Starting phenix.real_space_refine on Fri Jun 27 22:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uw5_26823/06_2025/7uw5_26823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uw5_26823/06_2025/7uw5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uw5_26823/06_2025/7uw5_26823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uw5_26823/06_2025/7uw5_26823.map" model { file = "/net/cci-nas-00/data/ceres_data/7uw5_26823/06_2025/7uw5_26823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uw5_26823/06_2025/7uw5_26823.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 24, 'TRP:plan': 6, 'ASP:plan': 15, 'PHE:plan': 14, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 639 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 11.46, per 1000 atoms: 0.35 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: 7.72 Conformation dependent library (CDL) restraints added in 4.5 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: 3.27 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: 12.50 Time building geometry restraints manager: 9.10 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: 0.30 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 63.030 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.019 0.001 TRP E 586 HIS 0.001 0.000 HIS B1029 PHE 0.021 0.001 PHE C 599 TYR 0.007 0.001 TYR G1057 ARG 0.005 0.000 ARG E 976 Details of bonding type rmsd hydrogen bonds : bond 0.07761 ( 3189) hydrogen bonds : angle 3.08915 ( 9378) covalent geometry : bond 0.00203 (32760) covalent geometry : angle 0.50002 (45010) *********************** 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 : 3.480 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: 0.8071 (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: 0.4633 time to fit residues: 483.1579 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 : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.6980 chunk 382 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 395 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 294 optimal weight: 0.8980 chunk 457 optimal weight: 10.0000 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 740 GLN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 ASN D 740 GLN ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN G 913 GLN ** G 933 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 = 0.4145 r_free = 0.4145 target = 0.172293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154785 restraints weight = 58418.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153083 restraints weight = 73279.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149319 restraints weight = 48319.111| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32760 Z= 0.142 Angle : 0.507 7.803 45010 Z= 0.255 Chirality : 0.038 0.146 5754 Planarity : 0.003 0.057 5817 Dihedral : 3.502 20.709 5215 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.72 % Allowed : 31.98 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.12), residues: 4935 helix: 3.81 (0.08), residues: 3717 sheet: 0.68 (0.29), residues: 329 loop : -1.51 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 826 HIS 0.005 0.001 HIS E1052 PHE 0.020 0.002 PHE G1042 TYR 0.011 0.001 TYR F1057 ARG 0.008 0.001 ARG E 976 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 3189) hydrogen bonds : angle 3.07262 ( 9378) covalent geometry : bond 0.00313 (32760) covalent geometry : angle 0.50746 (45010) *********************** 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 802 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 668 time to evaluate : 4.623 Fit side-chains revert: symmetry clash REVERT: A 795 MET cc_start: 0.7851 (mmp) cc_final: 0.7614 (mmm) REVERT: A 847 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6807 (mm) REVERT: A 854 MET cc_start: 0.6160 (mmp) cc_final: 0.5905 (mmp) REVERT: A 869 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7442 (t) REVERT: A 938 LEU cc_start: 0.8507 (tp) cc_final: 0.8117 (tt) REVERT: A 967 ARG cc_start: 0.7976 (tmm160) cc_final: 0.7677 (tmm160) REVERT: A 1048 SER cc_start: 0.8747 (t) cc_final: 0.8454 (m) REVERT: A 1062 ARG cc_start: 0.6114 (mtm110) cc_final: 0.5908 (mtm110) REVERT: B 795 MET cc_start: 0.7788 (mmp) cc_final: 0.7473 (mmm) REVERT: B 869 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7644 (t) REVERT: B 879 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 977 LYS cc_start: 0.8236 (mttt) cc_final: 0.7937 (mttm) REVERT: B 1002 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7937 (ptt90) REVERT: B 1048 SER cc_start: 0.8807 (t) cc_final: 0.8529 (m) REVERT: C 795 MET cc_start: 0.7862 (mmp) cc_final: 0.7630 (mmm) REVERT: C 847 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6824 (mm) REVERT: C 967 ARG cc_start: 0.8045 (tmm160) cc_final: 0.7749 (tmm160) REVERT: D 588 PHE cc_start: 0.5897 (t80) cc_final: 0.5633 (t80) REVERT: D 826 TRP cc_start: 0.7559 (p90) cc_final: 0.7305 (p90) REVERT: D 879 GLN cc_start: 0.7287 (tm-30) cc_final: 0.6922 (tm-30) REVERT: D 967 ARG cc_start: 0.7676 (tmm160) cc_final: 0.7390 (tmm160) REVERT: D 977 LYS cc_start: 0.8023 (mttt) cc_final: 0.7716 (mtpp) REVERT: D 1014 ASP cc_start: 0.7308 (t0) cc_final: 0.7022 (t70) REVERT: D 1030 PRO cc_start: 0.8401 (Cg_endo) cc_final: 0.7993 (Cg_exo) REVERT: E 752 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6940 (ttm170) REVERT: E 798 MET cc_start: 0.6458 (mmm) cc_final: 0.6164 (mmm) REVERT: E 947 ARG cc_start: 0.7558 (ptp90) cc_final: 0.7261 (ptp-170) REVERT: F 590 LYS cc_start: 0.6927 (tppt) cc_final: 0.6701 (ttmm) REVERT: F 869 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7260 (t) REVERT: F 879 GLN cc_start: 0.7322 (tm-30) cc_final: 0.7006 (tm-30) REVERT: F 947 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7476 (ptp-170) REVERT: F 977 LYS cc_start: 0.8348 (mttt) cc_final: 0.7965 (mttm) REVERT: F 1014 ASP cc_start: 0.7314 (t0) cc_final: 0.7051 (t0) REVERT: F 1048 SER cc_start: 0.8789 (t) cc_final: 0.8528 (m) REVERT: G 752 ARG cc_start: 0.7325 (ttm170) cc_final: 0.6976 (ttm170) REVERT: G 854 MET cc_start: 0.6061 (mmp) cc_final: 0.5775 (mmp) REVERT: G 869 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7418 (t) REVERT: G 938 LEU cc_start: 0.8477 (tp) cc_final: 0.8111 (tt) REVERT: G 967 ARG cc_start: 0.7886 (tmm160) cc_final: 0.7578 (ttp80) REVERT: G 1083 ASP cc_start: 0.7306 (t0) cc_final: 0.7051 (t0) outliers start: 134 outliers final: 94 residues processed: 742 average time/residue: 0.4339 time to fit residues: 505.6027 Evaluate side-chains 752 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 652 time to evaluate : 3.011 ------------------------------------------------------------------------------- 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 719 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 748 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 869 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 889 LEU 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 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 736 ASN Chi-restraints excluded: chain B residue 748 VAL 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 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 942 PHE 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 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 842 THR 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 954 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1017 LYS 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 717 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 748 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 951 THR Chi-restraints excluded: chain D residue 988 THR 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 988 THR 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 842 THR Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL 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 842 THR 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 886 THR Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 896 VAL Chi-restraints excluded: chain G residue 942 PHE Chi-restraints excluded: chain G residue 986 PHE Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1040 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 314 optimal weight: 8.9990 chunk 128 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 457 optimal weight: 9.9990 chunk 360 optimal weight: 80.0000 chunk 278 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 chunk 424 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 459 optimal weight: 0.9980 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN B 740 GLN ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 ASN D 740 GLN D 789 GLN D 933 ASN E 740 GLN E 933 ASN G 740 GLN G 933 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148287 restraints weight = 58839.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144487 restraints weight = 71295.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140589 restraints weight = 50557.009| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 32760 Z= 0.310 Angle : 0.680 9.636 45010 Z= 0.360 Chirality : 0.044 0.190 5754 Planarity : 0.004 0.054 5817 Dihedral : 4.414 24.384 5215 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 11.48 % Allowed : 30.38 % Favored : 58.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.12), residues: 4935 helix: 2.69 (0.08), residues: 3731 sheet: 0.86 (0.27), residues: 343 loop : -1.73 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 826 HIS 0.010 0.002 HIS C1052 PHE 0.042 0.003 PHE G1042 TYR 0.016 0.002 TYR F 883 ARG 0.010 0.001 ARG G1002 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 3189) hydrogen bonds : angle 3.86055 ( 9378) covalent geometry : bond 0.00687 (32760) covalent geometry : angle 0.67995 (45010) *********************** 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 891 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 662 time to evaluate : 3.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 LYS cc_start: 0.7522 (tppt) cc_final: 0.7108 (tppp) REVERT: A 847 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6795 (mm) REVERT: A 938 LEU cc_start: 0.8360 (tp) cc_final: 0.8128 (tt) REVERT: A 1048 SER cc_start: 0.8846 (t) cc_final: 0.8594 (m) REVERT: B 879 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 890 ASN cc_start: 0.7638 (t0) cc_final: 0.7385 (t0) REVERT: B 977 LYS cc_start: 0.8486 (mttt) cc_final: 0.7987 (mttm) REVERT: B 1002 ARG cc_start: 0.8453 (ptt-90) cc_final: 0.8186 (ptt90) REVERT: B 1063 ASP cc_start: 0.7529 (p0) cc_final: 0.7271 (p0) REVERT: C 599 PHE cc_start: 0.7083 (t80) cc_final: 0.6870 (t80) REVERT: C 791 LEU cc_start: 0.8131 (tt) cc_final: 0.7890 (tp) REVERT: C 843 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6290 (tpp) REVERT: C 889 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 1002 ARG cc_start: 0.8426 (ptt-90) cc_final: 0.8034 (ptt-90) REVERT: C 1031 ARG cc_start: 0.6202 (tpp80) cc_final: 0.5915 (ttm-80) REVERT: C 1063 ASP cc_start: 0.7532 (p0) cc_final: 0.7137 (p0) REVERT: D 588 PHE cc_start: 0.6216 (t80) cc_final: 0.5966 (t80) REVERT: D 641 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.6181 (m-70) REVERT: D 791 LEU cc_start: 0.7937 (tt) cc_final: 0.7668 (tp) REVERT: D 879 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7169 (tm-30) REVERT: D 977 LYS cc_start: 0.8467 (mttt) cc_final: 0.8092 (mtpp) REVERT: D 1002 ARG cc_start: 0.8544 (ptt-90) cc_final: 0.8255 (ptt90) REVERT: D 1014 ASP cc_start: 0.7203 (t0) cc_final: 0.6947 (t0) REVERT: E 752 ARG cc_start: 0.7353 (ttm170) cc_final: 0.7063 (ttm170) REVERT: E 798 MET cc_start: 0.6356 (mmm) cc_final: 0.5997 (mmm) REVERT: E 889 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7637 (mp) REVERT: E 938 LEU cc_start: 0.8328 (tp) cc_final: 0.8033 (tt) REVERT: E 999 THR cc_start: 0.8212 (t) cc_final: 0.7973 (p) REVERT: E 1063 ASP cc_start: 0.7373 (p0) cc_final: 0.7009 (p0) REVERT: E 1093 VAL cc_start: 0.8439 (m) cc_final: 0.8190 (t) REVERT: F 641 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.6118 (m-70) REVERT: F 793 ILE cc_start: 0.7908 (mm) cc_final: 0.7701 (mm) REVERT: F 879 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7288 (tm-30) REVERT: F 977 LYS cc_start: 0.8571 (mttt) cc_final: 0.8107 (mttm) REVERT: F 1002 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8146 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7367 (t0) cc_final: 0.7135 (t0) REVERT: F 1031 ARG cc_start: 0.6449 (tpp80) cc_final: 0.6103 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7113 (p0) cc_final: 0.6426 (p0) REVERT: G 1048 SER cc_start: 0.8822 (t) cc_final: 0.8588 (m) REVERT: G 1063 ASP cc_start: 0.7205 (p0) cc_final: 0.6975 (p0) outliers start: 229 outliers final: 165 residues processed: 812 average time/residue: 0.4326 time to fit residues: 557.2658 Evaluate side-chains 824 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 652 time to evaluate : 3.409 ------------------------------------------------------------------------------- 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 641 HIS 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 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 915 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 1007 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 THR 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 641 HIS 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 748 VAL Chi-restraints excluded: chain B residue 791 LEU 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 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 869 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 947 ARG 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 993 ASN Chi-restraints excluded: chain B residue 1017 LYS 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 641 HIS 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 734 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 843 MET 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 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 893 ILE 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 1007 LEU Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1023 LEU 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 809 ILE Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 843 MET 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 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 909 TRP Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1021 VAL 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 641 HIS Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 746 LEU 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 860 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 893 ILE 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 1021 VAL Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1048 SER 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 719 LEU Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 841 VAL Chi-restraints excluded: chain F residue 842 THR 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 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 993 ASN Chi-restraints excluded: chain F residue 1002 ARG Chi-restraints excluded: chain F residue 1007 LEU 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 641 HIS Chi-restraints excluded: chain G residue 717 THR Chi-restraints excluded: chain G residue 719 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 851 ILE Chi-restraints excluded: chain G residue 860 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 909 TRP Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN 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 415 optimal weight: 0.7980 chunk 489 optimal weight: 0.2980 chunk 253 optimal weight: 0.5980 chunk 267 optimal weight: 0.7980 chunk 442 optimal weight: 10.0000 chunk 418 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 99 optimal weight: 0.0970 chunk 43 optimal weight: 0.4980 chunk 413 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 GLN ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 983 ASN G 740 GLN ** 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 = 0.4113 r_free = 0.4113 target = 0.169791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151690 restraints weight = 58668.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148589 restraints weight = 69757.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.150214 restraints weight = 59614.194| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 32760 Z= 0.113 Angle : 0.476 8.725 45010 Z= 0.246 Chirality : 0.037 0.182 5754 Planarity : 0.003 0.068 5817 Dihedral : 3.638 20.006 5215 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Rotamer: Outliers : 5.86 % Allowed : 36.49 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.12), residues: 4935 helix: 3.51 (0.08), residues: 3661 sheet: 0.65 (0.27), residues: 343 loop : -1.57 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 826 HIS 0.002 0.000 HIS E1052 PHE 0.021 0.001 PHE D 848 TYR 0.008 0.001 TYR E1011 ARG 0.012 0.001 ARG D 861 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 3189) hydrogen bonds : angle 3.21795 ( 9378) covalent geometry : bond 0.00241 (32760) covalent geometry : angle 0.47641 (45010) *********************** 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 789 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 672 time to evaluate : 3.611 Fit side-chains revert: symmetry clash REVERT: A 847 LEU cc_start: 0.6950 (pp) cc_final: 0.6665 (mm) REVERT: A 900 THR cc_start: 0.8082 (m) cc_final: 0.7743 (m) REVERT: A 904 SER cc_start: 0.8103 (t) cc_final: 0.7712 (t) REVERT: A 938 LEU cc_start: 0.8572 (tp) cc_final: 0.8176 (tt) REVERT: A 986 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: A 1002 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (ptt-90) REVERT: A 1048 SER cc_start: 0.8815 (t) cc_final: 0.8497 (m) REVERT: B 869 VAL cc_start: 0.7950 (t) cc_final: 0.7720 (t) REVERT: B 879 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7184 (tm-30) REVERT: B 1002 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8160 (ptt90) REVERT: B 1063 ASP cc_start: 0.7338 (p0) cc_final: 0.6942 (p0) REVERT: C 843 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5646 (tpp) REVERT: C 879 GLN cc_start: 0.7403 (tm-30) cc_final: 0.6988 (tm-30) REVERT: C 964 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8063 (tt) REVERT: C 1002 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8107 (ptt-90) REVERT: C 1031 ARG cc_start: 0.6177 (tpp80) cc_final: 0.5944 (ttm-80) REVERT: C 1063 ASP cc_start: 0.7389 (p0) cc_final: 0.6754 (p0) REVERT: D 641 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.6137 (m-70) REVERT: D 879 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6797 (tm-30) REVERT: D 938 LEU cc_start: 0.8511 (tt) cc_final: 0.8268 (tp) REVERT: D 1002 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8256 (ptt90) REVERT: D 1014 ASP cc_start: 0.7065 (t0) cc_final: 0.6762 (t0) REVERT: E 590 LYS cc_start: 0.7167 (tppt) cc_final: 0.6932 (tppt) REVERT: E 938 LEU cc_start: 0.8468 (tp) cc_final: 0.8160 (tt) REVERT: E 1063 ASP cc_start: 0.7032 (p0) cc_final: 0.6792 (p0) REVERT: F 879 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6785 (tm-30) REVERT: F 977 LYS cc_start: 0.8448 (mttt) cc_final: 0.8119 (mtpp) REVERT: F 1002 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7980 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7085 (t0) cc_final: 0.6766 (t0) REVERT: F 1031 ARG cc_start: 0.6369 (tpp80) cc_final: 0.6019 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6855 (p0) cc_final: 0.6148 (p0) REVERT: G 810 TRP cc_start: 0.7468 (m-10) cc_final: 0.6979 (m100) REVERT: G 879 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6749 (tm-30) REVERT: G 938 LEU cc_start: 0.8391 (tp) cc_final: 0.8104 (tt) REVERT: G 1048 SER cc_start: 0.8784 (t) cc_final: 0.8463 (m) outliers start: 117 outliers final: 80 residues processed: 740 average time/residue: 0.4379 time to fit residues: 513.4399 Evaluate side-chains 753 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 664 time to evaluate : 3.186 ------------------------------------------------------------------------------- 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 843 MET Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 915 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 B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 791 LEU 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 889 LEU Chi-restraints excluded: chain B residue 892 ILE 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 988 THR Chi-restraints excluded: chain B residue 1002 ARG 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 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 843 MET 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 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 964 ILE Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1093 VAL 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 845 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1002 ARG Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 SER Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 786 VAL Chi-restraints excluded: chain E residue 796 LEU 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 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 1048 SER Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 717 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 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 970 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 G residue 637 LEU Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 861 ARG Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 868 GLU 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 1040 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 467 optimal weight: 4.9990 chunk 458 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 178 optimal weight: 0.2980 chunk 385 optimal weight: 9.9990 chunk 275 optimal weight: 0.0570 overall best weight: 1.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 GLN C1094 HIS 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 = 0.4041 r_free = 0.4041 target = 0.164309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137715 restraints weight = 58891.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139602 restraints weight = 39440.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140212 restraints weight = 27471.132| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32760 Z= 0.266 Angle : 0.626 10.565 45010 Z= 0.329 Chirality : 0.042 0.246 5754 Planarity : 0.004 0.063 5817 Dihedral : 4.174 22.456 5215 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 10.18 % Allowed : 32.48 % Favored : 57.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.12), residues: 4935 helix: 2.87 (0.08), residues: 3703 sheet: 0.70 (0.27), residues: 343 loop : -1.76 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 826 HIS 0.007 0.002 HIS C1052 PHE 0.039 0.003 PHE F1042 TYR 0.013 0.002 TYR D 883 ARG 0.007 0.001 ARG F 944 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 3189) hydrogen bonds : angle 3.68867 ( 9378) covalent geometry : bond 0.00589 (32760) covalent geometry : angle 0.62584 (45010) *********************** 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 878 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 675 time to evaluate : 3.311 Fit side-chains revert: symmetry clash REVERT: A 847 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6803 (mm) REVERT: A 938 LEU cc_start: 0.8449 (tp) cc_final: 0.8142 (tt) REVERT: A 1002 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8140 (ptt-90) REVERT: A 1048 SER cc_start: 0.8861 (t) cc_final: 0.8578 (m) REVERT: B 590 LYS cc_start: 0.7438 (tppt) cc_final: 0.7020 (ttmm) REVERT: B 879 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 1002 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8149 (ptt90) REVERT: B 1063 ASP cc_start: 0.7615 (p0) cc_final: 0.7223 (p0) REVERT: C 843 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6205 (tpp) REVERT: C 879 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7199 (tm-30) REVERT: D 641 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.6160 (m-70) REVERT: D 791 LEU cc_start: 0.7960 (tt) cc_final: 0.7652 (tp) REVERT: D 879 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7100 (tm-30) REVERT: D 889 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7479 (mt) REVERT: D 1002 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8212 (ptt90) REVERT: D 1014 ASP cc_start: 0.7189 (t0) cc_final: 0.6968 (t0) REVERT: E 590 LYS cc_start: 0.7610 (tppt) cc_final: 0.7158 (tppp) REVERT: E 889 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7608 (mp) REVERT: E 905 LEU cc_start: 0.8070 (tt) cc_final: 0.7865 (tt) REVERT: E 938 LEU cc_start: 0.8374 (tp) cc_final: 0.8127 (tt) REVERT: E 1031 ARG cc_start: 0.6361 (tpp-160) cc_final: 0.5976 (ttm-80) REVERT: E 1093 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8220 (t) REVERT: F 590 LYS cc_start: 0.7462 (tppt) cc_final: 0.7216 (ttmt) REVERT: F 641 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.6112 (m-70) REVERT: F 879 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7015 (tm-30) REVERT: F 977 LYS cc_start: 0.8611 (mttt) cc_final: 0.8279 (mtpp) REVERT: F 1002 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8137 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7095 (t0) cc_final: 0.6825 (t0) REVERT: F 1031 ARG cc_start: 0.6562 (tpp80) cc_final: 0.6072 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7189 (p0) cc_final: 0.6106 (p0) REVERT: G 590 LYS cc_start: 0.7385 (tppt) cc_final: 0.7049 (tppp) REVERT: G 938 LEU cc_start: 0.8322 (tp) cc_final: 0.8005 (tt) REVERT: G 1048 SER cc_start: 0.8831 (t) cc_final: 0.8572 (m) outliers start: 203 outliers final: 157 residues processed: 790 average time/residue: 0.4530 time to fit residues: 568.5881 Evaluate side-chains 837 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 669 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL 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 641 HIS 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 748 VAL Chi-restraints excluded: chain A residue 809 ILE 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 889 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 915 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 1027 THR Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1062 ARG Chi-restraints excluded: chain B residue 598 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 748 VAL Chi-restraints excluded: chain B residue 791 LEU 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 909 TRP 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 993 ASN Chi-restraints excluded: chain B residue 1002 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1023 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 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 809 ILE 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 851 ILE Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 885 ILE 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 1007 LEU Chi-restraints excluded: chain C residue 1043 THR 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 748 VAL Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 843 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE 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 988 THR Chi-restraints excluded: chain D residue 1002 ARG Chi-restraints excluded: chain D residue 1091 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 719 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 746 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 786 VAL Chi-restraints excluded: chain E residue 809 ILE 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 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 1023 LEU Chi-restraints excluded: chain E residue 1043 THR 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 748 VAL Chi-restraints excluded: chain F residue 786 VAL Chi-restraints excluded: chain F residue 809 ILE 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 870 LEU Chi-restraints excluded: chain F residue 885 ILE Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 946 VAL Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 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 1062 ARG 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 641 HIS Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 748 VAL Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 861 ARG Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 868 GLU 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 904 SER Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN 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 259 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 148 optimal weight: 10.0000 chunk 456 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 933 ASN F 933 ASN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147783 restraints weight = 58924.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143471 restraints weight = 66804.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141602 restraints weight = 51743.136| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32760 Z= 0.230 Angle : 0.592 10.589 45010 Z= 0.309 Chirality : 0.041 0.247 5754 Planarity : 0.004 0.064 5817 Dihedral : 4.106 22.891 5215 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.93 % Favored : 97.93 % Rotamer: Outliers : 9.97 % Allowed : 34.29 % Favored : 55.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.12), residues: 4935 helix: 2.79 (0.08), residues: 3703 sheet: 0.66 (0.26), residues: 343 loop : -1.75 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 826 HIS 0.005 0.001 HIS E1052 PHE 0.029 0.002 PHE E1042 TYR 0.011 0.002 TYR F 883 ARG 0.008 0.001 ARG G 944 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 3189) hydrogen bonds : angle 3.63398 ( 9378) covalent geometry : bond 0.00513 (32760) covalent geometry : angle 0.59182 (45010) *********************** 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 869 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 670 time to evaluate : 3.370 Fit side-chains revert: symmetry clash REVERT: A 795 MET cc_start: 0.7574 (mmm) cc_final: 0.7125 (mtp) REVERT: A 847 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6675 (mm) REVERT: A 938 LEU cc_start: 0.8463 (tp) cc_final: 0.8068 (tt) REVERT: A 1002 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8101 (ptt-90) REVERT: A 1048 SER cc_start: 0.8844 (t) cc_final: 0.8576 (m) REVERT: B 879 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 1002 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8169 (ptt90) REVERT: B 1063 ASP cc_start: 0.7557 (p0) cc_final: 0.7017 (p0) REVERT: C 843 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5959 (tpp) REVERT: C 870 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 879 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7139 (tm-30) REVERT: D 641 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6135 (m-70) REVERT: D 791 LEU cc_start: 0.7995 (tt) cc_final: 0.7683 (tp) REVERT: D 879 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7082 (tm-30) REVERT: D 976 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7650 (mmm-85) REVERT: D 1002 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8293 (ptt90) REVERT: D 1014 ASP cc_start: 0.7046 (t0) cc_final: 0.6773 (t0) REVERT: E 798 MET cc_start: 0.6248 (mmm) cc_final: 0.5918 (mmm) REVERT: E 938 LEU cc_start: 0.8402 (tp) cc_final: 0.8137 (tt) REVERT: E 994 TRP cc_start: 0.8584 (m-10) cc_final: 0.8291 (m-10) REVERT: E 1031 ARG cc_start: 0.6403 (tpp-160) cc_final: 0.5933 (ttm-80) REVERT: E 1063 ASP cc_start: 0.7473 (p0) cc_final: 0.6895 (p0) REVERT: E 1093 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8242 (t) REVERT: F 590 LYS cc_start: 0.7474 (tppt) cc_final: 0.7209 (ttmt) REVERT: F 641 HIS cc_start: 0.6325 (OUTLIER) cc_final: 0.6114 (m-70) REVERT: F 879 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7064 (tm-30) REVERT: F 1002 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8128 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7100 (t0) cc_final: 0.6793 (t0) REVERT: F 1031 ARG cc_start: 0.6504 (tpp80) cc_final: 0.6122 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7124 (p0) cc_final: 0.6373 (p0) REVERT: G 752 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7150 (ttm170) REVERT: G 938 LEU cc_start: 0.8357 (tp) cc_final: 0.8013 (tt) REVERT: G 1048 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8560 (m) REVERT: G 1063 ASP cc_start: 0.7116 (p0) cc_final: 0.6908 (p0) REVERT: G 1090 GLN cc_start: 0.8021 (mt0) cc_final: 0.7763 (mt0) outliers start: 199 outliers final: 157 residues processed: 789 average time/residue: 0.4157 time to fit residues: 520.5114 Evaluate side-chains 833 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 665 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL 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 809 ILE 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 904 SER Chi-restraints excluded: chain A residue 915 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 1007 LEU Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 598 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 748 VAL Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 795 MET 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 860 ILE 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 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 1002 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 598 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 809 ILE 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 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 885 ILE 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 936 SER 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 1007 LEU Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 598 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 729 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 809 ILE 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 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1002 ARG 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 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 746 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 809 ILE 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 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 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 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 809 ILE 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 851 ILE Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 885 ILE 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 970 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 993 ASN 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 F residue 1062 ARG Chi-restraints excluded: chain G residue 598 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 641 HIS Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 748 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 867 LEU Chi-restraints excluded: chain G residue 868 GLU 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 904 SER Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1021 VAL Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1048 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 121 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 13 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 402 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 472 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 890 ASN D 933 ASN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1082 ASN F 933 ASN ** 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 = 0.4064 r_free = 0.4064 target = 0.165834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149235 restraints weight = 58973.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143241 restraints weight = 62126.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142030 restraints weight = 54885.560| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32760 Z= 0.181 Angle : 0.560 11.124 45010 Z= 0.287 Chirality : 0.040 0.211 5754 Planarity : 0.003 0.062 5817 Dihedral : 3.926 22.446 5215 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.97 % Favored : 97.89 % Rotamer: Outliers : 9.12 % Allowed : 35.84 % Favored : 55.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.12), residues: 4935 helix: 2.96 (0.08), residues: 3703 sheet: 0.61 (0.26), residues: 343 loop : -1.75 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 826 HIS 0.005 0.001 HIS E1052 PHE 0.023 0.002 PHE E1042 TYR 0.009 0.001 TYR B 883 ARG 0.007 0.001 ARG G 944 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 3189) hydrogen bonds : angle 3.50598 ( 9378) covalent geometry : bond 0.00401 (32760) covalent geometry : angle 0.55995 (45010) *********************** 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 861 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 679 time to evaluate : 3.383 Fit side-chains revert: symmetry clash REVERT: A 809 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6107 (tp) REVERT: A 847 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6569 (mm) REVERT: A 938 LEU cc_start: 0.8407 (tp) cc_final: 0.8040 (tt) REVERT: A 1002 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8028 (ptt-90) REVERT: A 1048 SER cc_start: 0.8810 (t) cc_final: 0.8583 (m) REVERT: B 590 LYS cc_start: 0.7347 (tppt) cc_final: 0.7033 (ttmm) REVERT: B 879 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7272 (tm-30) REVERT: B 1002 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8196 (ptt90) REVERT: B 1063 ASP cc_start: 0.7557 (p0) cc_final: 0.7121 (p0) REVERT: C 843 MET cc_start: 0.6478 (tpt) cc_final: 0.6138 (tpp) REVERT: C 870 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7251 (mp) REVERT: C 879 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7128 (tm-30) REVERT: D 641 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.6218 (m-70) REVERT: D 795 MET cc_start: 0.7527 (mmm) cc_final: 0.7072 (ttp) REVERT: D 879 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7113 (tm-30) REVERT: D 976 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7778 (mmm-85) REVERT: D 1002 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8266 (ptt90) REVERT: D 1014 ASP cc_start: 0.7161 (t0) cc_final: 0.6916 (t0) REVERT: E 938 LEU cc_start: 0.8351 (tp) cc_final: 0.8079 (tt) REVERT: E 1031 ARG cc_start: 0.6402 (tpp-160) cc_final: 0.5946 (ttm-80) REVERT: E 1063 ASP cc_start: 0.7475 (p0) cc_final: 0.6779 (p0) REVERT: E 1093 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8190 (t) REVERT: F 590 LYS cc_start: 0.7426 (tppt) cc_final: 0.7208 (ttmt) REVERT: F 641 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.6069 (m-70) REVERT: F 879 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6942 (tm-30) REVERT: F 1014 ASP cc_start: 0.7249 (t0) cc_final: 0.6980 (t0) REVERT: F 1031 ARG cc_start: 0.6569 (tpp80) cc_final: 0.6178 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7201 (p0) cc_final: 0.6406 (p0) REVERT: G 752 ARG cc_start: 0.7446 (ttm170) cc_final: 0.7052 (ttm170) REVERT: G 938 LEU cc_start: 0.8356 (tp) cc_final: 0.8006 (tt) REVERT: G 1048 SER cc_start: 0.8832 (t) cc_final: 0.8566 (m) REVERT: G 1090 GLN cc_start: 0.8079 (mt0) cc_final: 0.7813 (mt0) outliers start: 182 outliers final: 149 residues processed: 789 average time/residue: 0.4215 time to fit residues: 530.1321 Evaluate side-chains 830 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 672 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL 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 737 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE 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 889 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 915 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 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 795 MET 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 868 GLU Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 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 1002 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 598 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 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 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 885 ILE 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 1007 LEU Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1088 PHE 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 729 VAL Chi-restraints excluded: chain D residue 748 VAL 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 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1002 ARG Chi-restraints excluded: chain D residue 1048 SER 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 736 ASN Chi-restraints excluded: chain E residue 746 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 809 ILE Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 860 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 1048 SER 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 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 786 VAL Chi-restraints excluded: chain F residue 809 ILE 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 899 MET Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 993 ASN Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1062 ARG Chi-restraints excluded: chain G residue 598 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 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 861 ARG Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 868 GLU 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 988 THR Chi-restraints excluded: chain G residue 1021 VAL Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1081 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 224 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 428 optimal weight: 0.7980 chunk 189 optimal weight: 0.4980 chunk 300 optimal weight: 40.0000 chunk 330 optimal weight: 0.9980 chunk 335 optimal weight: 0.6980 chunk 484 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN B 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 890 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150762 restraints weight = 59001.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145652 restraints weight = 64124.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143303 restraints weight = 56215.262| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32760 Z= 0.138 Angle : 0.528 10.925 45010 Z= 0.267 Chirality : 0.038 0.193 5754 Planarity : 0.003 0.061 5817 Dihedral : 3.725 22.223 5215 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.90 % Favored : 97.95 % Rotamer: Outliers : 7.87 % Allowed : 37.19 % Favored : 54.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.12), residues: 4935 helix: 3.20 (0.08), residues: 3703 sheet: 0.58 (0.26), residues: 343 loop : -1.73 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 826 HIS 0.004 0.001 HIS E1052 PHE 0.018 0.002 PHE C 848 TYR 0.008 0.001 TYR B 883 ARG 0.007 0.000 ARG G 944 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 3189) hydrogen bonds : angle 3.33541 ( 9378) covalent geometry : bond 0.00302 (32760) covalent geometry : angle 0.52772 (45010) *********************** 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 836 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 679 time to evaluate : 3.239 Fit side-chains REVERT: A 847 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6497 (mm) REVERT: A 938 LEU cc_start: 0.8474 (tp) cc_final: 0.8122 (tt) REVERT: A 1002 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8031 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7190 (t0) cc_final: 0.6957 (m-30) REVERT: A 1048 SER cc_start: 0.8812 (t) cc_final: 0.8567 (m) REVERT: B 879 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 843 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6054 (tpp) REVERT: C 870 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7255 (mp) REVERT: C 879 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 899 MET cc_start: 0.7407 (tpp) cc_final: 0.7184 (tpp) REVERT: C 1002 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7991 (ptt-90) REVERT: C 1031 ARG cc_start: 0.6354 (tpp-160) cc_final: 0.5914 (ttm-80) REVERT: C 1063 ASP cc_start: 0.7509 (p0) cc_final: 0.6922 (p0) REVERT: D 791 LEU cc_start: 0.7748 (tt) cc_final: 0.7538 (tp) REVERT: D 795 MET cc_start: 0.7537 (mmm) cc_final: 0.7143 (mtp) REVERT: D 861 ARG cc_start: 0.6867 (tmm160) cc_final: 0.6605 (tmm160) REVERT: D 879 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7105 (tm-30) REVERT: D 967 ARG cc_start: 0.7681 (tmm160) cc_final: 0.7408 (ttp80) REVERT: D 1002 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8268 (ptt90) REVERT: D 1014 ASP cc_start: 0.7117 (t0) cc_final: 0.6851 (t0) REVERT: E 938 LEU cc_start: 0.8364 (tp) cc_final: 0.8054 (tt) REVERT: E 994 TRP cc_start: 0.8632 (m-10) cc_final: 0.8338 (m-10) REVERT: E 1031 ARG cc_start: 0.6355 (tpp-160) cc_final: 0.5907 (ttm-80) REVERT: E 1063 ASP cc_start: 0.7471 (p0) cc_final: 0.6765 (p0) REVERT: F 869 VAL cc_start: 0.7490 (t) cc_final: 0.7217 (t) REVERT: F 879 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6911 (tm-30) REVERT: F 1002 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8126 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7291 (t0) cc_final: 0.7052 (t0) REVERT: F 1031 ARG cc_start: 0.6628 (tpp80) cc_final: 0.6232 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7222 (p0) cc_final: 0.6398 (p0) REVERT: G 590 LYS cc_start: 0.7208 (tppt) cc_final: 0.6876 (tppp) REVERT: G 752 ARG cc_start: 0.7373 (ttm170) cc_final: 0.6991 (ttm170) REVERT: G 810 TRP cc_start: 0.7440 (m-10) cc_final: 0.6971 (m100) REVERT: G 861 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6619 (tmm160) REVERT: G 879 GLN cc_start: 0.7374 (tm-30) cc_final: 0.6821 (tm-30) REVERT: G 938 LEU cc_start: 0.8361 (tp) cc_final: 0.8097 (tt) REVERT: G 1048 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8575 (m) REVERT: G 1090 GLN cc_start: 0.8075 (mt0) cc_final: 0.7801 (mt0) outliers start: 157 outliers final: 131 residues processed: 773 average time/residue: 0.4304 time to fit residues: 529.3224 Evaluate side-chains 813 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 673 time to evaluate : 3.136 ------------------------------------------------------------------------------- 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 842 THR Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE 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 889 LEU Chi-restraints excluded: chain A residue 915 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 809 ILE 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 885 ILE Chi-restraints excluded: chain B residue 889 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 988 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1014 ASP Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 625 HIS 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 748 VAL 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 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 904 SER 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 1021 VAL Chi-restraints excluded: chain C residue 1088 PHE Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 598 VAL 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 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 845 SER Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 870 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 960 THR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1002 ARG 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 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 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 1048 SER Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 637 LEU 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 843 MET 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 885 ILE Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 899 MET Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 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 1037 MET Chi-restraints excluded: chain F residue 1058 VAL Chi-restraints excluded: chain G residue 598 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 861 ARG Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 868 GLU 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 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1048 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 144 optimal weight: 50.0000 chunk 493 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 414 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 152 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 477 optimal weight: 0.0870 chunk 270 optimal weight: 0.7980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 890 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 = 0.4076 r_free = 0.4076 target = 0.166800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150253 restraints weight = 59110.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143922 restraints weight = 64613.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143165 restraints weight = 57453.276| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32760 Z= 0.146 Angle : 0.539 11.222 45010 Z= 0.272 Chirality : 0.039 0.186 5754 Planarity : 0.003 0.057 5817 Dihedral : 3.726 22.153 5215 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.01 % Favored : 97.85 % Rotamer: Outliers : 7.87 % Allowed : 37.54 % Favored : 54.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.12), residues: 4935 helix: 3.23 (0.08), residues: 3710 sheet: 0.60 (0.26), residues: 343 loop : -1.81 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 826 HIS 0.004 0.001 HIS E1052 PHE 0.021 0.002 PHE D 848 TYR 0.009 0.001 TYR B 883 ARG 0.008 0.001 ARG E 944 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 3189) hydrogen bonds : angle 3.32323 ( 9378) covalent geometry : bond 0.00320 (32760) covalent geometry : angle 0.53860 (45010) *********************** 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 835 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 678 time to evaluate : 3.241 Fit side-chains REVERT: A 847 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6540 (mm) REVERT: A 938 LEU cc_start: 0.8471 (tp) cc_final: 0.8091 (tt) REVERT: A 1002 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8080 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7183 (t0) cc_final: 0.6961 (m-30) REVERT: B 809 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6267 (tp) REVERT: B 879 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 843 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6085 (tpp) REVERT: C 870 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7239 (mp) REVERT: C 879 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7147 (tm-30) REVERT: C 899 MET cc_start: 0.7400 (tpp) cc_final: 0.7175 (tpp) REVERT: C 1002 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7977 (ptt-90) REVERT: D 795 MET cc_start: 0.7540 (mmm) cc_final: 0.7136 (mtp) REVERT: D 861 ARG cc_start: 0.6860 (tmm160) cc_final: 0.6508 (tmm160) REVERT: D 879 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7101 (tm-30) REVERT: D 1002 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8312 (ptt90) REVERT: D 1014 ASP cc_start: 0.7176 (t0) cc_final: 0.6898 (t0) REVERT: D 1031 ARG cc_start: 0.6598 (tpp-160) cc_final: 0.6199 (tpt90) REVERT: E 938 LEU cc_start: 0.8332 (tp) cc_final: 0.8066 (tt) REVERT: E 967 ARG cc_start: 0.7990 (tmm160) cc_final: 0.7672 (ttp80) REVERT: E 1031 ARG cc_start: 0.6346 (tpp-160) cc_final: 0.5864 (ttm-80) REVERT: E 1063 ASP cc_start: 0.7476 (p0) cc_final: 0.6457 (p0) REVERT: F 869 VAL cc_start: 0.7450 (t) cc_final: 0.7175 (t) REVERT: F 879 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6928 (tm-30) REVERT: F 1002 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8185 (ptt-90) REVERT: F 1031 ARG cc_start: 0.6537 (tpp80) cc_final: 0.6124 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7139 (p0) cc_final: 0.6312 (p0) REVERT: G 590 LYS cc_start: 0.7187 (tppt) cc_final: 0.6867 (tppp) REVERT: G 752 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7010 (ttm170) REVERT: G 810 TRP cc_start: 0.7418 (m-10) cc_final: 0.6969 (m100) REVERT: G 861 ARG cc_start: 0.6871 (tmm160) cc_final: 0.6576 (tmm160) REVERT: G 879 GLN cc_start: 0.7389 (tm-30) cc_final: 0.6812 (tm-30) REVERT: G 938 LEU cc_start: 0.8359 (tp) cc_final: 0.8088 (tt) REVERT: G 1048 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8595 (m) REVERT: G 1083 ASP cc_start: 0.7273 (t0) cc_final: 0.6935 (t0) outliers start: 157 outliers final: 141 residues processed: 773 average time/residue: 0.4265 time to fit residues: 526.4108 Evaluate side-chains 825 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 675 time to evaluate : 3.166 ------------------------------------------------------------------------------- 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 737 LEU 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 851 ILE 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 889 LEU Chi-restraints excluded: chain A residue 904 SER 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 795 MET Chi-restraints excluded: chain B residue 809 ILE 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 947 ARG Chi-restraints excluded: chain B residue 960 THR 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 1023 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 598 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 748 VAL 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 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 904 SER 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 1021 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 625 HIS 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 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 809 ILE 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 851 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 870 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 960 THR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1002 ARG Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 SER 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 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 746 LEU 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 1048 SER Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 637 LEU 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 746 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 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 885 ILE Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 899 MET 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 970 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 598 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 868 GLU 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 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1048 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 55 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 387 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 933 ASN ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4073 r_free = 0.4073 target = 0.166511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149601 restraints weight = 59150.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147559 restraints weight = 82031.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148611 restraints weight = 67970.244| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32760 Z= 0.161 Angle : 0.552 11.337 45010 Z= 0.279 Chirality : 0.039 0.192 5754 Planarity : 0.003 0.059 5817 Dihedral : 3.755 22.238 5215 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.97 % Favored : 97.89 % Rotamer: Outliers : 8.12 % Allowed : 37.44 % Favored : 54.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.12), residues: 4935 helix: 3.21 (0.08), residues: 3710 sheet: 0.60 (0.26), residues: 343 loop : -1.82 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 826 HIS 0.004 0.001 HIS E1052 PHE 0.021 0.002 PHE E1042 TYR 0.014 0.001 TYR B 716 ARG 0.008 0.001 ARG C 944 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 3189) hydrogen bonds : angle 3.34066 ( 9378) covalent geometry : bond 0.00357 (32760) covalent geometry : angle 0.55158 (45010) ********************** 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 839 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 677 time to evaluate : 3.187 Fit side-chains REVERT: A 588 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4993 (m-80) REVERT: A 847 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6597 (mm) REVERT: A 938 LEU cc_start: 0.8573 (tp) cc_final: 0.8135 (tt) REVERT: A 1002 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8074 (ptt-90) REVERT: B 809 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6216 (tp) REVERT: B 879 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7197 (tm-30) REVERT: C 843 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5717 (tpp) REVERT: C 870 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7116 (mp) REVERT: C 879 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7101 (tm-30) REVERT: C 1002 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: D 641 HIS cc_start: 0.6447 (OUTLIER) cc_final: 0.6128 (m-70) REVERT: D 795 MET cc_start: 0.7339 (mmm) cc_final: 0.6931 (mtp) REVERT: D 879 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6941 (tm-30) REVERT: D 1002 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8294 (ptt90) REVERT: D 1014 ASP cc_start: 0.7058 (t0) cc_final: 0.6717 (t0) REVERT: D 1031 ARG cc_start: 0.6495 (tpp-160) cc_final: 0.6148 (tpt90) REVERT: E 938 LEU cc_start: 0.8362 (tp) cc_final: 0.8064 (tt) REVERT: E 967 ARG cc_start: 0.7834 (tmm160) cc_final: 0.7626 (ttp80) REVERT: E 1031 ARG cc_start: 0.6271 (tpp-160) cc_final: 0.5832 (ttm-80) REVERT: E 1063 ASP cc_start: 0.7369 (p0) cc_final: 0.6410 (p0) REVERT: F 869 VAL cc_start: 0.7572 (t) cc_final: 0.7326 (t) REVERT: F 879 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6798 (tm-30) REVERT: F 1002 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8012 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7220 (t0) cc_final: 0.6897 (t0) REVERT: F 1031 ARG cc_start: 0.6551 (tpp80) cc_final: 0.6177 (ttm-80) REVERT: F 1063 ASP cc_start: 0.7008 (p0) cc_final: 0.6216 (p0) REVERT: G 590 LYS cc_start: 0.7092 (tppt) cc_final: 0.6822 (tppp) REVERT: G 752 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7303 (ttm170) REVERT: G 810 TRP cc_start: 0.7380 (m-10) cc_final: 0.6956 (m100) REVERT: G 861 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6570 (tmm160) REVERT: G 879 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6729 (tm-30) REVERT: G 938 LEU cc_start: 0.8350 (tp) cc_final: 0.8075 (tt) REVERT: G 1048 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8518 (m) REVERT: G 1083 ASP cc_start: 0.7238 (t0) cc_final: 0.6934 (t0) outliers start: 162 outliers final: 147 residues processed: 776 average time/residue: 0.4298 time to fit residues: 530.6532 Evaluate side-chains 836 residues out of total 4445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 677 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 PHE 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 748 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 851 ILE 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 795 MET Chi-restraints excluded: chain B residue 809 ILE 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 947 ARG Chi-restraints excluded: chain B residue 960 THR 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 1021 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 598 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 748 VAL 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 851 ILE 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 904 SER 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 1021 VAL Chi-restraints excluded: chain C residue 1088 PHE Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 598 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 719 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 809 ILE 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 851 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 870 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 960 THR Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1002 ARG Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 SER 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 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 746 LEU 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 F residue 625 HIS Chi-restraints excluded: chain F residue 637 LEU 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 746 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 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 885 ILE Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 899 MET Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 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 1037 MET Chi-restraints excluded: chain F residue 1058 VAL Chi-restraints excluded: chain F residue 1062 ARG Chi-restraints excluded: chain G residue 598 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 861 ARG Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 868 GLU 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 988 THR Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1048 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 235 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 478 optimal weight: 0.8980 chunk 494 optimal weight: 0.8980 chunk 487 optimal weight: 0.0970 chunk 151 optimal weight: 0.0670 chunk 343 optimal weight: 0.4980 chunk 274 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 13 optimal weight: 40.0000 chunk 211 optimal weight: 0.0470 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 983 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 983 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153729 restraints weight = 58798.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150656 restraints weight = 78194.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.151956 restraints weight = 66181.615| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 32760 Z= 0.103 Angle : 0.506 12.041 45010 Z= 0.252 Chirality : 0.037 0.159 5754 Planarity : 0.003 0.060 5817 Dihedral : 3.453 21.452 5215 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.72 % Favored : 98.14 % Rotamer: Outliers : 4.46 % Allowed : 41.40 % Favored : 54.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.12), residues: 4935 helix: 3.56 (0.08), residues: 3696 sheet: 0.65 (0.27), residues: 329 loop : -1.67 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 826 HIS 0.003 0.001 HIS D1052 PHE 0.023 0.001 PHE D 848 TYR 0.012 0.001 TYR B 716 ARG 0.008 0.001 ARG C 861 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 3189) hydrogen bonds : angle 3.09650 ( 9378) covalent geometry : bond 0.00217 (32760) covalent geometry : angle 0.50563 (45010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13372.54 seconds wall clock time: 231 minutes 56.32 seconds (13916.32 seconds total)