favored : 59.50 % 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: 4.05 (0.12), residues: 4935 helix: 3.69 (0.08), residues: 3717 sheet: 0.82 (0.28), residues: 343 loop : -1.49 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 944 TYR 0.007 0.001 TYR C 730 PHE 0.017 0.001 PHE G1042 TRP 0.026 0.001 TRP A 826 HIS 0.003 0.001 HIS E1052 Details of bonding type rmsd covalent geometry : bond 0.00261 (32760) covalent geometry : angle 0.46525 (45010) hydrogen bonds : bond 0.03441 ( 3189) hydrogen bonds : angle 3.08757 ( 9378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 672 time to evaluate : 0.916 Fit side-chains REVERT: A 938 LEU cc_start: 0.8601 (tp) cc_final: 0.8177 (tt) REVERT: A 977 LYS cc_start: 0.8401 (mttt) cc_final: 0.8170 (mttm) REVERT: A 1048 SER cc_start: 0.8697 (t) cc_final: 0.8385 (m) REVERT: B 869 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7686 (t) REVERT: B 879 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 977 LYS cc_start: 0.8337 (mttt) cc_final: 0.7754 (mttm) REVERT: B 1014 ASP cc_start: 0.7207 (t0) cc_final: 0.6960 (t0) REVERT: B 1048 SER cc_start: 0.8816 (t) cc_final: 0.8597 (m) REVERT: B 1063 ASP cc_start: 0.7167 (p0) cc_final: 0.6828 (p0) REVERT: C 847 LEU cc_start: 0.7073 (pp) cc_final: 0.6723 (mm) REVERT: D 879 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6890 (tm-30) REVERT: D 977 LYS cc_start: 0.8212 (mttt) cc_final: 0.7923 (mtpp) REVERT: D 1014 ASP cc_start: 0.7123 (t0) cc_final: 0.6754 (t0) REVERT: D 1030 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8298 (Cg_exo) REVERT: E 798 MET cc_start: 0.6461 (mmm) cc_final: 0.6211 (mmm) REVERT: E 938 LEU cc_start: 0.8595 (tp) cc_final: 0.8175 (tt) REVERT: E 1063 ASP cc_start: 0.6888 (p0) cc_final: 0.6299 (p0) REVERT: F 641 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5952 (m-70) REVERT: F 869 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7266 (t) REVERT: F 879 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6856 (tm-30) REVERT: F 977 LYS cc_start: 0.8427 (mttt) cc_final: 0.8170 (mttm) REVERT: F 1002 ARG cc_start: 0.8325 (ptt-90) cc_final: 0.7995 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7285 (t0) cc_final: 0.6994 (t0) REVERT: G 752 ARG cc_start: 0.7376 (ttm170) cc_final: 0.6996 (ttm170) REVERT: G 869 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7433 (t) REVERT: G 879 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6855 (tm-30) REVERT: G 938 LEU cc_start: 0.8416 (tp) cc_final: 0.8143 (tt) REVERT: G 967 ARG cc_start: 0.7819 (tmm160) cc_final: 0.7521 (ttp80) REVERT: G 1083 ASP cc_start: 0.7247 (t0) cc_final: 0.6993 (t0) outliers start: 129 outliers final: 95 residues processed: 744 average time/residue: 0.1939 time to fit residues: 225.6737 Evaluate side-chains 766 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 667 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1062 ARG Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 986 PHE Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 954 ILE Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 791 LEU Chi-restraints excluded: chain F residue 843 MET Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1032 VAL Chi-restraints excluded: chain G residue 590 LYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 795 MET Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1017 LYS Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 314 optimal weight: 7.9990 chunk 425 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 388 optimal weight: 0.0370 chunk 361 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 488 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 487 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 495 optimal weight: 0.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 890 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN D 933 ASN F 933 ASN ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN G 890 ASN G 933 ASN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152570 restraints weight = 58821.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147726 restraints weight = 64392.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.144796 restraints weight = 57368.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145120 restraints weight = 55750.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145338 restraints weight = 48488.587| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32760 Z= 0.150 Angle : 0.501 9.179 45010 Z= 0.259 Chirality : 0.038 0.211 5754 Planarity : 0.003 0.127 5817 Dihedral : 3.616 20.106 5215 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 8.57 % Allowed : 32.93 % Favored : 58.50 % 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: 3.89 (0.12), residues: 4935 helix: 3.61 (0.08), residues: 3696 sheet: 0.76 (0.27), residues: 343 loop : -1.59 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 861 TYR 0.009 0.001 TYR D 883 PHE 0.024 0.002 PHE G1042 TRP 0.028 0.001 TRP E 826 HIS 0.004 0.001 HIS D1052 Details of bonding type rmsd covalent geometry : bond 0.00331 (32760) covalent geometry : angle 0.50067 (45010) hydrogen bonds : bond 0.03765 ( 3189) hydrogen bonds : angle 3.18891 ( 9378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 670 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 938 LEU cc_start: 0.8550 (tp) cc_final: 0.8126 (tt) REVERT: A 977 LYS cc_start: 0.8495 (mttt) cc_final: 0.8171 (mttm) REVERT: A 1002 ARG cc_start: 0.8405 (ptt-90) cc_final: 0.8142 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7252 (t0) cc_final: 0.6907 (t0) REVERT: A 1048 SER cc_start: 0.8729 (t) cc_final: 0.8483 (m) REVERT: B 869 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7665 (t) REVERT: B 879 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 1014 ASP cc_start: 0.7216 (t0) cc_final: 0.7013 (t0) REVERT: B 1063 ASP cc_start: 0.7354 (p0) cc_final: 0.6999 (p0) REVERT: C 843 MET cc_start: 0.6325 (tpt) cc_final: 0.6021 (tpp) REVERT: C 847 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6815 (mm) REVERT: C 1002 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8101 (ptt-90) REVERT: D 641 HIS cc_start: 0.6514 (OUTLIER) cc_final: 0.6198 (m-70) REVERT: D 826 TRP cc_start: 0.7626 (p90) cc_final: 0.7342 (p90) REVERT: D 879 GLN cc_start: 0.7378 (tm-30) cc_final: 0.6973 (tm-30) REVERT: D 977 LYS cc_start: 0.8333 (mttt) cc_final: 0.8006 (mtpp) REVERT: D 1014 ASP cc_start: 0.7067 (t0) cc_final: 0.6721 (t0) REVERT: D 1030 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8377 (Cg_exo) REVERT: D 1048 SER cc_start: 0.8788 (t) cc_final: 0.8535 (m) REVERT: E 798 MET cc_start: 0.6484 (mmm) cc_final: 0.6268 (mmm) REVERT: E 854 MET cc_start: 0.6391 (mmp) cc_final: 0.6021 (mmp) REVERT: E 938 LEU cc_start: 0.8494 (tp) cc_final: 0.8190 (tt) REVERT: F 641 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6044 (m-70) REVERT: F 869 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7266 (t) REVERT: F 879 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6865 (tm-30) REVERT: F 977 LYS cc_start: 0.8457 (mttt) cc_final: 0.8078 (mttm) REVERT: F 1002 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8045 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7236 (t0) cc_final: 0.6942 (t0) REVERT: G 752 ARG cc_start: 0.7396 (ttm170) cc_final: 0.6951 (ttm170) REVERT: G 810 TRP cc_start: 0.7516 (m-10) cc_final: 0.6986 (m100) REVERT: G 854 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5803 (mmp) REVERT: G 879 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6866 (tm-30) REVERT: G 938 LEU cc_start: 0.8395 (tp) cc_final: 0.8120 (tt) REVERT: G 1002 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8013 (ptt-90) REVERT: G 1048 SER cc_start: 0.8926 (t) cc_final: 0.8595 (m) REVERT: G 1063 ASP cc_start: 0.7091 (p0) cc_final: 0.6841 (p0) outliers start: 171 outliers final: 125 residues processed: 766 average time/residue: 0.1853 time to fit residues: 226.2241 Evaluate side-chains 794 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 660 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 625 HIS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 842 THR Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 843 MET Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1032 VAL Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 854 MET Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 251 optimal weight: 10.0000 chunk 228 optimal weight: 50.0000 chunk 396 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 470 optimal weight: 0.9980 chunk 153 optimal weight: 50.0000 chunk 344 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 429 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN D 933 ASN E 740 GLN ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN F 983 ASN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.169408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149299 restraints weight = 58889.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146577 restraints weight = 71709.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148571 restraints weight = 53022.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148532 restraints weight = 31623.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148866 restraints weight = 29342.194| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32760 Z= 0.133 Angle : 0.486 9.185 45010 Z= 0.249 Chirality : 0.038 0.196 5754 Planarity : 0.003 0.057 5817 Dihedral : 3.517 19.942 5215 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.10 % Rotamer: Outliers : 7.57 % Allowed : 34.39 % Favored : 58.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.97 (0.12), residues: 4935 helix: 3.72 (0.08), residues: 3661 sheet: 0.75 (0.27), residues: 343 loop : -1.59 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 944 TYR 0.010 0.001 TYR F 739 PHE 0.019 0.001 PHE B1042 TRP 0.029 0.001 TRP E 826 HIS 0.003 0.001 HIS C1052 Details of bonding type rmsd covalent geometry : bond 0.00294 (32760) covalent geometry : angle 0.48617 (45010) hydrogen bonds : bond 0.03554 ( 3189) hydrogen bonds : angle 3.12246 ( 9378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 671 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 826 TRP cc_start: 0.7755 (p90) cc_final: 0.7540 (p90) REVERT: A 938 LEU cc_start: 0.8525 (tp) cc_final: 0.8105 (tt) REVERT: A 977 LYS cc_start: 0.8526 (mttt) cc_final: 0.8112 (mttm) REVERT: A 1002 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8140 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7260 (t0) cc_final: 0.6946 (t0) REVERT: A 1048 SER cc_start: 0.8723 (t) cc_final: 0.8469 (m) REVERT: B 869 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7623 (t) REVERT: B 879 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 1063 ASP cc_start: 0.7423 (p0) cc_final: 0.6997 (p0) REVERT: C 843 MET cc_start: 0.6227 (tpt) cc_final: 0.5892 (tpp) REVERT: C 1002 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7917 (ptt-90) REVERT: D 879 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6954 (tm-30) REVERT: D 977 LYS cc_start: 0.8332 (mttt) cc_final: 0.8011 (mtpp) REVERT: D 1014 ASP cc_start: 0.7111 (t0) cc_final: 0.6776 (t0) REVERT: D 1030 PRO cc_start: 0.8631 (Cg_endo) cc_final: 0.8385 (Cg_exo) REVERT: D 1048 SER cc_start: 0.8795 (t) cc_final: 0.8574 (m) REVERT: E 854 MET cc_start: 0.6365 (mmp) cc_final: 0.6055 (mmp) REVERT: E 912 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7387 (mp) REVERT: E 938 LEU cc_start: 0.8496 (tp) cc_final: 0.8176 (tt) REVERT: E 1063 ASP cc_start: 0.6739 (p0) cc_final: 0.6396 (p0) REVERT: F 641 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5998 (m-70) REVERT: F 869 VAL cc_start: 0.7510 (OUTLIER) cc_final: 0.7211 (t) REVERT: F 879 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6865 (tm-30) REVERT: F 977 LYS cc_start: 0.8510 (mttt) cc_final: 0.8154 (mttm) REVERT: F 1002 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8057 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7248 (t0) cc_final: 0.6971 (t0) REVERT: F 1063 ASP cc_start: 0.6746 (p0) cc_final: 0.6495 (p0) REVERT: G 752 ARG cc_start: 0.7410 (ttm170) cc_final: 0.6950 (ttm170) REVERT: G 810 TRP cc_start: 0.7480 (m-10) cc_final: 0.7009 (m100) REVERT: G 869 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7334 (t) REVERT: G 879 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6832 (tm-30) REVERT: G 938 LEU cc_start: 0.8366 (tp) cc_final: 0.8098 (tt) REVERT: G 1002 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8027 (ptt-90) REVERT: G 1048 SER cc_start: 0.8910 (t) cc_final: 0.8603 (m) outliers start: 151 outliers final: 116 residues processed: 756 average time/residue: 0.1831 time to fit residues: 220.0458 Evaluate side-chains 791 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 666 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 842 THR Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 912 LEU Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 886 THR Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1032 VAL Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 915 LEU Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 464 optimal weight: 9.9990 chunk 280 optimal weight: 0.7980 chunk 327 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 447 optimal weight: 4.9990 chunk 404 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 GLN C1094 HIS D 740 GLN D 890 ASN D 933 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN G 740 GLN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.152265 restraints weight = 58854.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146682 restraints weight = 66705.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145120 restraints weight = 53209.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145330 restraints weight = 49736.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145581 restraints weight = 41640.411| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32760 Z= 0.139 Angle : 0.503 9.586 45010 Z= 0.256 Chirality : 0.038 0.185 5754 Planarity : 0.003 0.054 5817 Dihedral : 3.546 20.494 5215 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.90 % Favored : 98.01 % Rotamer: Outliers : 8.22 % Allowed : 34.39 % Favored : 57.39 % 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: 3.91 (0.12), residues: 4935 helix: 3.67 (0.08), residues: 3661 sheet: 0.74 (0.27), residues: 343 loop : -1.57 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 944 TYR 0.009 0.001 TYR C1057 PHE 0.021 0.002 PHE A1042 TRP 0.030 0.001 TRP G 857 HIS 0.004 0.001 HIS B1052 Details of bonding type rmsd covalent geometry : bond 0.00306 (32760) covalent geometry : angle 0.50266 (45010) hydrogen bonds : bond 0.03655 ( 3189) hydrogen bonds : angle 3.15657 ( 9378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 680 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 938 LEU cc_start: 0.8460 (tp) cc_final: 0.8087 (tt) REVERT: A 977 LYS cc_start: 0.8590 (mttt) cc_final: 0.8153 (mttm) REVERT: A 1002 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8137 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7354 (t0) cc_final: 0.7089 (t0) REVERT: B 854 MET cc_start: 0.6378 (mmp) cc_final: 0.6154 (mmp) REVERT: B 869 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7501 (t) REVERT: B 879 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 1063 ASP cc_start: 0.7463 (p0) cc_final: 0.7081 (p0) REVERT: C 843 MET cc_start: 0.6476 (tpt) cc_final: 0.6138 (tpp) REVERT: C 899 MET cc_start: 0.7348 (tpp) cc_final: 0.7104 (tpp) REVERT: C 1002 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8149 (ptt90) REVERT: D 641 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.6116 (m-70) REVERT: D 879 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7106 (tm-30) REVERT: D 977 LYS cc_start: 0.8434 (mttt) cc_final: 0.7995 (mtpp) REVERT: D 1014 ASP cc_start: 0.7168 (t0) cc_final: 0.6875 (t0) REVERT: D 1030 PRO cc_start: 0.8630 (Cg_endo) cc_final: 0.8396 (Cg_exo) REVERT: E 854 MET cc_start: 0.6614 (mmp) cc_final: 0.6307 (mmp) REVERT: E 938 LEU cc_start: 0.8458 (tp) cc_final: 0.8145 (tt) REVERT: E 994 TRP cc_start: 0.8486 (m-10) cc_final: 0.7661 (m-10) REVERT: E 1031 ARG cc_start: 0.5798 (ttm-80) cc_final: 0.5471 (ttt-90) REVERT: E 1093 VAL cc_start: 0.8386 (m) cc_final: 0.8137 (t) REVERT: F 641 HIS cc_start: 0.6214 (OUTLIER) cc_final: 0.5981 (m-70) REVERT: F 869 VAL cc_start: 0.7394 (OUTLIER) cc_final: 0.7087 (t) REVERT: F 879 GLN cc_start: 0.7411 (tm-30) cc_final: 0.6954 (tm-30) REVERT: F 977 LYS cc_start: 0.8557 (mttt) cc_final: 0.7736 (mttm) REVERT: F 1002 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8062 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7339 (t0) cc_final: 0.7100 (t0) REVERT: F 1063 ASP cc_start: 0.7040 (p0) cc_final: 0.6747 (p0) REVERT: G 752 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6725 (ttm170) REVERT: G 810 TRP cc_start: 0.7451 (m-10) cc_final: 0.6982 (m100) REVERT: G 869 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7210 (t) REVERT: G 879 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6893 (tm-30) REVERT: G 938 LEU cc_start: 0.8360 (tp) cc_final: 0.8102 (tt) REVERT: G 1002 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8014 (ptt-90) REVERT: G 1048 SER cc_start: 0.8919 (t) cc_final: 0.8641 (m) REVERT: G 1083 ASP cc_start: 0.7333 (t0) cc_final: 0.7026 (t0) outliers start: 164 outliers final: 136 residues processed: 775 average time/residue: 0.1901 time to fit residues: 234.8039 Evaluate side-chains 822 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 677 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1071 LEU Chi-restraints excluded: chain E residue 625 HIS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 842 THR Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 851 ILE Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 886 THR Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 338 optimal weight: 0.9990 chunk 387 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 212 optimal weight: 0.0980 chunk 121 optimal weight: 0.1980 chunk 241 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN B 983 ASN ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1090 GLN ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN G 740 GLN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150999 restraints weight = 59157.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149313 restraints weight = 70708.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149788 restraints weight = 45875.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148707 restraints weight = 35409.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149289 restraints weight = 35208.212| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 32760 Z= 0.102 Angle : 0.473 9.368 45010 Z= 0.239 Chirality : 0.037 0.149 5754 Planarity : 0.003 0.055 5817 Dihedral : 3.354 19.761 5215 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 5.96 % Allowed : 37.34 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.16 (0.12), residues: 4935 helix: 3.86 (0.08), residues: 3661 sheet: 0.75 (0.27), residues: 343 loop : -1.53 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.006 0.001 TYR G 730 PHE 0.013 0.001 PHE F 848 TRP 0.032 0.001 TRP A 826 HIS 0.002 0.000 HIS G1094 Details of bonding type rmsd covalent geometry : bond 0.00219 (32760) covalent geometry : angle 0.47347 (45010) hydrogen bonds : bond 0.03237 ( 3189) hydrogen bonds : angle 3.00012 ( 9378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 670 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 826 TRP cc_start: 0.7675 (p90) cc_final: 0.7448 (p90) REVERT: A 869 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7268 (t) REVERT: A 938 LEU cc_start: 0.8523 (tp) cc_final: 0.8112 (tt) REVERT: A 977 LYS cc_start: 0.8470 (mttt) cc_final: 0.8089 (mttm) REVERT: A 1002 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8079 (ptt-90) REVERT: A 1031 ARG cc_start: 0.5791 (tpp80) cc_final: 0.5586 (ttm-80) REVERT: A 1048 SER cc_start: 0.8670 (t) cc_final: 0.8429 (m) REVERT: B 869 VAL cc_start: 0.7814 (t) cc_final: 0.7546 (t) REVERT: B 879 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 983 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7264 (m110) REVERT: B 1063 ASP cc_start: 0.7304 (p0) cc_final: 0.6885 (p0) REVERT: C 843 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5874 (tpp) REVERT: C 973 ASP cc_start: 0.8053 (t0) cc_final: 0.7835 (t0) REVERT: C 1002 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8071 (ptt-90) REVERT: D 641 HIS cc_start: 0.6449 (OUTLIER) cc_final: 0.6167 (m-70) REVERT: D 869 VAL cc_start: 0.7422 (t) cc_final: 0.7111 (t) REVERT: D 879 GLN cc_start: 0.7348 (tm-30) cc_final: 0.6940 (tm-30) REVERT: D 977 LYS cc_start: 0.8313 (mttt) cc_final: 0.8008 (mtpp) REVERT: D 1002 ARG cc_start: 0.8432 (ptt90) cc_final: 0.8211 (ptt90) REVERT: D 1014 ASP cc_start: 0.7067 (t0) cc_final: 0.6744 (t0) REVERT: D 1030 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8286 (Cg_exo) REVERT: E 854 MET cc_start: 0.6490 (mmp) cc_final: 0.6206 (mmp) REVERT: E 938 LEU cc_start: 0.8516 (tp) cc_final: 0.8162 (tt) REVERT: F 590 LYS cc_start: 0.7178 (tppt) cc_final: 0.6898 (ttmm) REVERT: F 641 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.6093 (m-70) REVERT: F 879 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6808 (tm-30) REVERT: F 977 LYS cc_start: 0.8447 (mttt) cc_final: 0.8101 (mtpp) REVERT: F 1002 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8067 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7332 (t0) cc_final: 0.7031 (t0) REVERT: F 1031 ARG cc_start: 0.6572 (tpt170) cc_final: 0.6294 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6820 (p0) cc_final: 0.6330 (p0) REVERT: G 752 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6883 (ttm170) REVERT: G 810 TRP cc_start: 0.7416 (m-10) cc_final: 0.6943 (m100) REVERT: G 879 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6745 (tm-30) REVERT: G 938 LEU cc_start: 0.8400 (tp) cc_final: 0.8119 (tt) REVERT: G 1002 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7975 (ptt-90) REVERT: G 1048 SER cc_start: 0.8909 (t) cc_final: 0.8601 (m) REVERT: G 1083 ASP cc_start: 0.7290 (t0) cc_final: 0.6947 (t0) outliers start: 119 outliers final: 92 residues processed: 738 average time/residue: 0.1902 time to fit residues: 222.9393 Evaluate side-chains 764 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 663 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 983 ASN Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 843 MET Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 843 MET Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 791 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 843 MET Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 845 SER Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 212 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 377 optimal weight: 0.9990 chunk 447 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 497 optimal weight: 0.0870 overall best weight: 1.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN D 890 ASN D 933 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1090 GLN ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN G 740 GLN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.167639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151417 restraints weight = 59036.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146361 restraints weight = 68494.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143989 restraints weight = 61475.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143866 restraints weight = 64953.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144393 restraints weight = 52269.467| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32760 Z= 0.163 Angle : 0.539 10.577 45010 Z= 0.274 Chirality : 0.039 0.174 5754 Planarity : 0.003 0.051 5817 Dihedral : 3.610 21.045 5215 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.95 % Favored : 97.93 % Rotamer: Outliers : 7.47 % Allowed : 36.24 % Favored : 56.29 % 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: 3.81 (0.12), residues: 4935 helix: 3.55 (0.08), residues: 3703 sheet: 0.67 (0.26), residues: 357 loop : -1.68 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 944 TYR 0.009 0.001 TYR F 883 PHE 0.030 0.002 PHE F1042 TRP 0.033 0.002 TRP E 826 HIS 0.005 0.001 HIS C1094 Details of bonding type rmsd covalent geometry : bond 0.00361 (32760) covalent geometry : angle 0.53928 (45010) hydrogen bonds : bond 0.03835 ( 3189) hydrogen bonds : angle 3.19880 ( 9378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 682 time to evaluate : 0.954 Fit side-chains REVERT: A 938 LEU cc_start: 0.8427 (tp) cc_final: 0.8065 (tt) REVERT: A 977 LYS cc_start: 0.8572 (mttt) cc_final: 0.8168 (mttm) REVERT: A 1002 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8146 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7379 (t0) cc_final: 0.7123 (t0) REVERT: A 1031 ARG cc_start: 0.6273 (tpp80) cc_final: 0.5923 (ttm-80) REVERT: B 795 MET cc_start: 0.7767 (mmm) cc_final: 0.7566 (mmm) REVERT: B 869 VAL cc_start: 0.7776 (t) cc_final: 0.7526 (t) REVERT: B 879 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 1063 ASP cc_start: 0.7469 (p0) cc_final: 0.7089 (p0) REVERT: C 843 MET cc_start: 0.6518 (tpt) cc_final: 0.6189 (tpp) REVERT: C 889 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 1002 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8045 (ptt-90) REVERT: C 1063 ASP cc_start: 0.7084 (p0) cc_final: 0.6657 (p0) REVERT: D 641 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.6214 (m-70) REVERT: D 879 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7146 (tm-30) REVERT: D 977 LYS cc_start: 0.8448 (mttt) cc_final: 0.8137 (mtpp) REVERT: D 1002 ARG cc_start: 0.8527 (ptt90) cc_final: 0.8291 (ptt90) REVERT: D 1014 ASP cc_start: 0.7266 (t0) cc_final: 0.6981 (t0) REVERT: D 1030 PRO cc_start: 0.8622 (Cg_endo) cc_final: 0.8350 (Cg_exo) REVERT: E 854 MET cc_start: 0.6625 (mmp) cc_final: 0.6321 (mmp) REVERT: E 938 LEU cc_start: 0.8421 (tp) cc_final: 0.8118 (tt) REVERT: E 1031 ARG cc_start: 0.5741 (ttm-80) cc_final: 0.5521 (ttt-90) REVERT: E 1063 ASP cc_start: 0.6737 (p0) cc_final: 0.5631 (p0) REVERT: E 1093 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8164 (t) REVERT: F 641 HIS cc_start: 0.6260 (OUTLIER) cc_final: 0.6019 (m-70) REVERT: F 879 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7008 (tm-30) REVERT: F 1002 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8104 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7339 (t0) cc_final: 0.7090 (t0) REVERT: F 1063 ASP cc_start: 0.7116 (p0) cc_final: 0.6808 (p0) REVERT: G 752 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6751 (ttm170) REVERT: G 810 TRP cc_start: 0.7437 (m-10) cc_final: 0.7014 (m100) REVERT: G 879 GLN cc_start: 0.7468 (tm-30) cc_final: 0.6920 (tm-30) REVERT: G 938 LEU cc_start: 0.8345 (tp) cc_final: 0.8094 (tt) REVERT: G 1002 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8024 (ptt-90) REVERT: G 1048 SER cc_start: 0.8931 (t) cc_final: 0.8635 (m) REVERT: G 1083 ASP cc_start: 0.7347 (t0) cc_final: 0.7013 (t0) outliers start: 149 outliers final: 121 residues processed: 769 average time/residue: 0.1918 time to fit residues: 236.2241 Evaluate side-chains 807 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 678 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1071 LEU Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 625 HIS Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 842 THR Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1093 VAL Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 851 ILE Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 746 LEU Chi-restraints excluded: chain G residue 748 VAL Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 388 optimal weight: 0.9990 chunk 338 optimal weight: 0.5980 chunk 454 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 414 optimal weight: 0.7980 chunk 494 optimal weight: 0.7980 chunk 267 optimal weight: 0.7980 chunk 258 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN B 983 ASN D 933 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN G 740 GLN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151143 restraints weight = 58738.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147865 restraints weight = 75527.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148956 restraints weight = 62866.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149322 restraints weight = 44953.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149276 restraints weight = 44652.014| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32760 Z= 0.132 Angle : 0.516 10.113 45010 Z= 0.261 Chirality : 0.038 0.163 5754 Planarity : 0.003 0.051 5817 Dihedral : 3.523 20.328 5215 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.74 % Favored : 98.14 % Rotamer: Outliers : 6.57 % Allowed : 37.19 % Favored : 56.24 % 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: 3.83 (0.12), residues: 4935 helix: 3.53 (0.08), residues: 3731 sheet: 0.69 (0.26), residues: 357 loop : -1.70 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 861 TYR 0.007 0.001 TYR B 883 PHE 0.020 0.001 PHE F1042 TRP 0.034 0.001 TRP D 826 HIS 0.003 0.001 HIS C1052 Details of bonding type rmsd covalent geometry : bond 0.00291 (32760) covalent geometry : angle 0.51574 (45010) hydrogen bonds : bond 0.03567 ( 3189) hydrogen bonds : angle 3.14090 ( 9378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 676 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 826 TRP cc_start: 0.7668 (p90) cc_final: 0.7315 (p90) REVERT: A 938 LEU cc_start: 0.8515 (tp) cc_final: 0.8146 (tt) REVERT: A 977 LYS cc_start: 0.8460 (mttt) cc_final: 0.8153 (mttm) REVERT: A 1002 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8119 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7259 (t0) cc_final: 0.6938 (t0) REVERT: B 795 MET cc_start: 0.7600 (mmm) cc_final: 0.7362 (mmm) REVERT: B 869 VAL cc_start: 0.7903 (t) cc_final: 0.7664 (t) REVERT: B 879 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 1063 ASP cc_start: 0.7274 (p0) cc_final: 0.6870 (p0) REVERT: C 843 MET cc_start: 0.6060 (tpt) cc_final: 0.5771 (tpp) REVERT: C 1002 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8074 (ptt-90) REVERT: D 641 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6148 (m-70) REVERT: D 791 LEU cc_start: 0.8042 (tt) cc_final: 0.7703 (tp) REVERT: D 879 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6933 (tm-30) REVERT: D 976 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7576 (mmm-85) REVERT: D 977 LYS cc_start: 0.8274 (mttt) cc_final: 0.8048 (mtpp) REVERT: D 1002 ARG cc_start: 0.8466 (ptt90) cc_final: 0.8253 (ptt90) REVERT: D 1014 ASP cc_start: 0.7058 (t0) cc_final: 0.6705 (t0) REVERT: D 1030 PRO cc_start: 0.8627 (Cg_endo) cc_final: 0.8328 (Cg_exo) REVERT: E 854 MET cc_start: 0.6411 (mmp) cc_final: 0.6125 (mmp) REVERT: E 938 LEU cc_start: 0.8505 (tp) cc_final: 0.8199 (tt) REVERT: E 967 ARG cc_start: 0.7780 (tmm160) cc_final: 0.7560 (ttp80) REVERT: E 1063 ASP cc_start: 0.6498 (p0) cc_final: 0.5467 (p0) REVERT: E 1093 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8198 (t) REVERT: F 641 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.6135 (m-70) REVERT: F 869 VAL cc_start: 0.7575 (t) cc_final: 0.7293 (t) REVERT: F 879 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6833 (tm-30) REVERT: F 1002 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8119 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7208 (t0) cc_final: 0.6865 (t0) REVERT: F 1031 ARG cc_start: 0.6698 (tpt170) cc_final: 0.6410 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6772 (p0) cc_final: 0.6268 (p0) REVERT: G 752 ARG cc_start: 0.7543 (ttm170) cc_final: 0.7038 (ttm170) REVERT: G 795 MET cc_start: 0.7363 (mmm) cc_final: 0.7028 (ttm) REVERT: G 879 GLN cc_start: 0.7292 (tm-30) cc_final: 0.6715 (tm-30) REVERT: G 938 LEU cc_start: 0.8378 (tp) cc_final: 0.8090 (tt) REVERT: G 1002 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8027 (ptt-90) REVERT: G 1048 SER cc_start: 0.8917 (t) cc_final: 0.8575 (m) outliers start: 131 outliers final: 117 residues processed: 751 average time/residue: 0.1902 time to fit residues: 227.4996 Evaluate side-chains 797 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 673 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 625 HIS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1093 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 843 MET Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1037 MET Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 229 optimal weight: 40.0000 chunk 95 optimal weight: 20.0000 chunk 300 optimal weight: 50.0000 chunk 92 optimal weight: 0.8980 chunk 376 optimal weight: 10.0000 chunk 356 optimal weight: 0.0970 chunk 396 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 214 optimal weight: 0.1980 chunk 379 optimal weight: 0.8980 chunk 83 optimal weight: 50.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN D 890 ASN D 933 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146526 restraints weight = 59703.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144748 restraints weight = 68683.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146114 restraints weight = 47700.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.146518 restraints weight = 33999.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146640 restraints weight = 30241.667| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32760 Z= 0.138 Angle : 0.531 10.445 45010 Z= 0.267 Chirality : 0.038 0.167 5754 Planarity : 0.003 0.051 5817 Dihedral : 3.562 20.775 5215 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.07 % Favored : 97.81 % Rotamer: Outliers : 6.47 % Allowed : 37.49 % Favored : 56.04 % 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: 3.79 (0.12), residues: 4935 helix: 3.49 (0.08), residues: 3731 sheet: 0.71 (0.26), residues: 357 loop : -1.69 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 861 TYR 0.008 0.001 TYR B 883 PHE 0.019 0.002 PHE C1042 TRP 0.033 0.001 TRP B 826 HIS 0.003 0.001 HIS C1052 Details of bonding type rmsd covalent geometry : bond 0.00303 (32760) covalent geometry : angle 0.53115 (45010) hydrogen bonds : bond 0.03653 ( 3189) hydrogen bonds : angle 3.16525 ( 9378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9870 Ramachandran restraints generated. 4935 Oldfield, 0 Emsley, 4935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 679 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 590 LYS cc_start: 0.7292 (tppt) cc_final: 0.7055 (tppt) REVERT: A 938 LEU cc_start: 0.8477 (tp) cc_final: 0.8157 (tt) REVERT: A 977 LYS cc_start: 0.8473 (mttt) cc_final: 0.8138 (mttm) REVERT: A 1002 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8140 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7330 (t0) cc_final: 0.6981 (t0) REVERT: A 1063 ASP cc_start: 0.6915 (p0) cc_final: 0.6606 (p0) REVERT: B 795 MET cc_start: 0.7704 (mmm) cc_final: 0.7473 (mmm) REVERT: B 869 VAL cc_start: 0.7868 (t) cc_final: 0.7619 (t) REVERT: B 879 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 1063 ASP cc_start: 0.7338 (p0) cc_final: 0.6934 (p0) REVERT: C 590 LYS cc_start: 0.7160 (tppt) cc_final: 0.6765 (ttmm) REVERT: C 843 MET cc_start: 0.6224 (tpt) cc_final: 0.5926 (tpp) REVERT: C 870 LEU cc_start: 0.7450 (mp) cc_final: 0.7212 (mp) REVERT: C 1063 ASP cc_start: 0.6871 (p0) cc_final: 0.6394 (p0) REVERT: D 641 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6168 (m-70) REVERT: D 791 LEU cc_start: 0.7983 (tt) cc_final: 0.7684 (tp) REVERT: D 879 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7033 (tm-30) REVERT: D 976 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: D 977 LYS cc_start: 0.8369 (mttt) cc_final: 0.8099 (mtpp) REVERT: D 1014 ASP cc_start: 0.7169 (t0) cc_final: 0.6835 (t0) REVERT: D 1030 PRO cc_start: 0.8622 (Cg_endo) cc_final: 0.8314 (Cg_exo) REVERT: E 854 MET cc_start: 0.6451 (mmp) cc_final: 0.6175 (mmp) REVERT: E 938 LEU cc_start: 0.8467 (tp) cc_final: 0.8174 (tt) REVERT: E 967 ARG cc_start: 0.7857 (tmm160) cc_final: 0.7569 (ttp80) REVERT: E 1093 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (t) REVERT: F 641 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.6151 (m-70) REVERT: F 869 VAL cc_start: 0.7501 (t) cc_final: 0.7218 (t) REVERT: F 879 GLN cc_start: 0.7361 (tm-30) cc_final: 0.6878 (tm-30) REVERT: F 888 ILE cc_start: 0.8673 (tp) cc_final: 0.8441 (tt) REVERT: F 1002 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8161 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7224 (t0) cc_final: 0.6918 (t0) REVERT: F 1031 ARG cc_start: 0.6679 (tpt170) cc_final: 0.6287 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6975 (p0) cc_final: 0.6179 (p0) REVERT: G 752 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6937 (ttm170) REVERT: G 879 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6780 (tm-30) REVERT: G 938 LEU cc_start: 0.8364 (tp) cc_final: 0.8087 (tt) REVERT: G 1002 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8058 (ptt-90) REVERT: G 1048 SER cc_start: 0.8931 (t) cc_final: 0.8609 (m) REVERT: G 1083 ASP cc_start: 0.7306 (t0) cc_final: 0.6964 (t0) outliers start: 129 outliers final: 118 residues processed: 756 average time/residue: 0.1910 time to fit residues: 229.4792 Evaluate side-chains 799 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 675 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 625 HIS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1093 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 845 SER Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 933 ASN Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 341 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 191 optimal weight: 0.7980 chunk 432 optimal weight: 50.0000 chunk 183 optimal weight: 2.9990 chunk 326 optimal weight: 0.6980 chunk 485 optimal weight: 1.9990 chunk 442 optimal weight: 30.0000 chunk 425 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN D 933 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.167889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.150067 restraints weight = 59252.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147757 restraints weight = 66462.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145470 restraints weight = 43049.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145424 restraints weight = 39062.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145692 restraints weight = 33894.324| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 32760 Z= 0.162 Angle : 0.637 59.197 45010 Z= 0.349 Chirality : 0.039 0.431 5754 Planarity : 0.003 0.053 5817 Dihedral : 3.600 37.587 5215 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.01 % Favored : 97.85 % Rotamer: Outliers : 7.22 % Allowed : 36.99 % Favored : 55.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.76 (0.12), residues: 4935 helix: 3.47 (0.08), residues: 3731 sheet: 0.71 (0.26), residues: 357 loop : -1.70 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 792 TYR 0.008 0.001 TYR B 883 PHE 0.020 0.002 PHE C1042 TRP 0.031 0.001 TRP B 826 HIS 0.003 0.001 HIS C1052 Details of bonding type rmsd covalent geometry : bond 0.00345 (32760) covalent geometry : angle 0.63664 (45010) hydrogen bonds : bond 0.03688 ( 3189) hydrogen bonds : angle 3.17102 ( 9378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5837.90 seconds wall clock time: 100 minutes 29.78 seconds (6029.78 seconds total)