Starting phenix.real_space_refine (version: dev) on Tue Dec 13 16:32:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/12_2022/5wrg_6679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/12_2022/5wrg_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_6679/12_2022/5wrg_6679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/12_2022/5wrg_6679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/12_2022/5wrg_6679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/12_2022/5wrg_6679.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 9.42, per 1000 atoms: 0.58 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: 6.34 Conformation dependent library (CDL) restraints added in 2.5 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: 0.82 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: 5.08 Time building geometry restraints manager: 6.93 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=" 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 angle pdb=" N PRO A 547 " pdb=" CA PRO A 547 " pdb=" C PRO A 547 " ideal model delta sigma weight residual 113.40 124.28 -10.88 1.34e+00 5.57e-01 6.59e+01 angle pdb=" C ILE C 696 " pdb=" N PRO C 697 " pdb=" CA PRO C 697 " ideal model delta sigma weight residual 119.84 129.40 -9.56 1.25e+00 6.40e-01 5.85e+01 angle pdb=" C ILE B 696 " pdb=" N PRO B 697 " pdb=" CA PRO B 697 " ideal model delta sigma weight residual 119.84 129.39 -9.55 1.25e+00 6.40e-01 5.84e+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 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. 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: 1.650 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: 6.220 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.140 Process input model: 42.820 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 1.375 14.042 22605 Z= 0.727 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 % 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 *********************** 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 : 1.857 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 outliers start: 9 outliers final: 3 residues processed: 417 average time/residue: 0.2934 time to fit residues: 175.8054 Evaluate side-chains 220 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 217 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1320 time to fit residues: 3.3208 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 171 optimal weight: 0.0870 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 198 optimal weight: 0.1980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 B 401 GLN B 435 ASN B 437 ASN B 910 ASN B 987 GLN B1018 GLN C 401 GLN C 435 ASN C 437 ASN C 910 ASN C 987 GLN C1018 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16608 Z= 0.205 Angle : 1.038 24.105 22605 Z= 0.475 Chirality : 0.047 0.191 2646 Planarity : 0.005 0.047 2958 Dihedral : 7.973 47.704 2343 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.93 % Favored : 83.93 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.58 % Twisted Proline : 6.06 % Twisted General : 0.53 % 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: -1.64 (0.18), residues: 564 sheet: -1.71 (0.33), residues: 249 loop : -3.83 (0.14), residues: 1365 *********************** 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 308 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 2.719 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 outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.2944 time to fit residues: 137.7051 Evaluate side-chains 218 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5913 ------------------------------------------------------------------------------- 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: 0.0270 chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 215 optimal weight: 0.0170 chunk 177 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN B 987 GLN B1018 GLN C 939 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 16608 Z= 0.177 Angle : 1.006 24.195 22605 Z= 0.450 Chirality : 0.047 0.191 2646 Planarity : 0.005 0.042 2958 Dihedral : 7.209 46.642 2343 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.84 % Favored : 83.98 % Rotamer Outliers : 0.00 % 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: -3.79 (0.16), residues: 2178 helix: -0.72 (0.21), residues: 555 sheet: -1.48 (0.33), residues: 249 loop : -3.77 (0.14), residues: 1374 *********************** 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: 0 poor density : 276 time to evaluate : 1.992 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 outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2641 time to fit residues: 110.3102 Evaluate side-chains 198 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5557 ------------------------------------------------------------------------------- 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: 7.9990 chunk 149 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 766 GLN ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN B 910 ASN B 917 GLN C 381 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN C 917 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 16608 Z= 0.314 Angle : 1.055 22.511 22605 Z= 0.484 Chirality : 0.047 0.199 2646 Planarity : 0.005 0.040 2958 Dihedral : 7.332 48.722 2343 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 19.24 % Favored : 80.62 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.63 % Twisted Proline : 5.05 % Twisted General : 0.19 % 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: -3.70 (0.17), residues: 2178 helix: -0.54 (0.21), residues: 582 sheet: -1.80 (0.32), residues: 258 loop : -3.74 (0.15), residues: 1338 *********************** 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 252 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.108 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 outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.2792 time to fit residues: 105.9273 Evaluate side-chains 184 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1336 time to fit residues: 2.8182 ------------------------------------------------------------------------------- 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: 1.9990 chunk 120 optimal weight: 0.8980 chunk 3 optimal weight: 0.0010 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 910 ASN B 902 GLN B 947 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 16608 Z= 0.239 Angle : 1.022 23.934 22605 Z= 0.459 Chirality : 0.047 0.194 2646 Planarity : 0.004 0.036 2958 Dihedral : 7.129 47.813 2343 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 17.22 % Favored : 82.60 % Rotamer Outliers : 0.00 % 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: -3.61 (0.17), residues: 2178 helix: -0.39 (0.21), residues: 606 sheet: -1.55 (0.32), residues: 246 loop : -3.81 (0.14), residues: 1326 *********************** 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 251 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.796 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 outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2737 time to fit residues: 102.1308 Evaluate side-chains 186 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6075 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 0.0670 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN B 947 GLN C 437 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.5017 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= 0.182 Angle : 1.009 24.384 22605 Z= 0.445 Chirality : 0.047 0.193 2646 Planarity : 0.004 0.040 2958 Dihedral : 6.833 46.968 2343 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.71 % Favored : 83.15 % Rotamer Outliers : 0.06 % 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: -3.44 (0.17), residues: 2178 helix: -0.20 (0.22), residues: 606 sheet: -1.47 (0.33), residues: 249 loop : -3.74 (0.14), residues: 1323 *********************** 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 257 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 2.013 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 outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.2750 time to fit residues: 105.7271 Evaluate side-chains 188 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6017 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN C 437 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** 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: 0.7099 moved from start: 0.5288 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= 0.197 Angle : 1.004 23.944 22605 Z= 0.446 Chirality : 0.046 0.187 2646 Planarity : 0.004 0.042 2958 Dihedral : 6.706 47.092 2343 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.80 % Favored : 83.06 % Rotamer Outliers : 0.12 % 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: -3.28 (0.17), residues: 2178 helix: 0.07 (0.22), residues: 594 sheet: -1.18 (0.34), residues: 234 loop : -3.70 (0.15), residues: 1350 *********************** 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 246 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 245 average time/residue: 0.2740 time to fit residues: 101.3874 Evaluate side-chains 182 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6404 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 0.0980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN B 942 ASN B 947 GLN ** C 599 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: 0.7110 moved from start: 0.5515 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= 0.209 Angle : 1.013 24.783 22605 Z= 0.450 Chirality : 0.046 0.252 2646 Planarity : 0.004 0.048 2958 Dihedral : 6.691 47.548 2343 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.80 % Favored : 83.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.63 % Twisted Proline : 3.03 % 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: -3.19 (0.17), residues: 2178 helix: 0.18 (0.22), residues: 591 sheet: -1.18 (0.34), residues: 234 loop : -3.65 (0.15), residues: 1353 *********************** 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 : 1.911 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 outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2699 time to fit residues: 99.9123 Evaluate side-chains 185 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4503 ------------------------------------------------------------------------------- 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: 0.6980 chunk 202 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 942 ASN C 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 16608 Z= 0.348 Angle : 1.119 24.035 22605 Z= 0.516 Chirality : 0.049 0.239 2646 Planarity : 0.005 0.063 2958 Dihedral : 7.430 46.045 2343 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 19.42 % Favored : 80.39 % Rotamer Outliers : 0.00 % 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: -3.57 (0.17), residues: 2178 helix: -0.40 (0.21), residues: 612 sheet: -1.46 (0.33), residues: 225 loop : -3.77 (0.15), residues: 1341 *********************** 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 225 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.850 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 outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2855 time to fit residues: 96.1698 Evaluate side-chains 164 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5118 ------------------------------------------------------------------------------- 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: 0.7980 chunk 126 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 144 optimal weight: 0.0000 chunk 218 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 0.0020 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 522 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN B 947 GLN C 437 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6296 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= 0.203 Angle : 1.048 25.358 22605 Z= 0.464 Chirality : 0.047 0.253 2646 Planarity : 0.004 0.042 2958 Dihedral : 6.915 46.944 2343 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.02 % Favored : 83.84 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.68 % Twisted Proline : 3.03 % Twisted General : 0.19 % 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: -3.33 (0.17), residues: 2178 helix: 0.10 (0.22), residues: 591 sheet: -1.59 (0.31), residues: 249 loop : -3.70 (0.14), residues: 1338 ********************** 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 244 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.993 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 outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.2909 time to fit residues: 107.6649 Evaluate side-chains 180 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6144 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 0.0770 chunk 160 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 32 optimal weight: 0.0470 chunk 152 optimal weight: 0.0030 overall best weight: 1.0250 ------------------------------------------------------------------------------- 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** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN B 951 ASN C 435 ASN C 437 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN C 960 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.109445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081647 restraints weight = 61249.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083297 restraints weight = 41896.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.084376 restraints weight = 31490.376| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16608 Z= 0.211 Angle : 1.039 24.642 22605 Z= 0.463 Chirality : 0.047 0.197 2646 Planarity : 0.004 0.049 2958 Dihedral : 6.773 45.949 2343 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 17.49 % Favored : 82.37 % Rotamer Outliers : 0.00 % 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: -3.22 (0.17), residues: 2178 helix: 0.16 (0.22), residues: 594 sheet: -1.22 (0.33), residues: 231 loop : -3.66 (0.15), residues: 1353 =============================================================================== Job complete usr+sys time: 3132.77 seconds wall clock time: 58 minutes 3.45 seconds (3483.45 seconds total)