Starting phenix.real_space_refine on Sun Mar 17 01:22:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/03_2024/5wrg_6679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/03_2024/5wrg_6679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/03_2024/5wrg_6679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/03_2024/5wrg_6679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/03_2024/5wrg_6679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/03_2024/5wrg_6679.pdb" } resolution = 4.3 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= 0.000 sd= 0.004 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 87 5.16 5 C 10281 2.51 5 N 2760 2.21 5 O 3189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16317 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5439 Classifications: {'peptide': 736} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76} Link IDs: {'CIS': 26, 'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 5439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5439 Classifications: {'peptide': 736} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76} Link IDs: {'CIS': 26, 'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 5439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5439 Classifications: {'peptide': 736} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76} Link IDs: {'CIS': 26, 'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Time building chain proxies: 8.78, per 1000 atoms: 0.54 Number of scatterers: 16317 At special positions: 0 Unit cell: (109.56, 108.24, 149.16, 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 87 16.00 O 3189 8.00 N 2760 7.00 C 10281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.05 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.05 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.02 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.05 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.05 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.02 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.05 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.05 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.02 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 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: 6.42 Conformation dependent library (CDL) restraints added in 3.1 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 28.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.952A pdb=" N LEU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.867A pdb=" N LEU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.812A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 402 through 409 removed outlier: 4.131A pdb=" N ALA A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 734 Processing helix chain 'A' and resid 743 through 765 removed outlier: 3.931A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 removed outlier: 3.897A pdb=" N ASP A 802 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 860 removed outlier: 3.874A pdb=" N ALA A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 860 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 891 removed outlier: 3.504A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 Processing helix chain 'A' and resid 901 through 917 removed outlier: 3.677A pdb=" N ALA A 906 " --> pdb=" O GLN A 902 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 915 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 949 removed outlier: 3.591A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 940 " --> pdb=" O GLN A 936 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.102A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1011 removed outlier: 3.601A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 removed outlier: 3.951A pdb=" N LEU B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.868A pdb=" N LEU B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.812A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 402 through 409 removed outlier: 4.130A pdb=" N ALA B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 734 Processing helix chain 'B' and resid 743 through 765 removed outlier: 3.931A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 759 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 removed outlier: 3.899A pdb=" N ASP B 802 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 860 removed outlier: 3.874A pdb=" N ALA B 858 " --> pdb=" O ALA B 854 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 859 " --> pdb=" O TYR B 855 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 860 " --> pdb=" O THR B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 removed outlier: 3.504A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 898 Processing helix chain 'B' and resid 901 through 917 removed outlier: 3.678A pdb=" N ALA B 906 " --> pdb=" O GLN B 902 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 912 " --> pdb=" O GLN B 908 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN B 915 " --> pdb=" O LYS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 949 removed outlier: 3.591A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 940 " --> pdb=" O GLN B 936 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 4.101A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1011 removed outlier: 3.599A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 removed outlier: 3.952A pdb=" N LEU C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.868A pdb=" N LEU C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.811A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 402 through 409 removed outlier: 4.131A pdb=" N ALA C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 609 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 734 Processing helix chain 'C' and resid 743 through 765 removed outlier: 3.931A pdb=" N LEU C 749 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 759 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 806 removed outlier: 3.898A pdb=" N ASP C 802 " --> pdb=" O SER C 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 860 removed outlier: 3.874A pdb=" N ALA C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 859 " --> pdb=" O TYR C 855 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 860 " --> pdb=" O THR C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 891 removed outlier: 3.504A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 898 Processing helix chain 'C' and resid 901 through 917 removed outlier: 3.677A pdb=" N ALA C 906 " --> pdb=" O GLN C 902 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN C 915 " --> pdb=" O LYS C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 949 removed outlier: 3.591A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA C 940 " --> pdb=" O GLN C 936 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 4.101A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1011 removed outlier: 3.600A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 995 " --> pdb=" O THR C 991 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.700A pdb=" N GLY A 580 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 595 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 344 removed outlier: 4.461A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 386 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 418 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441 removed outlier: 3.697A pdb=" N ASN A 479 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.681A pdb=" N SER A 574 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 700 through 701 Processing sheet with id=AA7, first strand: chain 'A' and resid 704 through 710 removed outlier: 3.555A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AA9, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.699A pdb=" N GLY B 580 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 595 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 341 through 344 removed outlier: 4.461A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 386 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 418 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 441 removed outlier: 3.698A pdb=" N ASN B 479 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 537 through 539 removed outlier: 3.681A pdb=" N SER B 574 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 539 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AB6, first strand: chain 'B' and resid 704 through 710 removed outlier: 3.556A pdb=" N GLU B 707 " --> pdb=" O PHE B1044 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AB8, first strand: chain 'C' and resid 266 through 267 Processing sheet with id=AB9, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.700A pdb=" N GLY C 580 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 595 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 344 removed outlier: 4.461A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER C 386 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS C 419 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 418 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 440 through 441 removed outlier: 3.697A pdb=" N ASN C 479 " --> pdb=" O TYR C 440 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.681A pdb=" N SER C 574 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC5, first strand: chain 'C' and resid 704 through 710 removed outlier: 3.555A pdb=" N GLU C 707 " --> pdb=" O PHE C1044 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 716 through 718 465 hydrogen bonds defined for protein. 1296 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: 4.50 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5001 1.33 - 1.45: 2872 1.45 - 1.57: 8618 1.57 - 1.69: 3 1.69 - 1.81: 114 Bond restraints: 16608 Sorted by residual: bond pdb=" CA PRO A 547 " pdb=" C PRO A 547 " ideal model delta sigma weight residual 1.516 1.569 -0.052 1.42e-02 4.96e+03 1.36e+01 bond pdb=" CA PRO B 547 " pdb=" C PRO B 547 " ideal model delta sigma weight residual 1.516 1.568 -0.052 1.42e-02 4.96e+03 1.35e+01 bond pdb=" CA PRO C 547 " pdb=" C PRO C 547 " ideal model delta sigma weight residual 1.516 1.568 -0.052 1.42e-02 4.96e+03 1.32e+01 bond pdb=" CA VAL B 675 " pdb=" C VAL B 675 " ideal model delta sigma weight residual 1.525 1.585 -0.060 2.10e-02 2.27e+03 8.04e+00 bond pdb=" CA VAL A 675 " pdb=" C VAL A 675 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.72e+00 ... (remaining 16603 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.66: 510 106.66 - 114.18: 9316 114.18 - 121.70: 8713 121.70 - 129.22: 3958 129.22 - 136.74: 108 Bond angle restraints: 22605 Sorted by residual: angle pdb=" C GLU C1013 " pdb=" N CYS C1014 " pdb=" CA CYS C1014 " ideal model delta sigma weight residual 121.70 136.74 -15.04 1.80e+00 3.09e-01 6.98e+01 angle pdb=" C GLU A1013 " pdb=" N CYS A1014 " pdb=" CA CYS A1014 " ideal model delta sigma weight residual 121.70 136.71 -15.01 1.80e+00 3.09e-01 6.95e+01 angle pdb=" C GLU B1013 " pdb=" N CYS B1014 " pdb=" CA CYS B1014 " ideal model delta sigma weight residual 121.70 136.67 -14.97 1.80e+00 3.09e-01 6.91e+01 angle pdb=" N PRO C 547 " pdb=" CA PRO C 547 " pdb=" C PRO C 547 " ideal model delta sigma weight residual 113.40 124.33 -10.93 1.34e+00 5.57e-01 6.66e+01 angle pdb=" N PRO B 547 " pdb=" CA PRO B 547 " pdb=" C PRO B 547 " ideal model delta sigma weight residual 113.40 124.31 -10.91 1.34e+00 5.57e-01 6.63e+01 ... (remaining 22600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 9312 16.79 - 33.58: 530 33.58 - 50.37: 94 50.37 - 67.17: 15 67.17 - 83.96: 27 Dihedral angle restraints: 9978 sinusoidal: 3561 harmonic: 6417 Sorted by residual: dihedral pdb=" CA CYS B 524 " pdb=" C CYS B 524 " pdb=" N VAL B 525 " pdb=" CA VAL B 525 " ideal model delta harmonic sigma weight residual -180.00 -96.04 -83.96 0 5.00e+00 4.00e-02 2.82e+02 dihedral pdb=" CA CYS A 524 " pdb=" C CYS A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual -180.00 -96.07 -83.93 0 5.00e+00 4.00e-02 2.82e+02 dihedral pdb=" CA CYS C 524 " pdb=" C CYS C 524 " pdb=" N VAL C 525 " pdb=" CA VAL C 525 " ideal model delta harmonic sigma weight residual -180.00 -96.11 -83.89 0 5.00e+00 4.00e-02 2.81e+02 ... (remaining 9975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2319 0.092 - 0.184: 274 0.184 - 0.277: 41 0.277 - 0.369: 9 0.369 - 0.461: 3 Chirality restraints: 2646 Sorted by residual: chirality pdb=" CB VAL A 525 " pdb=" CA VAL A 525 " pdb=" CG1 VAL A 525 " pdb=" CG2 VAL A 525 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CB VAL C 525 " pdb=" CA VAL C 525 " pdb=" CG1 VAL C 525 " pdb=" CG2 VAL C 525 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CB VAL B 525 " pdb=" CA VAL B 525 " pdb=" CG1 VAL B 525 " pdb=" CG2 VAL B 525 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 2643 not shown) Planarity restraints: 2958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 741 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C PHE C 741 " -0.078 2.00e-02 2.50e+03 pdb=" O PHE C 741 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS C 742 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 741 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C PHE B 741 " 0.078 2.00e-02 2.50e+03 pdb=" O PHE B 741 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS B 742 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 741 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C PHE A 741 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE A 741 " -0.029 2.00e-02 2.50e+03 pdb=" N CYS A 742 " -0.026 2.00e-02 2.50e+03 ... (remaining 2955 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1551 2.73 - 3.27: 16254 3.27 - 3.82: 26901 3.82 - 4.36: 30472 4.36 - 4.90: 48791 Nonbonded interactions: 123969 Sorted by model distance: nonbonded pdb=" O TYR A 646 " pdb=" OH TYR A 677 " model vdw 2.191 2.440 nonbonded pdb=" O TYR C 646 " pdb=" OH TYR C 677 " model vdw 2.192 2.440 nonbonded pdb=" O TYR B 646 " pdb=" OH TYR B 677 " model vdw 2.192 2.440 nonbonded pdb=" O PHE C 741 " pdb=" N GLN C 744 " model vdw 2.263 2.520 nonbonded pdb=" O PHE A 741 " pdb=" N GLN A 744 " model vdw 2.264 2.520 ... (remaining 123964 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' } 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: 1.250 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: 0.010 Extract box with map and model: 5.710 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 43.160 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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 : 0.007 0.060 16608 Z= 0.461 Angle : 1.399 15.044 22605 Z= 0.769 Chirality : 0.066 0.461 2646 Planarity : 0.007 0.049 2958 Dihedral : 12.061 83.958 5766 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.69 % Allowed : 17.95 % Favored : 81.36 % Rotamer: Outliers : 0.53 % Allowed : 4.27 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.15 % Twisted Proline : 9.09 % Twisted General : 1.58 % 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: -5.05 (0.15), residues: 2178 helix: -3.26 (0.14), residues: 534 sheet: -2.15 (0.33), residues: 228 loop : -3.86 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.003 0.001 HIS B 641 PHE 0.028 0.003 PHE B1024 TYR 0.018 0.003 TYR C 899 ARG 0.008 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 408 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.8259 (mmt) cc_final: 0.8019 (mmt) REVERT: A 838 ASN cc_start: 0.8566 (p0) cc_final: 0.8107 (p0) REVERT: A 851 MET cc_start: 0.8697 (tpt) cc_final: 0.8461 (tpp) REVERT: A 974 GLN cc_start: 0.8454 (mm110) cc_final: 0.8156 (mm-40) REVERT: A 984 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7578 (tm-30) REVERT: B 340 TRP cc_start: 0.7825 (p-90) cc_final: 0.7127 (p-90) REVERT: B 518 ASP cc_start: 0.6730 (m-30) cc_final: 0.6440 (p0) REVERT: B 557 ASP cc_start: 0.8269 (m-30) cc_final: 0.8007 (m-30) REVERT: B 715 LYS cc_start: 0.8288 (tttt) cc_final: 0.8070 (ttmt) REVERT: B 740 SER cc_start: 0.7861 (t) cc_final: 0.7025 (t) REVERT: C 532 LEU cc_start: 0.8370 (pt) cc_final: 0.7780 (mp) REVERT: C 558 PHE cc_start: 0.8459 (m-10) cc_final: 0.8239 (m-10) REVERT: C 708 VAL cc_start: 0.9375 (m) cc_final: 0.8748 (m) REVERT: C 733 ASN cc_start: 0.8867 (t0) cc_final: 0.8452 (t0) REVERT: C 743 THR cc_start: 0.9290 (p) cc_final: 0.9052 (t) REVERT: C 932 ASP cc_start: 0.8279 (t70) cc_final: 0.8023 (t70) outliers start: 9 outliers final: 3 residues processed: 417 average time/residue: 0.3090 time to fit residues: 183.7876 Evaluate side-chains 228 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 198 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 435 ASN A 437 ASN A 910 ASN A 960 ASN B 401 GLN B 435 ASN B 437 ASN B 910 ASN B1018 GLN B1046 HIS C 401 GLN C 435 ASN C 437 ASN C 910 ASN C 987 GLN C1018 GLN ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16608 Z= 0.222 Angle : 0.946 13.133 22605 Z= 0.501 Chirality : 0.050 0.220 2646 Planarity : 0.005 0.047 2958 Dihedral : 8.256 48.546 2343 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.21 % Favored : 83.65 % Rotamer: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.49 % Twisted Proline : 6.06 % Twisted General : 0.67 % 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: -4.26 (0.16), residues: 2178 helix: -1.74 (0.18), residues: 579 sheet: -1.74 (0.33), residues: 249 loop : -3.80 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 476 HIS 0.002 0.000 HIS B1040 PHE 0.018 0.002 PHE A 741 TYR 0.019 0.001 TYR C 738 ARG 0.012 0.001 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 307 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.8374 (mmt) cc_final: 0.8108 (mmm) REVERT: A 942 ASN cc_start: 0.8295 (m-40) cc_final: 0.8034 (m110) REVERT: A 969 VAL cc_start: 0.9272 (t) cc_final: 0.8309 (t) REVERT: A 976 ASP cc_start: 0.8836 (m-30) cc_final: 0.8633 (p0) REVERT: A 984 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 263 MET cc_start: 0.1061 (mmm) cc_final: 0.0693 (tpp) REVERT: B 518 ASP cc_start: 0.6850 (m-30) cc_final: 0.6519 (p0) REVERT: B 558 PHE cc_start: 0.8532 (m-10) cc_final: 0.8324 (m-10) REVERT: B 636 LEU cc_start: 0.8495 (tp) cc_final: 0.8255 (tp) REVERT: B 987 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8420 (tp-100) REVERT: B 999 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 532 LEU cc_start: 0.8125 (pt) cc_final: 0.7507 (mp) REVERT: C 650 ILE cc_start: 0.9373 (mt) cc_final: 0.9013 (mt) REVERT: C 733 ASN cc_start: 0.8961 (t0) cc_final: 0.8620 (t0) REVERT: C 1000 ILE cc_start: 0.9619 (mt) cc_final: 0.9154 (mm) outliers start: 3 outliers final: 0 residues processed: 310 average time/residue: 0.2947 time to fit residues: 136.0949 Evaluate side-chains 222 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 0.0060 chunk 67 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 759 ASN A 910 ASN A 960 ASN B 910 ASN B1018 GLN C 939 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16608 Z= 0.220 Angle : 0.910 14.165 22605 Z= 0.478 Chirality : 0.049 0.247 2646 Planarity : 0.005 0.047 2958 Dihedral : 7.490 48.909 2343 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.85 % Favored : 82.97 % Rotamer: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 6.06 % Twisted General : 0.29 % 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 (0.16), residues: 2178 helix: -0.80 (0.20), residues: 579 sheet: -1.54 (0.33), residues: 243 loop : -3.82 (0.14), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.002 0.000 HIS C1030 PHE 0.023 0.001 PHE A 293 TYR 0.014 0.001 TYR A 723 ARG 0.006 0.001 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 ILE cc_start: 0.8994 (mt) cc_final: 0.8774 (mm) REVERT: A 709 MET cc_start: 0.8132 (mmt) cc_final: 0.7781 (mmm) REVERT: A 969 VAL cc_start: 0.9080 (t) cc_final: 0.8824 (t) REVERT: A 976 ASP cc_start: 0.8968 (m-30) cc_final: 0.8690 (p0) REVERT: A 984 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 988 THR cc_start: 0.9337 (m) cc_final: 0.9130 (m) REVERT: B 518 ASP cc_start: 0.7381 (m-30) cc_final: 0.6828 (p0) REVERT: B 557 ASP cc_start: 0.7896 (m-30) cc_final: 0.7694 (m-30) REVERT: B 558 PHE cc_start: 0.8629 (m-10) cc_final: 0.8223 (m-10) REVERT: B 715 LYS cc_start: 0.8326 (tttt) cc_final: 0.7833 (ttmt) REVERT: C 263 MET cc_start: 0.2365 (tpt) cc_final: 0.2010 (tpt) REVERT: C 532 LEU cc_start: 0.8058 (pt) cc_final: 0.7385 (mp) REVERT: C 650 ILE cc_start: 0.9346 (mt) cc_final: 0.9118 (mt) REVERT: C 733 ASN cc_start: 0.9094 (t0) cc_final: 0.8735 (t0) REVERT: C 952 PHE cc_start: 0.6566 (m-10) cc_final: 0.6319 (m-80) REVERT: C 1000 ILE cc_start: 0.9769 (mt) cc_final: 0.9367 (mm) outliers start: 2 outliers final: 1 residues processed: 276 average time/residue: 0.2745 time to fit residues: 112.2933 Evaluate side-chains 193 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 766 GLN A 917 GLN A 960 ASN B 917 GLN B 947 GLN C 301 GLN C 910 ASN C 917 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16608 Z= 0.277 Angle : 0.932 14.111 22605 Z= 0.488 Chirality : 0.049 0.297 2646 Planarity : 0.005 0.043 2958 Dihedral : 7.392 49.092 2343 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 18.46 % Favored : 81.40 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.58 % Twisted Proline : 5.05 % Twisted General : 0.24 % 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: -3.68 (0.17), residues: 2178 helix: -0.45 (0.22), residues: 582 sheet: -1.77 (0.31), residues: 252 loop : -3.77 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 423 HIS 0.004 0.001 HIS C1030 PHE 0.021 0.002 PHE A 451 TYR 0.014 0.001 TYR C 723 ARG 0.012 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 ILE cc_start: 0.9028 (mt) cc_final: 0.8746 (mm) REVERT: A 707 GLU cc_start: 0.8627 (pp20) cc_final: 0.7613 (pp20) REVERT: A 969 VAL cc_start: 0.9164 (t) cc_final: 0.8810 (t) REVERT: A 976 ASP cc_start: 0.9030 (m-30) cc_final: 0.8746 (p0) REVERT: B 518 ASP cc_start: 0.7236 (m-30) cc_final: 0.6427 (p0) REVERT: B 557 ASP cc_start: 0.7878 (m-30) cc_final: 0.7632 (m-30) REVERT: B 722 MET cc_start: 0.8203 (tpp) cc_final: 0.7952 (tpp) REVERT: B 999 GLU cc_start: 0.8109 (tp30) cc_final: 0.7858 (tp30) REVERT: B 1022 VAL cc_start: 0.8882 (p) cc_final: 0.8639 (t) REVERT: C 532 LEU cc_start: 0.8009 (pt) cc_final: 0.7695 (mp) REVERT: C 650 ILE cc_start: 0.9376 (mt) cc_final: 0.9139 (mt) REVERT: C 733 ASN cc_start: 0.9142 (t0) cc_final: 0.8800 (t0) REVERT: C 1000 ILE cc_start: 0.9731 (mt) cc_final: 0.9270 (mm) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2762 time to fit residues: 106.0614 Evaluate side-chains 189 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 960 ASN B 947 GLN C 301 GLN C 381 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16608 Z= 0.263 Angle : 0.924 14.001 22605 Z= 0.485 Chirality : 0.049 0.262 2646 Planarity : 0.005 0.045 2958 Dihedral : 7.350 48.527 2343 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 18.09 % Favored : 81.77 % Rotamer: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 6.06 % Twisted General : 0.14 % 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: -3.56 (0.17), residues: 2178 helix: -0.28 (0.22), residues: 597 sheet: -1.72 (0.31), residues: 252 loop : -3.76 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 423 HIS 0.003 0.001 HIS B1040 PHE 0.015 0.002 PHE A 451 TYR 0.013 0.001 TYR B 598 ARG 0.006 0.001 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8817 (pptt) cc_final: 0.8492 (ptmm) REVERT: A 532 LEU cc_start: 0.8516 (pt) cc_final: 0.8186 (mp) REVERT: A 650 ILE cc_start: 0.9049 (mt) cc_final: 0.8745 (mm) REVERT: A 707 GLU cc_start: 0.8589 (pp20) cc_final: 0.7444 (pp20) REVERT: A 969 VAL cc_start: 0.9182 (t) cc_final: 0.8922 (t) REVERT: A 976 ASP cc_start: 0.9001 (m-30) cc_final: 0.8682 (p0) REVERT: B 340 TRP cc_start: 0.8133 (p-90) cc_final: 0.7427 (p-90) REVERT: B 518 ASP cc_start: 0.7427 (m-30) cc_final: 0.6593 (p0) REVERT: B 983 LEU cc_start: 0.9254 (tt) cc_final: 0.8852 (tp) REVERT: C 381 ASN cc_start: 0.7081 (m110) cc_final: 0.6480 (m110) REVERT: C 532 LEU cc_start: 0.7832 (pt) cc_final: 0.7509 (mp) REVERT: C 722 MET cc_start: 0.9177 (tpp) cc_final: 0.8956 (tpp) REVERT: C 733 ASN cc_start: 0.9174 (t0) cc_final: 0.8954 (t0) REVERT: C 992 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8682 (tm-30) REVERT: C 1000 ILE cc_start: 0.9640 (mt) cc_final: 0.9278 (mm) REVERT: C 1011 MET cc_start: 0.8354 (tmm) cc_final: 0.8135 (tmm) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.2861 time to fit residues: 107.9180 Evaluate side-chains 185 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 960 ASN B 947 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1005 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16608 Z= 0.222 Angle : 0.902 14.205 22605 Z= 0.472 Chirality : 0.048 0.248 2646 Planarity : 0.004 0.040 2958 Dihedral : 7.126 47.231 2343 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 17.40 % Favored : 82.46 % Rotamer: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.58 % Twisted Proline : 3.03 % Twisted General : 0.29 % 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: -3.43 (0.17), residues: 2178 helix: -0.11 (0.22), residues: 588 sheet: -1.63 (0.32), residues: 252 loop : -3.69 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 423 HIS 0.006 0.001 HIS A 641 PHE 0.016 0.001 PHE A 529 TYR 0.012 0.001 TYR B 598 ARG 0.007 0.001 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 PHE cc_start: 0.7291 (m-10) cc_final: 0.7018 (m-10) REVERT: A 532 LEU cc_start: 0.8428 (pt) cc_final: 0.7999 (mp) REVERT: A 557 ASP cc_start: 0.8345 (m-30) cc_final: 0.8103 (m-30) REVERT: A 650 ILE cc_start: 0.8990 (mt) cc_final: 0.8675 (mm) REVERT: A 709 MET cc_start: 0.8123 (mmp) cc_final: 0.7731 (mmm) REVERT: A 976 ASP cc_start: 0.8994 (m-30) cc_final: 0.8706 (p0) REVERT: A 1011 MET cc_start: 0.8195 (tmm) cc_final: 0.7906 (tmm) REVERT: B 340 TRP cc_start: 0.8107 (p-90) cc_final: 0.7355 (p-90) REVERT: B 518 ASP cc_start: 0.7415 (m-30) cc_final: 0.6591 (p0) REVERT: B 961 ASP cc_start: 0.8711 (t0) cc_final: 0.8505 (p0) REVERT: B 983 LEU cc_start: 0.9255 (tt) cc_final: 0.8834 (tp) REVERT: C 373 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8280 (mmtm) REVERT: C 381 ASN cc_start: 0.6869 (m110) cc_final: 0.6320 (m110) REVERT: C 532 LEU cc_start: 0.7973 (pt) cc_final: 0.7697 (mp) REVERT: C 650 ILE cc_start: 0.9304 (mt) cc_final: 0.9063 (mt) REVERT: C 722 MET cc_start: 0.9094 (tpp) cc_final: 0.8788 (tpp) REVERT: C 992 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8541 (tm-30) REVERT: C 1011 MET cc_start: 0.8137 (tmm) cc_final: 0.7884 (tmm) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.2696 time to fit residues: 104.2649 Evaluate side-chains 190 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 0.0270 chunk 118 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 301 GLN B 947 GLN C 437 ASN C 599 GLN C 744 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16608 Z= 0.204 Angle : 0.896 14.163 22605 Z= 0.466 Chirality : 0.048 0.235 2646 Planarity : 0.004 0.035 2958 Dihedral : 6.889 46.822 2343 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.25 % Favored : 83.61 % Rotamer: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.17), residues: 2178 helix: -0.01 (0.22), residues: 597 sheet: -1.55 (0.32), residues: 255 loop : -3.69 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 476 HIS 0.002 0.001 HIS B1030 PHE 0.016 0.001 PHE C 558 TYR 0.011 0.001 TYR A 300 ARG 0.006 0.000 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.6636 (pm20) cc_final: 0.6400 (pm20) REVERT: A 451 PHE cc_start: 0.7416 (m-10) cc_final: 0.7160 (m-10) REVERT: A 532 LEU cc_start: 0.8404 (pt) cc_final: 0.8113 (mp) REVERT: A 558 PHE cc_start: 0.8869 (m-10) cc_final: 0.8568 (m-10) REVERT: A 650 ILE cc_start: 0.8995 (mt) cc_final: 0.8621 (mm) REVERT: A 707 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 719 ASP cc_start: 0.8554 (t0) cc_final: 0.8227 (t0) REVERT: A 976 ASP cc_start: 0.8956 (m-30) cc_final: 0.8702 (p0) REVERT: A 1011 MET cc_start: 0.8326 (tmm) cc_final: 0.7993 (tmm) REVERT: B 407 ASP cc_start: 0.8159 (t0) cc_final: 0.7734 (t0) REVERT: B 518 ASP cc_start: 0.7315 (m-30) cc_final: 0.6709 (p0) REVERT: B 557 ASP cc_start: 0.7399 (m-30) cc_final: 0.7189 (m-30) REVERT: B 738 TYR cc_start: 0.5711 (p90) cc_final: 0.5393 (p90) REVERT: B 983 LEU cc_start: 0.9270 (tt) cc_final: 0.8975 (tp) REVERT: B 992 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8313 (tm-30) REVERT: C 381 ASN cc_start: 0.6915 (m110) cc_final: 0.6323 (m110) REVERT: C 532 LEU cc_start: 0.7889 (pt) cc_final: 0.7547 (mp) REVERT: C 650 ILE cc_start: 0.9293 (mt) cc_final: 0.9050 (mt) REVERT: C 718 VAL cc_start: 0.9281 (t) cc_final: 0.9009 (m) REVERT: C 992 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8546 (tm-30) REVERT: C 1011 MET cc_start: 0.8293 (tmm) cc_final: 0.7993 (tmm) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.2587 time to fit residues: 98.6681 Evaluate side-chains 192 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 0.2980 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 165 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 ASN B 947 GLN C 435 ASN C 437 ASN C 902 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16608 Z= 0.213 Angle : 0.893 14.128 22605 Z= 0.466 Chirality : 0.048 0.237 2646 Planarity : 0.004 0.042 2958 Dihedral : 6.852 47.321 2343 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.48 % Favored : 83.38 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.58 % Twisted Proline : 3.03 % Twisted General : 0.29 % 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: -3.24 (0.17), residues: 2178 helix: 0.07 (0.22), residues: 597 sheet: -1.13 (0.34), residues: 228 loop : -3.65 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 340 HIS 0.006 0.001 HIS A1030 PHE 0.013 0.001 PHE C 578 TYR 0.013 0.001 TYR A 723 ARG 0.007 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.1698 (mmm) cc_final: 0.0902 (mmm) REVERT: A 451 PHE cc_start: 0.7444 (m-10) cc_final: 0.7164 (m-10) REVERT: A 532 LEU cc_start: 0.8481 (pt) cc_final: 0.8197 (mp) REVERT: A 558 PHE cc_start: 0.8898 (m-10) cc_final: 0.8544 (m-10) REVERT: A 650 ILE cc_start: 0.8923 (mt) cc_final: 0.8605 (mm) REVERT: A 976 ASP cc_start: 0.8965 (m-30) cc_final: 0.8726 (p0) REVERT: A 1011 MET cc_start: 0.8266 (tmm) cc_final: 0.7890 (tmm) REVERT: B 340 TRP cc_start: 0.8061 (p-90) cc_final: 0.7283 (p-90) REVERT: B 407 ASP cc_start: 0.8105 (t0) cc_final: 0.7644 (t0) REVERT: B 518 ASP cc_start: 0.7936 (m-30) cc_final: 0.7248 (p0) REVERT: B 738 TYR cc_start: 0.5964 (p90) cc_final: 0.5642 (p90) REVERT: B 983 LEU cc_start: 0.9314 (tt) cc_final: 0.8902 (tp) REVERT: B 992 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8293 (tm-30) REVERT: C 381 ASN cc_start: 0.6937 (m110) cc_final: 0.6357 (m110) REVERT: C 532 LEU cc_start: 0.7901 (pt) cc_final: 0.7596 (mp) REVERT: C 650 ILE cc_start: 0.9280 (mt) cc_final: 0.9007 (mt) REVERT: C 992 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8657 (tm-30) REVERT: C 1011 MET cc_start: 0.8288 (tmm) cc_final: 0.8072 (tmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2588 time to fit residues: 95.3897 Evaluate side-chains 184 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 196 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN ** B 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 942 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16608 Z= 0.335 Angle : 0.982 14.037 22605 Z= 0.515 Chirality : 0.050 0.286 2646 Planarity : 0.005 0.052 2958 Dihedral : 7.306 48.239 2343 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 19.70 % Favored : 80.17 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 6.06 % Twisted General : 0.14 % 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: -3.45 (0.17), residues: 2178 helix: -0.25 (0.21), residues: 621 sheet: -1.37 (0.34), residues: 228 loop : -3.74 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 423 HIS 0.006 0.001 HIS A1030 PHE 0.036 0.002 PHE B 551 TYR 0.018 0.002 TYR C 723 ARG 0.013 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.8028 (p90) cc_final: 0.7740 (p90) REVERT: A 451 PHE cc_start: 0.7447 (m-10) cc_final: 0.7146 (m-10) REVERT: A 558 PHE cc_start: 0.8984 (m-10) cc_final: 0.8618 (m-10) REVERT: A 1011 MET cc_start: 0.8439 (tmm) cc_final: 0.7974 (tmm) REVERT: B 263 MET cc_start: 0.4428 (mmp) cc_final: 0.3638 (tmm) REVERT: B 340 TRP cc_start: 0.8246 (p-90) cc_final: 0.7354 (p-90) REVERT: B 407 ASP cc_start: 0.7901 (t0) cc_final: 0.7439 (t0) REVERT: B 709 MET cc_start: 0.7791 (mmm) cc_final: 0.7561 (mmm) REVERT: B 738 TYR cc_start: 0.6442 (p90) cc_final: 0.5726 (p90) REVERT: B 762 GLU cc_start: 0.8472 (tp30) cc_final: 0.8111 (tp30) REVERT: B 958 VAL cc_start: 0.8958 (p) cc_final: 0.8542 (p) REVERT: B 983 LEU cc_start: 0.9344 (tt) cc_final: 0.9121 (tt) REVERT: B 992 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8287 (tm-30) REVERT: C 532 LEU cc_start: 0.8286 (pt) cc_final: 0.8079 (mp) REVERT: C 650 ILE cc_start: 0.9385 (mt) cc_final: 0.9084 (mt) REVERT: C 722 MET cc_start: 0.8954 (tpp) cc_final: 0.8607 (tpp) REVERT: C 727 ASP cc_start: 0.8511 (m-30) cc_final: 0.8244 (m-30) REVERT: C 992 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8623 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2618 time to fit residues: 90.5215 Evaluate side-chains 170 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN C 437 ASN ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16608 Z= 0.226 Angle : 0.926 14.317 22605 Z= 0.481 Chirality : 0.049 0.251 2646 Planarity : 0.004 0.047 2958 Dihedral : 7.023 46.644 2343 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.25 % Favored : 83.56 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.58 % Twisted Proline : 3.03 % Twisted General : 0.29 % 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: -3.29 (0.17), residues: 2178 helix: 0.01 (0.22), residues: 600 sheet: -1.28 (0.34), residues: 231 loop : -3.67 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 423 HIS 0.006 0.001 HIS A1030 PHE 0.024 0.001 PHE B 551 TYR 0.012 0.001 TYR B 598 ARG 0.012 0.001 ARG B 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 PHE cc_start: 0.7320 (m-10) cc_final: 0.6951 (m-10) REVERT: A 532 LEU cc_start: 0.8607 (pt) cc_final: 0.8402 (mp) REVERT: A 558 PHE cc_start: 0.8938 (m-10) cc_final: 0.8664 (m-10) REVERT: A 1011 MET cc_start: 0.8336 (tmm) cc_final: 0.7945 (tmm) REVERT: B 300 TYR cc_start: 0.6961 (m-10) cc_final: 0.6761 (m-10) REVERT: B 340 TRP cc_start: 0.8129 (p-90) cc_final: 0.7286 (p-90) REVERT: B 407 ASP cc_start: 0.7820 (t0) cc_final: 0.7364 (t0) REVERT: B 557 ASP cc_start: 0.7572 (m-30) cc_final: 0.7347 (m-30) REVERT: B 650 ILE cc_start: 0.9244 (mt) cc_final: 0.8984 (mt) REVERT: B 709 MET cc_start: 0.7626 (mmm) cc_final: 0.7372 (mmm) REVERT: B 738 TYR cc_start: 0.6236 (p90) cc_final: 0.5565 (p90) REVERT: B 983 LEU cc_start: 0.9290 (tt) cc_final: 0.8943 (tp) REVERT: C 296 ASP cc_start: 0.5852 (m-30) cc_final: 0.5652 (m-30) REVERT: C 532 LEU cc_start: 0.8177 (pt) cc_final: 0.7937 (mp) REVERT: C 650 ILE cc_start: 0.9345 (mt) cc_final: 0.9022 (mt) REVERT: C 722 MET cc_start: 0.8928 (tpp) cc_final: 0.8548 (tpp) REVERT: C 727 ASP cc_start: 0.8498 (m-30) cc_final: 0.8170 (m-30) REVERT: C 745 LEU cc_start: 0.9573 (mt) cc_final: 0.9350 (mt) REVERT: C 992 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8504 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2665 time to fit residues: 92.6657 Evaluate side-chains 177 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 987 GLN C 435 ASN C 437 ASN ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.110052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082258 restraints weight = 60344.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083962 restraints weight = 41664.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.085035 restraints weight = 31433.873| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16608 Z= 0.216 Angle : 0.903 13.967 22605 Z= 0.470 Chirality : 0.048 0.243 2646 Planarity : 0.004 0.040 2958 Dihedral : 6.838 46.660 2343 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 17.40 % Favored : 82.46 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 3.03 % Twisted General : 0.14 % 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: -3.27 (0.17), residues: 2178 helix: 0.01 (0.22), residues: 606 sheet: -1.18 (0.34), residues: 237 loop : -3.69 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 340 HIS 0.007 0.001 HIS A1030 PHE 0.020 0.001 PHE C 558 TYR 0.011 0.001 TYR B 475 ARG 0.009 0.001 ARG B 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3196.39 seconds wall clock time: 58 minutes 40.56 seconds (3520.56 seconds total)