Starting phenix.real_space_refine on Fri Mar 22 04:57:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw5_26823/03_2024/7uw5_26823.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw5_26823/03_2024/7uw5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw5_26823/03_2024/7uw5_26823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw5_26823/03_2024/7uw5_26823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw5_26823/03_2024/7uw5_26823.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw5_26823/03_2024/7uw5_26823.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32340 Number of models: 1 Model: "" Number of chains: 7 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "G" 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 Time building chain proxies: 17.29, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 13.70 Conformation dependent library (CDL) restraints added in 6.5 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: 3.22 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: 11.64 Time building geometry restraints manager: 14.77 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: 100.56 - 107.26: 623 107.26 - 113.96: 19242 113.96 - 120.66: 14202 120.66 - 127.36: 10635 127.36 - 134.06: 308 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 2.520 nonbonded pdb=" NH1 ARG B1002 " pdb=" OD1 ASP C 975 " model vdw 2.218 2.520 nonbonded pdb=" NH1 ARG F1002 " pdb=" OD1 ASP G 975 " model vdw 2.218 2.520 nonbonded pdb=" NH1 ARG D1002 " pdb=" OD1 ASP E 975 " model vdw 2.218 2.520 nonbonded pdb=" NH1 ARG E1002 " pdb=" OD1 ASP F 975 " model vdw 2.218 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.030 Extract box with map and model: 14.760 Check model and map are aligned: 0.500 Set scattering table: 0.330 Process input model: 83.980 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.660 ------------------------------------------------------------------------------- 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= 0.140 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 666 time to evaluate : 3.529 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: 0.4524 time to fit residues: 469.6230 Evaluate side-chains 649 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 3.571 ------------------------------------------------------------------------------- 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: 0.5980 chunk 382 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 395 optimal weight: 0.0570 chunk 152 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 457 optimal weight: 9.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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** A1090 GLN B 740 GLN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 GLN C 933 ASN C1090 GLN D 740 GLN ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32760 Z= 0.231 Angle : 0.515 7.989 45010 Z= 0.260 Chirality : 0.038 0.157 5754 Planarity : 0.003 0.035 5817 Dihedral : 3.546 21.537 5215 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 7.12 % Allowed : 33.03 % Favored : 59.85 % 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: 4.13 (0.12), residues: 4935 helix: 3.77 (0.08), residues: 3717 sheet: 0.65 (0.28), residues: 343 loop : -1.51 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 826 HIS 0.005 0.001 HIS E1052 PHE 0.022 0.002 PHE G1042 TYR 0.008 0.001 TYR C 730 ARG 0.007 0.001 ARG F 944 *********************** 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 810 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 668 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 795 MET cc_start: 0.7822 (mmp) cc_final: 0.7530 (tpp) REVERT: A 854 MET cc_start: 0.6102 (mmp) cc_final: 0.5841 (mmp) REVERT: A 938 LEU cc_start: 0.8531 (tp) cc_final: 0.8198 (tt) REVERT: A 1048 SER cc_start: 0.8731 (t) cc_final: 0.8432 (m) REVERT: B 795 MET cc_start: 0.7686 (mmp) cc_final: 0.7418 (mmm) REVERT: B 869 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7714 (t) REVERT: B 879 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 1002 ARG cc_start: 0.8245 (ptt-90) cc_final: 0.7758 (ptt-90) REVERT: B 1048 SER cc_start: 0.8723 (t) cc_final: 0.8514 (m) REVERT: C 795 MET cc_start: 0.7835 (mmp) cc_final: 0.7618 (mmm) REVERT: C 847 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6797 (mm) REVERT: D 826 TRP cc_start: 0.7570 (p90) cc_final: 0.7308 (p90) REVERT: D 879 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6889 (tm-30) REVERT: D 977 LYS cc_start: 0.8034 (mttt) cc_final: 0.7814 (mtpp) REVERT: D 1002 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.8001 (ptt90) REVERT: D 1014 ASP cc_start: 0.7199 (t0) cc_final: 0.6776 (t0) REVERT: D 1030 PRO cc_start: 0.8506 (Cg_endo) cc_final: 0.8126 (Cg_exo) REVERT: E 752 ARG cc_start: 0.7361 (ttm170) cc_final: 0.7110 (ttm170) REVERT: E 798 MET cc_start: 0.6423 (mmm) cc_final: 0.6120 (mmm) REVERT: E 947 ARG cc_start: 0.7538 (ptp90) cc_final: 0.7270 (ptp-170) REVERT: F 590 LYS cc_start: 0.6837 (tppt) cc_final: 0.6635 (ttmm) REVERT: F 869 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7328 (t) REVERT: F 879 GLN cc_start: 0.7341 (tm-30) cc_final: 0.7027 (tm-30) REVERT: F 977 LYS cc_start: 0.8356 (mttt) cc_final: 0.8133 (mttm) REVERT: F 1014 ASP cc_start: 0.7137 (t0) cc_final: 0.6889 (t0) REVERT: G 752 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6817 (ttm170) REVERT: G 854 MET cc_start: 0.6042 (mmp) cc_final: 0.5766 (mmp) REVERT: G 869 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7475 (t) REVERT: G 938 LEU cc_start: 0.8486 (tp) cc_final: 0.8157 (tt) REVERT: G 977 LYS cc_start: 0.8130 (mttt) cc_final: 0.7873 (mttm) REVERT: G 1002 ARG cc_start: 0.8313 (ptt-90) cc_final: 0.8037 (ptt-90) REVERT: G 1083 ASP cc_start: 0.7275 (t0) cc_final: 0.7038 (t0) outliers start: 142 outliers final: 100 residues processed: 751 average time/residue: 0.4208 time to fit residues: 497.7313 Evaluate side-chains 756 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 652 time to evaluate : 3.341 ------------------------------------------------------------------------------- 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 729 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 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 A residue 1089 ASN 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 841 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 947 ARG 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 1040 VAL Chi-restraints excluded: chain B residue 1089 ASN 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 993 ASN 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 841 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 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 847 LEU 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 F residue 993 ASN Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 734 ILE Chi-restraints excluded: chain G residue 748 VAL Chi-restraints excluded: chain G residue 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 942 PHE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 0.9990 chunk 142 optimal weight: 0.0370 chunk 380 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 458 optimal weight: 8.9990 chunk 495 optimal weight: 0.9980 chunk 408 optimal weight: 0.7980 chunk 454 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 367 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 D 740 GLN D 933 ASN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 GLN ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32760 Z= 0.188 Angle : 0.462 7.492 45010 Z= 0.236 Chirality : 0.037 0.138 5754 Planarity : 0.002 0.034 5817 Dihedral : 3.417 20.776 5215 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 6.57 % Allowed : 34.64 % Favored : 58.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.23 (0.12), residues: 4935 helix: 3.81 (0.08), residues: 3717 sheet: 0.91 (0.28), residues: 343 loop : -1.44 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 826 HIS 0.003 0.001 HIS E1052 PHE 0.017 0.001 PHE G1042 TYR 0.010 0.001 TYR D1057 ARG 0.007 0.000 ARG B 944 *********************** 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 792 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 661 time to evaluate : 3.653 Fit side-chains revert: symmetry clash REVERT: A 938 LEU cc_start: 0.8597 (tp) cc_final: 0.8176 (tt) REVERT: A 1048 SER cc_start: 0.8751 (t) cc_final: 0.8443 (m) REVERT: B 869 VAL cc_start: 0.7927 (t) cc_final: 0.7658 (t) REVERT: B 879 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 1014 ASP cc_start: 0.7166 (t0) cc_final: 0.6923 (t0) REVERT: B 1063 ASP cc_start: 0.7042 (p0) cc_final: 0.6718 (p0) REVERT: C 847 LEU cc_start: 0.7042 (pp) cc_final: 0.6724 (mm) REVERT: C 870 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7660 (tp) REVERT: C 964 ILE cc_start: 0.8245 (tt) cc_final: 0.8036 (tt) REVERT: C 1002 ARG cc_start: 0.8247 (ptt-90) cc_final: 0.8045 (ptt-90) REVERT: D 641 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5940 (m-70) REVERT: D 879 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6833 (tm-30) REVERT: D 977 LYS cc_start: 0.8173 (mttt) cc_final: 0.7935 (mtpp) REVERT: D 1002 ARG cc_start: 0.8345 (ptt-90) cc_final: 0.8138 (ptt90) REVERT: D 1014 ASP cc_start: 0.7039 (t0) cc_final: 0.6701 (t0) REVERT: D 1030 PRO cc_start: 0.8557 (Cg_endo) cc_final: 0.8213 (Cg_exo) REVERT: E 752 ARG cc_start: 0.7354 (ttm170) cc_final: 0.7064 (ttm170) REVERT: E 938 LEU cc_start: 0.8627 (tp) cc_final: 0.8212 (tt) REVERT: E 947 ARG cc_start: 0.7574 (ptp90) cc_final: 0.7304 (ptp-170) REVERT: F 590 LYS cc_start: 0.6942 (tppt) cc_final: 0.6735 (ttmm) REVERT: F 879 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6909 (tm-30) REVERT: F 977 LYS cc_start: 0.8440 (mttt) cc_final: 0.8162 (mtpp) REVERT: F 1014 ASP cc_start: 0.7098 (t0) cc_final: 0.6815 (t0) REVERT: F 1063 ASP cc_start: 0.6414 (p0) cc_final: 0.6142 (p0) REVERT: G 854 MET cc_start: 0.6007 (mmp) cc_final: 0.5738 (mmp) REVERT: G 938 LEU cc_start: 0.8475 (tp) cc_final: 0.8152 (tt) REVERT: G 1002 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.7993 (ptt-90) REVERT: G 1048 SER cc_start: 0.8789 (t) cc_final: 0.8461 (m) REVERT: G 1083 ASP cc_start: 0.7281 (t0) cc_final: 0.7021 (t0) outliers start: 131 outliers final: 92 residues processed: 738 average time/residue: 0.4828 time to fit residues: 567.5050 Evaluate side-chains 745 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 651 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1067 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 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 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 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 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 909 TRP Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain E residue 719 LEU Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 842 THR Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 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 G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 796 LEU Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 867 LEU 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 961 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 2.9990 chunk 344 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 307 optimal weight: 0.0970 chunk 460 optimal weight: 0.5980 chunk 487 optimal weight: 0.9980 chunk 240 optimal weight: 0.3980 chunk 436 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** D 740 GLN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 GLN ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2003 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= 0.166 Angle : 0.449 8.469 45010 Z= 0.229 Chirality : 0.037 0.180 5754 Planarity : 0.002 0.034 5817 Dihedral : 3.328 19.420 5215 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 7.12 % Allowed : 35.49 % Favored : 57.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.27 (0.12), residues: 4935 helix: 3.85 (0.08), residues: 3717 sheet: 0.92 (0.28), residues: 343 loop : -1.44 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 826 HIS 0.002 0.001 HIS D1052 PHE 0.015 0.001 PHE G1042 TYR 0.005 0.001 TYR F 883 ARG 0.008 0.000 ARG E1062 *********************** 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 800 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 658 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 938 LEU cc_start: 0.8575 (tp) cc_final: 0.8173 (tt) REVERT: A 1048 SER cc_start: 0.8722 (t) cc_final: 0.8402 (m) REVERT: B 869 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7586 (t) REVERT: B 879 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 1014 ASP cc_start: 0.7150 (t0) cc_final: 0.6917 (t0) REVERT: B 1063 ASP cc_start: 0.7266 (p0) cc_final: 0.6838 (p0) REVERT: C 847 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6692 (mm) REVERT: C 870 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7575 (tp) REVERT: C 964 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8030 (tt) REVERT: D 826 TRP cc_start: 0.7573 (p90) cc_final: 0.7289 (p90) REVERT: D 879 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6822 (tm-30) REVERT: D 977 LYS cc_start: 0.8185 (mttt) cc_final: 0.7984 (mtpp) REVERT: D 1014 ASP cc_start: 0.7027 (t0) cc_final: 0.6669 (t0) REVERT: D 1030 PRO cc_start: 0.8609 (Cg_endo) cc_final: 0.8240 (Cg_exo) REVERT: E 752 ARG cc_start: 0.7310 (ttm170) cc_final: 0.7010 (ttm170) REVERT: E 798 MET cc_start: 0.6532 (mmm) cc_final: 0.6310 (mmm) REVERT: E 938 LEU cc_start: 0.8566 (tp) cc_final: 0.8167 (tt) REVERT: E 947 ARG cc_start: 0.7611 (ptp90) cc_final: 0.7404 (ptp-170) REVERT: E 1063 ASP cc_start: 0.6519 (p0) cc_final: 0.6159 (p0) REVERT: F 590 LYS cc_start: 0.6966 (tppt) cc_final: 0.6710 (ttmm) REVERT: F 641 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5996 (m-70) REVERT: F 879 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6840 (tm-30) REVERT: F 977 LYS cc_start: 0.8429 (mttt) cc_final: 0.8098 (mttm) REVERT: F 1014 ASP cc_start: 0.7054 (t0) cc_final: 0.6779 (t0) REVERT: G 854 MET cc_start: 0.6004 (mmp) cc_final: 0.5729 (mmp) REVERT: G 869 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7355 (t) REVERT: G 879 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6793 (tm-30) REVERT: G 938 LEU cc_start: 0.8469 (tp) cc_final: 0.8154 (tt) REVERT: G 1002 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8018 (ptt-90) REVERT: G 1048 SER cc_start: 0.8742 (t) cc_final: 0.8450 (m) REVERT: G 1083 ASP cc_start: 0.7283 (t0) cc_final: 0.7008 (t0) outliers start: 142 outliers final: 108 residues processed: 737 average time/residue: 0.4325 time to fit residues: 500.0866 Evaluate side-chains 764 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 649 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1067 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 717 THR Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 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 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 737 LEU 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 867 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1089 ASN 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 796 LEU Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1089 ASN 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 796 LEU 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 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 993 ASN Chi-restraints excluded: chain F residue 1089 ASN 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 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 942 PHE 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 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 415 optimal weight: 0.6980 chunk 336 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 437 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** C 890 ASN D 740 GLN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 GLN ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2381 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= 0.216 Angle : 0.489 8.874 45010 Z= 0.250 Chirality : 0.038 0.186 5754 Planarity : 0.003 0.029 5817 Dihedral : 3.477 19.787 5215 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 9.17 % Allowed : 33.88 % Favored : 56.94 % 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: 4.07 (0.12), residues: 4935 helix: 3.69 (0.08), residues: 3717 sheet: 0.91 (0.28), residues: 343 loop : -1.48 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 826 HIS 0.004 0.001 HIS E1052 PHE 0.022 0.002 PHE G1042 TYR 0.008 0.001 TYR F 883 ARG 0.007 0.001 ARG G 944 *********************** 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 847 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 664 time to evaluate : 3.786 Fit side-chains revert: symmetry clash REVERT: A 938 LEU cc_start: 0.8557 (tp) cc_final: 0.8131 (tt) REVERT: A 977 LYS cc_start: 0.8465 (mttt) cc_final: 0.8172 (mttm) REVERT: A 1014 ASP cc_start: 0.7104 (t0) cc_final: 0.6780 (t0) REVERT: A 1048 SER cc_start: 0.8756 (t) cc_final: 0.8429 (m) REVERT: B 869 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7649 (t) REVERT: B 879 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 977 LYS cc_start: 0.8280 (mttt) cc_final: 0.7808 (mttm) REVERT: B 1014 ASP cc_start: 0.7023 (t0) cc_final: 0.6822 (t0) REVERT: B 1063 ASP cc_start: 0.7357 (p0) cc_final: 0.6926 (p0) REVERT: C 847 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6772 (mm) REVERT: C 889 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7498 (mp) REVERT: C 964 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.8012 (tt) REVERT: C 1002 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8048 (ptt90) REVERT: C 1063 ASP cc_start: 0.6939 (p0) cc_final: 0.6587 (p0) REVERT: D 641 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6107 (m-70) REVERT: D 795 MET cc_start: 0.7465 (mmm) cc_final: 0.7179 (mmm) REVERT: D 879 GLN cc_start: 0.7315 (tm-30) cc_final: 0.6891 (tm-30) REVERT: D 977 LYS cc_start: 0.8264 (mttt) cc_final: 0.8025 (mtpp) REVERT: D 1014 ASP cc_start: 0.7032 (t0) cc_final: 0.6685 (t0) REVERT: D 1030 PRO cc_start: 0.8646 (Cg_endo) cc_final: 0.8370 (Cg_exo) REVERT: D 1073 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7669 (mtt-85) REVERT: E 752 ARG cc_start: 0.7330 (ttm170) cc_final: 0.7110 (ttm170) REVERT: E 798 MET cc_start: 0.6513 (mmm) cc_final: 0.6302 (mmm) REVERT: E 854 MET cc_start: 0.6369 (mmp) cc_final: 0.6007 (mmp) REVERT: E 938 LEU cc_start: 0.8506 (tp) cc_final: 0.8189 (tt) REVERT: E 1002 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8013 (ptt-90) REVERT: E 1063 ASP cc_start: 0.6572 (p0) cc_final: 0.6303 (p0) REVERT: F 641 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.6018 (m-70) REVERT: F 869 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7265 (t) REVERT: F 879 GLN cc_start: 0.7321 (tm-30) cc_final: 0.6887 (tm-30) REVERT: F 977 LYS cc_start: 0.8494 (mttt) cc_final: 0.8187 (mttm) REVERT: F 1002 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8142 (ptt-90) REVERT: F 1007 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7706 (pt) REVERT: F 1014 ASP cc_start: 0.7076 (t0) cc_final: 0.6818 (t0) REVERT: G 861 ARG cc_start: 0.6810 (mtt180) cc_final: 0.6597 (ttt180) REVERT: G 869 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7394 (t) REVERT: G 879 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6849 (tm-30) REVERT: G 938 LEU cc_start: 0.8411 (tp) cc_final: 0.8138 (tt) REVERT: G 1002 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8103 (ptt-90) REVERT: G 1048 SER cc_start: 0.8763 (t) cc_final: 0.8454 (m) REVERT: G 1063 ASP cc_start: 0.7047 (p0) cc_final: 0.6741 (p0) REVERT: G 1073 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7731 (mtt-85) outliers start: 183 outliers final: 147 residues processed: 767 average time/residue: 0.4275 time to fit residues: 516.1369 Evaluate side-chains 821 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 659 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 909 TRP 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 1067 THR Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 988 THR Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1074 THR 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 847 LEU Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 870 LEU 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 964 ILE Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1002 ARG Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1021 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 737 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1073 ARG Chi-restraints excluded: chain D residue 1089 ASN 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 737 LEU 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 842 THR Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 851 ILE Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 885 ILE Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1037 MET Chi-restraints excluded: chain E residue 1043 THR Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 843 MET Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 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 1007 LEU Chi-restraints excluded: chain F residue 1048 SER Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 915 LEU Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1073 ARG Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 3.9990 chunk 438 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 286 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 487 optimal weight: 0.8980 chunk 404 optimal weight: 0.8980 chunk 225 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** C 740 GLN D 740 GLN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN ** G 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32760 Z= 0.193 Angle : 0.478 8.906 45010 Z= 0.243 Chirality : 0.038 0.162 5754 Planarity : 0.002 0.028 5817 Dihedral : 3.423 19.134 5215 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.84 % Favored : 98.14 % Rotamer: Outliers : 8.57 % Allowed : 34.59 % Favored : 56.84 % 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: 4.13 (0.12), residues: 4935 helix: 3.78 (0.08), residues: 3682 sheet: 0.87 (0.27), residues: 343 loop : -1.46 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 826 HIS 0.003 0.001 HIS D1052 PHE 0.019 0.001 PHE G1042 TYR 0.007 0.001 TYR B 883 ARG 0.008 0.000 ARG E 944 *********************** 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 841 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 670 time to evaluate : 3.449 Fit side-chains revert: symmetry clash REVERT: A 869 VAL cc_start: 0.7637 (t) cc_final: 0.7357 (t) REVERT: A 938 LEU cc_start: 0.8538 (tp) cc_final: 0.8113 (tt) REVERT: A 977 LYS cc_start: 0.8435 (mttt) cc_final: 0.8141 (mttm) REVERT: A 1014 ASP cc_start: 0.7083 (t0) cc_final: 0.6774 (t0) REVERT: A 1048 SER cc_start: 0.8761 (t) cc_final: 0.8432 (m) REVERT: B 869 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7643 (t) REVERT: B 879 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 1063 ASP cc_start: 0.7398 (p0) cc_final: 0.6976 (p0) REVERT: C 889 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 964 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 1063 ASP cc_start: 0.6968 (p0) cc_final: 0.6721 (p0) REVERT: D 641 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.6144 (m-70) REVERT: D 795 MET cc_start: 0.7411 (mmm) cc_final: 0.6941 (mmm) REVERT: D 879 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6881 (tm-30) REVERT: D 977 LYS cc_start: 0.8280 (mttt) cc_final: 0.8044 (mtpp) REVERT: D 992 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8563 (mt) REVERT: D 1014 ASP cc_start: 0.7014 (t0) cc_final: 0.6676 (t0) REVERT: D 1030 PRO cc_start: 0.8640 (Cg_endo) cc_final: 0.8387 (Cg_exo) REVERT: D 1073 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7702 (mtt-85) REVERT: E 752 ARG cc_start: 0.7332 (ttm170) cc_final: 0.7103 (ttm170) REVERT: E 854 MET cc_start: 0.6319 (mmp) cc_final: 0.5992 (mmp) REVERT: E 938 LEU cc_start: 0.8518 (tp) cc_final: 0.8179 (tt) REVERT: E 1002 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8091 (ptt-90) REVERT: E 1093 VAL cc_start: 0.8415 (m) cc_final: 0.8133 (t) REVERT: F 641 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.6015 (m-70) REVERT: F 826 TRP cc_start: 0.7414 (p90) cc_final: 0.7152 (p90) REVERT: F 879 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6832 (tm-30) REVERT: F 977 LYS cc_start: 0.8491 (mttt) cc_final: 0.8215 (mtpp) REVERT: F 1002 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8103 (ptt-90) REVERT: F 1014 ASP cc_start: 0.7047 (t0) cc_final: 0.6823 (t0) REVERT: G 810 TRP cc_start: 0.7481 (m-10) cc_final: 0.7042 (m100) REVERT: G 869 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7366 (t) REVERT: G 938 LEU cc_start: 0.8403 (tp) cc_final: 0.8124 (tt) REVERT: G 1002 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8132 (ptt-90) REVERT: G 1048 SER cc_start: 0.8764 (t) cc_final: 0.8458 (m) REVERT: G 1073 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7702 (mtt-85) REVERT: G 1083 ASP cc_start: 0.7273 (t0) cc_final: 0.6987 (t0) outliers start: 171 outliers final: 137 residues processed: 769 average time/residue: 0.4519 time to fit residues: 551.0498 Evaluate side-chains 814 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 665 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 746 LEU 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 886 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1067 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 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 843 MET 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 885 ILE 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 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 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 B residue 1089 ASN Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 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 964 ILE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 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 915 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1073 ARG Chi-restraints excluded: chain D residue 1089 ASN 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 729 VAL Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 737 LEU Chi-restraints excluded: chain E residue 786 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 886 THR Chi-restraints excluded: chain E residue 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 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 1048 SER Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 746 LEU Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 847 LEU Chi-restraints excluded: chain G residue 851 ILE Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 961 VAL Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1073 ARG Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 356 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 410 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 485 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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** ** C 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 HIS D 740 GLN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN G 933 ASN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 : 0.004 0.060 32760 Z= 0.273 Angle : 0.553 10.117 45010 Z= 0.283 Chirality : 0.040 0.173 5754 Planarity : 0.003 0.045 5817 Dihedral : 3.753 21.420 5215 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.79 % Rotamer: Outliers : 9.17 % Allowed : 34.84 % Favored : 55.99 % 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: 3.64 (0.12), residues: 4935 helix: 3.39 (0.08), residues: 3710 sheet: 0.86 (0.27), residues: 343 loop : -1.67 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 826 HIS 0.005 0.001 HIS E1052 PHE 0.027 0.002 PHE A1042 TYR 0.014 0.001 TYR C1057 ARG 0.008 0.001 ARG D 976 *********************** 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 853 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 670 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 938 LEU cc_start: 0.8469 (tp) cc_final: 0.8119 (tt) REVERT: A 977 LYS cc_start: 0.8498 (mttt) cc_final: 0.8200 (mttm) REVERT: A 1002 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7141 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7088 (t0) cc_final: 0.6836 (t0) REVERT: A 1063 ASP cc_start: 0.6914 (p0) cc_final: 0.6512 (p0) REVERT: B 869 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7692 (t) REVERT: B 879 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 1063 ASP cc_start: 0.7501 (p0) cc_final: 0.7076 (p0) REVERT: C 843 MET cc_start: 0.6408 (tpt) cc_final: 0.6082 (tpp) REVERT: C 1002 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7976 (ptt-90) REVERT: C 1063 ASP cc_start: 0.7197 (p0) cc_final: 0.6891 (p0) REVERT: D 641 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.6109 (m-70) REVERT: D 854 MET cc_start: 0.6288 (mmp) cc_final: 0.6015 (mmp) REVERT: D 879 GLN cc_start: 0.7415 (tm-30) cc_final: 0.6968 (tm-30) REVERT: D 889 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7551 (mt) REVERT: D 977 LYS cc_start: 0.8374 (mttt) cc_final: 0.8101 (mtpp) REVERT: D 1014 ASP cc_start: 0.7014 (t0) cc_final: 0.6697 (t0) REVERT: D 1030 PRO cc_start: 0.8707 (Cg_endo) cc_final: 0.8472 (Cg_exo) REVERT: D 1073 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: E 938 LEU cc_start: 0.8488 (tp) cc_final: 0.8194 (tt) REVERT: E 967 ARG cc_start: 0.7855 (tmm160) cc_final: 0.7516 (ttp80) REVERT: E 1002 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (ptt-90) REVERT: E 1093 VAL cc_start: 0.8488 (m) cc_final: 0.8227 (t) REVERT: F 641 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.6052 (m-70) REVERT: F 791 LEU cc_start: 0.7780 (tt) cc_final: 0.7520 (tp) REVERT: F 869 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7283 (t) REVERT: F 879 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6947 (tm-30) REVERT: F 977 LYS cc_start: 0.8588 (mttt) cc_final: 0.8334 (mtpp) REVERT: F 1014 ASP cc_start: 0.7033 (t0) cc_final: 0.6815 (t0) REVERT: F 1031 ARG cc_start: 0.6491 (tpt170) cc_final: 0.6113 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6570 (p0) cc_final: 0.6180 (p0) REVERT: G 590 LYS cc_start: 0.7010 (tppt) cc_final: 0.6722 (tppp) REVERT: G 795 MET cc_start: 0.7451 (mmm) cc_final: 0.7098 (ttm) REVERT: G 938 LEU cc_start: 0.8355 (tp) cc_final: 0.8088 (tt) REVERT: G 1002 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8204 (ptt-90) REVERT: G 1014 ASP cc_start: 0.7093 (t0) cc_final: 0.6731 (t0) REVERT: G 1048 SER cc_start: 0.8800 (t) cc_final: 0.8463 (m) REVERT: G 1063 ASP cc_start: 0.7095 (p0) cc_final: 0.6752 (p0) REVERT: G 1073 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7806 (mtt-85) REVERT: G 1083 ASP cc_start: 0.7276 (t0) cc_final: 0.6982 (t0) outliers start: 183 outliers final: 153 residues processed: 779 average time/residue: 0.4268 time to fit residues: 525.4767 Evaluate side-chains 824 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 660 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 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 886 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1089 ASN 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 791 LEU Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 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 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 B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ASN 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 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 904 SER Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL 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 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 843 MET 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 915 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1073 ARG Chi-restraints excluded: chain D residue 1089 ASN 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 729 VAL Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 737 LEU 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 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 988 THR Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1023 LEU Chi-restraints excluded: chain E residue 1037 MET Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1089 ASN 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 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 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 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1048 SER Chi-restraints excluded: chain F residue 1089 ASN 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 717 THR Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 737 LEU Chi-restraints excluded: chain G residue 746 LEU Chi-restraints excluded: chain G residue 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 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1073 ARG Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 50.0000 chunk 193 optimal weight: 0.6980 chunk 290 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 330 optimal weight: 0.5980 chunk 240 optimal weight: 0.0040 chunk 45 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN ** C 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 GLN G 890 ASN ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32760 Z= 0.244 Angle : 0.528 10.140 45010 Z= 0.269 Chirality : 0.039 0.220 5754 Planarity : 0.003 0.032 5817 Dihedral : 3.669 20.760 5215 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.80 % Favored : 98.07 % Rotamer: Outliers : 8.72 % Allowed : 36.59 % Favored : 54.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.62 (0.12), residues: 4935 helix: 3.35 (0.08), residues: 3731 sheet: 0.80 (0.27), residues: 343 loop : -1.69 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 857 HIS 0.003 0.001 HIS D1052 PHE 0.023 0.002 PHE A1042 TYR 0.009 0.001 TYR F 883 ARG 0.008 0.001 ARG A 944 *********************** 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 837 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 663 time to evaluate : 3.410 Fit side-chains revert: symmetry clash REVERT: A 826 TRP cc_start: 0.7795 (p90) cc_final: 0.7357 (p90) REVERT: A 938 LEU cc_start: 0.8497 (tp) cc_final: 0.8211 (tt) REVERT: A 977 LYS cc_start: 0.8489 (mttt) cc_final: 0.8182 (mttm) REVERT: A 1002 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7176 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7064 (t0) cc_final: 0.6833 (t0) REVERT: A 1063 ASP cc_start: 0.6924 (p0) cc_final: 0.6336 (p0) REVERT: B 869 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7655 (t) REVERT: B 879 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 1063 ASP cc_start: 0.7508 (p0) cc_final: 0.7097 (p0) REVERT: C 843 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.6040 (tpp) REVERT: C 1063 ASP cc_start: 0.7137 (p0) cc_final: 0.6865 (p0) REVERT: D 641 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.6135 (m-70) REVERT: D 879 GLN cc_start: 0.7387 (tm-30) cc_final: 0.6983 (tm-30) REVERT: D 977 LYS cc_start: 0.8311 (mttt) cc_final: 0.8041 (mtpp) REVERT: D 992 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8542 (mt) REVERT: D 1014 ASP cc_start: 0.7021 (t0) cc_final: 0.6763 (t0) REVERT: D 1030 PRO cc_start: 0.8674 (Cg_endo) cc_final: 0.8432 (Cg_exo) REVERT: D 1073 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7722 (mtt-85) REVERT: E 854 MET cc_start: 0.6528 (mmp) cc_final: 0.6029 (mmp) REVERT: E 912 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7352 (mp) REVERT: E 938 LEU cc_start: 0.8496 (tp) cc_final: 0.8185 (tt) REVERT: E 967 ARG cc_start: 0.7840 (tmm160) cc_final: 0.7490 (ttp80) REVERT: E 1002 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8247 (ptt-90) REVERT: E 1031 ARG cc_start: 0.6111 (tpp80) cc_final: 0.5645 (ttm-80) REVERT: E 1063 ASP cc_start: 0.6966 (p0) cc_final: 0.6231 (p0) REVERT: E 1093 VAL cc_start: 0.8486 (m) cc_final: 0.8209 (t) REVERT: F 641 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.6029 (m-70) REVERT: F 791 LEU cc_start: 0.7720 (tt) cc_final: 0.7477 (tp) REVERT: F 826 TRP cc_start: 0.7167 (p90) cc_final: 0.6948 (p90) REVERT: F 869 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7271 (t) REVERT: F 879 GLN cc_start: 0.7367 (tm-30) cc_final: 0.6889 (tm-30) REVERT: F 1002 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7998 (ptt-90) REVERT: F 1031 ARG cc_start: 0.6536 (tpt170) cc_final: 0.6204 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6696 (p0) cc_final: 0.6410 (p0) REVERT: G 795 MET cc_start: 0.7401 (mmm) cc_final: 0.7183 (mtp) REVERT: G 879 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6814 (tm-30) REVERT: G 938 LEU cc_start: 0.8371 (tp) cc_final: 0.8101 (tt) REVERT: G 1002 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8173 (ptt-90) REVERT: G 1014 ASP cc_start: 0.7078 (t0) cc_final: 0.6840 (t0) REVERT: G 1048 SER cc_start: 0.8797 (t) cc_final: 0.8481 (m) REVERT: G 1073 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7786 (mtt-85) outliers start: 174 outliers final: 147 residues processed: 762 average time/residue: 0.4380 time to fit residues: 529.6641 Evaluate side-chains 821 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 661 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU 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 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 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 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 B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ASN 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 860 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 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 842 THR Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 SER Chi-restraints excluded: chain D residue 1073 ARG Chi-restraints excluded: chain D residue 1089 ASN 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 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 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 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 912 LEU Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 869 VAL Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 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 1048 SER Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain G residue 625 HIS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 729 VAL Chi-restraints excluded: chain G residue 746 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 885 ILE Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 993 ASN Chi-restraints excluded: chain G residue 1002 ARG Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1073 ARG Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 50.0000 chunk 465 optimal weight: 7.9990 chunk 424 optimal weight: 0.6980 chunk 452 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 355 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 409 optimal weight: 0.0980 chunk 428 optimal weight: 0.0170 chunk 451 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 32760 Z= 0.167 Angle : 0.494 9.901 45010 Z= 0.247 Chirality : 0.038 0.176 5754 Planarity : 0.002 0.028 5817 Dihedral : 3.459 20.589 5215 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.82 % Favored : 98.03 % Rotamer: Outliers : 6.72 % Allowed : 39.15 % 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: 3.87 (0.12), residues: 4935 helix: 3.56 (0.08), residues: 3731 sheet: 0.74 (0.27), residues: 343 loop : -1.64 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 857 HIS 0.003 0.001 HIS C1052 PHE 0.016 0.001 PHE G1042 TYR 0.007 0.001 TYR B 883 ARG 0.007 0.000 ARG A 944 *********************** 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 802 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 668 time to evaluate : 3.103 Fit side-chains revert: symmetry clash REVERT: A 826 TRP cc_start: 0.7776 (p90) cc_final: 0.7374 (p90) REVERT: A 869 VAL cc_start: 0.7639 (t) cc_final: 0.7415 (t) REVERT: A 938 LEU cc_start: 0.8585 (tp) cc_final: 0.8194 (tt) REVERT: A 977 LYS cc_start: 0.8431 (mttt) cc_final: 0.8146 (mttm) REVERT: A 1002 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7200 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7048 (t0) cc_final: 0.6771 (t0) REVERT: A 1048 SER cc_start: 0.8632 (t) cc_final: 0.8387 (m) REVERT: A 1063 ASP cc_start: 0.6702 (p0) cc_final: 0.6284 (p0) REVERT: B 869 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7601 (t) REVERT: B 879 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 1063 ASP cc_start: 0.7491 (p0) cc_final: 0.7018 (p0) REVERT: C 590 LYS cc_start: 0.6841 (tppt) cc_final: 0.6512 (ttmm) REVERT: C 843 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5926 (tpp) REVERT: C 870 LEU cc_start: 0.7603 (mp) cc_final: 0.7340 (mp) REVERT: C 1063 ASP cc_start: 0.7090 (p0) cc_final: 0.6878 (p0) REVERT: D 641 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.6184 (m-70) REVERT: D 792 ARG cc_start: 0.6734 (mtt180) cc_final: 0.6441 (mtt90) REVERT: D 869 VAL cc_start: 0.7459 (t) cc_final: 0.7182 (t) REVERT: D 879 GLN cc_start: 0.7319 (tm-30) cc_final: 0.6918 (tm-30) REVERT: D 977 LYS cc_start: 0.8283 (mttt) cc_final: 0.8019 (mtpp) REVERT: D 992 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8516 (mt) REVERT: D 1014 ASP cc_start: 0.7003 (t0) cc_final: 0.6684 (t0) REVERT: D 1030 PRO cc_start: 0.8652 (Cg_endo) cc_final: 0.8398 (Cg_exo) REVERT: E 854 MET cc_start: 0.6476 (mmp) cc_final: 0.6033 (mmp) REVERT: E 912 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7251 (mp) REVERT: E 938 LEU cc_start: 0.8534 (tp) cc_final: 0.8187 (tt) REVERT: E 967 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7492 (ttp80) REVERT: E 1031 ARG cc_start: 0.5971 (tpp80) cc_final: 0.5543 (ttm-80) REVERT: E 1063 ASP cc_start: 0.6948 (p0) cc_final: 0.6158 (p0) REVERT: E 1093 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8131 (t) REVERT: F 641 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.6143 (m-70) REVERT: F 869 VAL cc_start: 0.7531 (t) cc_final: 0.7249 (t) REVERT: F 879 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6809 (tm-30) REVERT: F 1031 ARG cc_start: 0.6488 (tpt170) cc_final: 0.6170 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6676 (p0) cc_final: 0.6246 (p0) REVERT: G 879 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6708 (tm-30) REVERT: G 938 LEU cc_start: 0.8399 (tp) cc_final: 0.8111 (tt) REVERT: G 1048 SER cc_start: 0.8759 (t) cc_final: 0.8472 (m) REVERT: G 1063 ASP cc_start: 0.7103 (p0) cc_final: 0.6872 (p0) outliers start: 134 outliers final: 108 residues processed: 748 average time/residue: 0.4286 time to fit residues: 508.1623 Evaluate side-chains 774 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 658 time to evaluate : 3.647 ------------------------------------------------------------------------------- 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 746 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 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 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1089 ASN 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 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 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 1007 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 843 MET Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 986 PHE Chi-restraints excluded: chain C residue 988 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1017 LYS Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1089 ASN 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 746 LEU Chi-restraints excluded: chain E residue 786 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 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 912 LEU Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1093 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 737 LEU Chi-restraints excluded: chain F residue 842 THR Chi-restraints excluded: chain F residue 847 LEU Chi-restraints excluded: chain F residue 867 LEU Chi-restraints excluded: chain F residue 889 LEU Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1048 SER Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 637 LEU Chi-restraints excluded: chain G residue 746 LEU Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 6.9990 chunk 478 optimal weight: 0.0370 chunk 292 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 332 optimal weight: 0.7980 chunk 502 optimal weight: 0.8980 chunk 462 optimal weight: 2.9990 chunk 399 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 308 optimal weight: 8.9990 chunk 245 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 GLN ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 933 ASN ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32760 Z= 0.184 Angle : 0.506 10.066 45010 Z= 0.253 Chirality : 0.038 0.177 5754 Planarity : 0.003 0.030 5817 Dihedral : 3.450 20.872 5215 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.88 % Favored : 97.97 % Rotamer: Outliers : 6.52 % Allowed : 39.75 % Favored : 53.73 % 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: 3.85 (0.12), residues: 4935 helix: 3.55 (0.08), residues: 3731 sheet: 0.73 (0.27), residues: 343 loop : -1.65 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 857 HIS 0.003 0.001 HIS E1052 PHE 0.018 0.001 PHE A1042 TYR 0.007 0.001 TYR F 883 ARG 0.009 0.001 ARG C 792 ********************** 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 790 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 660 time to evaluate : 3.400 Fit side-chains revert: symmetry clash REVERT: A 826 TRP cc_start: 0.7764 (p90) cc_final: 0.7348 (p90) REVERT: A 938 LEU cc_start: 0.8595 (tp) cc_final: 0.8181 (tt) REVERT: A 977 LYS cc_start: 0.8451 (mttt) cc_final: 0.8173 (mttm) REVERT: A 1002 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7248 (ptt-90) REVERT: A 1014 ASP cc_start: 0.7049 (t0) cc_final: 0.6784 (t0) REVERT: A 1063 ASP cc_start: 0.6745 (p0) cc_final: 0.6390 (p0) REVERT: B 869 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7617 (t) REVERT: B 879 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 1023 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6993 (mp) REVERT: B 1063 ASP cc_start: 0.7425 (p0) cc_final: 0.7025 (p0) REVERT: C 590 LYS cc_start: 0.6875 (tppt) cc_final: 0.6623 (ttmm) REVERT: C 843 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5954 (tpp) REVERT: C 870 LEU cc_start: 0.7573 (mp) cc_final: 0.7306 (mp) REVERT: C 1063 ASP cc_start: 0.7137 (p0) cc_final: 0.6925 (p0) REVERT: D 641 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6166 (m-70) REVERT: D 869 VAL cc_start: 0.7434 (t) cc_final: 0.7151 (t) REVERT: D 879 GLN cc_start: 0.7345 (tm-30) cc_final: 0.6938 (tm-30) REVERT: D 977 LYS cc_start: 0.8267 (mttt) cc_final: 0.7957 (mtpp) REVERT: D 992 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8551 (mt) REVERT: D 1014 ASP cc_start: 0.7007 (t0) cc_final: 0.6694 (t0) REVERT: D 1030 PRO cc_start: 0.8661 (Cg_endo) cc_final: 0.8352 (Cg_exo) REVERT: E 854 MET cc_start: 0.6501 (mmp) cc_final: 0.6041 (mmp) REVERT: E 912 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7335 (mp) REVERT: E 938 LEU cc_start: 0.8525 (tp) cc_final: 0.8186 (tt) REVERT: E 967 ARG cc_start: 0.7835 (tmm160) cc_final: 0.7488 (ttp80) REVERT: E 1093 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8154 (t) REVERT: F 641 HIS cc_start: 0.6370 (OUTLIER) cc_final: 0.6145 (m-70) REVERT: F 869 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7252 (t) REVERT: F 879 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6817 (tm-30) REVERT: F 1031 ARG cc_start: 0.6471 (tpt170) cc_final: 0.6167 (ttm-80) REVERT: F 1063 ASP cc_start: 0.6679 (p0) cc_final: 0.6375 (p0) REVERT: G 879 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6717 (tm-30) REVERT: G 938 LEU cc_start: 0.8400 (tp) cc_final: 0.8121 (tt) REVERT: G 1048 SER cc_start: 0.8778 (t) cc_final: 0.8478 (m) REVERT: G 1063 ASP cc_start: 0.7081 (p0) cc_final: 0.6833 (p0) REVERT: G 1073 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: G 1083 ASP cc_start: 0.7286 (t0) cc_final: 0.6943 (t0) outliers start: 130 outliers final: 117 residues processed: 742 average time/residue: 0.4417 time to fit residues: 519.7064 Evaluate side-chains 787 residues out of total 4445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 659 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1089 ASN 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 791 LEU Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 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 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 B residue 1074 THR Chi-restraints excluded: chain B residue 1089 ASN Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain C residue 843 MET Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 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 1093 VAL Chi-restraints excluded: chain D residue 625 HIS Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 842 THR Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 889 LEU Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 988 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1071 LEU Chi-restraints excluded: chain D residue 1089 ASN 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 746 LEU Chi-restraints excluded: chain E residue 748 VAL Chi-restraints excluded: chain E residue 786 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 889 LEU Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 912 LEU Chi-restraints excluded: chain E residue 988 THR Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1093 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 641 HIS Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 737 LEU 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 889 LEU Chi-restraints excluded: chain F residue 933 ASN Chi-restraints excluded: chain F residue 954 ILE Chi-restraints excluded: chain F residue 960 THR Chi-restraints excluded: chain F residue 970 THR Chi-restraints excluded: chain F residue 988 THR Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1023 LEU Chi-restraints excluded: chain F residue 1048 SER Chi-restraints excluded: chain F residue 1089 ASN 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 746 LEU Chi-restraints excluded: chain G residue 842 THR Chi-restraints excluded: chain G residue 867 LEU Chi-restraints excluded: chain G residue 885 ILE Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain G residue 988 THR Chi-restraints excluded: chain G residue 1040 VAL Chi-restraints excluded: chain G residue 1073 ARG Chi-restraints excluded: chain G residue 1089 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 0.1980 chunk 425 optimal weight: 0.4980 chunk 122 optimal weight: 0.2980 chunk 368 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 400 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 411 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 73 optimal weight: 8.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.169153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.152142 restraints weight = 58535.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148940 restraints weight = 76898.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150043 restraints weight = 64606.820| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 32760 Z= 0.183 Angle : 0.618 59.193 45010 Z= 0.341 Chirality : 0.038 0.598 5754 Planarity : 0.003 0.060 5817 Dihedral : 3.494 39.964 5215 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.82 % Favored : 98.01 % Rotamer: Outliers : 6.67 % Allowed : 39.85 % Favored : 53.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.86 (0.12), residues: 4935 helix: 3.55 (0.08), residues: 3731 sheet: 0.72 (0.27), residues: 343 loop : -1.65 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 857 HIS 0.003 0.001 HIS D1052 PHE 0.016 0.001 PHE A1042 TYR 0.046 0.001 TYR D1057 ARG 0.019 0.000 ARG E 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8292.00 seconds wall clock time: 147 minutes 11.04 seconds (8831.04 seconds total)