Starting phenix.real_space_refine on Thu Nov 16 18:28:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/11_2023/5wrg_6679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/11_2023/5wrg_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_6679/11_2023/5wrg_6679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/11_2023/5wrg_6679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/11_2023/5wrg_6679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wrg_6679/11_2023/5wrg_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-1.21rc1-5144/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: 8.96, per 1000 atoms: 0.55 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 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: 1.64 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: 5.25 Time building geometry restraints manager: 6.83 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.760 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 44.280 Find NCS groups from input model: 0.980 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.600 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.877 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: 0.3153 time to fit residues: 187.1418 Evaluate side-chains 220 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 217 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1482 time to fit residues: 3.4182 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2904 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= 0.218 Angle : 0.949 13.311 22605 Z= 0.503 Chirality : 0.050 0.224 2646 Planarity : 0.005 0.047 2958 Dihedral : 8.319 48.253 2343 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.84 % Favored : 84.02 % Rotamer: Outliers : 0.18 % Allowed : 3.26 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.49 % Twisted Proline : 6.06 % Twisted General : 0.62 % 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: -1.62 (0.18), residues: 558 sheet: -1.69 (0.33), residues: 249 loop : -3.84 (0.14), residues: 1371 *********************** 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 301 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 298 time to evaluate : 1.863 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: 3 outliers final: 0 residues processed: 301 average time/residue: 0.2804 time to fit residues: 124.7914 Evaluate side-chains 213 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4119 ------------------------------------------------------------------------------- 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: 10.0000 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 0.0040 chunk 135 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 197 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A 910 ASN A 992 GLN B 910 ASN B1018 GLN C 939 GLN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16608 Z= 0.205 Angle : 0.898 14.209 22605 Z= 0.472 Chirality : 0.049 0.241 2646 Planarity : 0.005 0.047 2958 Dihedral : 7.400 48.256 2343 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.57 % Favored : 83.24 % Rotamer: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 6.06 % 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: -3.79 (0.16), residues: 2178 helix: -0.66 (0.21), residues: 555 sheet: -1.58 (0.33), residues: 252 loop : -3.79 (0.14), residues: 1371 *********************** 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 272 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 1.900 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 outliers start: 3 outliers final: 1 residues processed: 272 average time/residue: 0.2948 time to fit residues: 118.8627 Evaluate side-chains 184 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1413 time to fit residues: 2.8265 ------------------------------------------------------------------------------- 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: 1.9990 chunk 103 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 133 optimal weight: 0.0040 chunk 199 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 301 GLN C 599 GLN C 910 ASN C1046 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16608 Z= 0.200 Angle : 0.889 14.327 22605 Z= 0.464 Chirality : 0.048 0.265 2646 Planarity : 0.004 0.041 2958 Dihedral : 7.113 47.317 2343 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.02 % Favored : 83.79 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: -3.58 (0.17), residues: 2178 helix: -0.34 (0.22), residues: 579 sheet: -1.40 (0.33), residues: 246 loop : -3.77 (0.14), residues: 1353 *********************** 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 251 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.942 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: 251 average time/residue: 0.2859 time to fit residues: 106.8818 Evaluate side-chains 182 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6745 ------------------------------------------------------------------------------- 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: 8.9990 chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 0.0470 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN B 917 GLN C 599 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16608 Z= 0.237 Angle : 0.902 13.992 22605 Z= 0.470 Chirality : 0.049 0.239 2646 Planarity : 0.004 0.036 2958 Dihedral : 7.067 48.229 2343 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 17.68 % Favored : 82.14 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 4.04 % 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: -3.40 (0.17), residues: 2178 helix: -0.05 (0.22), residues: 576 sheet: -1.48 (0.32), residues: 255 loop : -3.69 (0.15), residues: 1347 *********************** 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 246 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.923 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 outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2798 time to fit residues: 103.8047 Evaluate side-chains 185 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8212 ------------------------------------------------------------------------------- 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: 0.1980 chunk 41 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN B 902 GLN B 917 GLN B 947 GLN C 301 GLN C 437 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16608 Z= 0.193 Angle : 0.881 14.528 22605 Z= 0.457 Chirality : 0.048 0.233 2646 Planarity : 0.004 0.041 2958 Dihedral : 6.787 45.985 2343 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.15 % Favored : 84.71 % Rotamer: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % 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: -3.32 (0.17), residues: 2178 helix: -0.11 (0.22), residues: 597 sheet: -1.19 (0.33), residues: 249 loop : -3.68 (0.14), residues: 1332 *********************** 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 259 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.791 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 outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.2874 time to fit residues: 111.1213 Evaluate side-chains 189 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6467 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.0670 chunk 118 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- 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 A 917 GLN B 301 GLN B 917 GLN B 939 GLN C 435 ASN C 437 ASN C 960 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16608 Z= 0.243 Angle : 0.899 14.032 22605 Z= 0.468 Chirality : 0.048 0.253 2646 Planarity : 0.004 0.034 2958 Dihedral : 6.880 48.143 2343 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 17.45 % Favored : 82.42 % Rotamer: Outliers : 0.06 % Allowed : 1.96 % Favored : 97.98 % 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: -3.25 (0.17), residues: 2178 helix: 0.02 (0.22), residues: 597 sheet: -1.01 (0.34), residues: 237 loop : -3.69 (0.14), residues: 1344 *********************** 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 239 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 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 outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2802 time to fit residues: 99.9947 Evaluate side-chains 177 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.979 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6336 ------------------------------------------------------------------------------- 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: 9.9990 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 134 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 19 optimal weight: 0.0770 chunk 165 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN C 437 ASN ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16608 Z= 0.197 Angle : 0.880 14.643 22605 Z= 0.455 Chirality : 0.048 0.228 2646 Planarity : 0.004 0.043 2958 Dihedral : 6.687 46.507 2343 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.92 % Favored : 84.94 % 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: -3.16 (0.17), residues: 2178 helix: 0.14 (0.22), residues: 591 sheet: -0.92 (0.34), residues: 237 loop : -3.63 (0.14), residues: 1350 *********************** 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 239 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.931 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: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2660 time to fit residues: 96.6584 Evaluate side-chains 172 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3488 ------------------------------------------------------------------------------- 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: 2.9990 chunk 202 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 301 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN B 942 ASN C 381 ASN ** C 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 942 ASN C 960 ASN ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16608 Z= 0.449 Angle : 1.074 13.933 22605 Z= 0.562 Chirality : 0.053 0.340 2646 Planarity : 0.006 0.061 2958 Dihedral : 7.640 47.256 2343 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 20.16 % Favored : 79.57 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.72 % Twisted Proline : 6.06 % 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: -3.75 (0.16), residues: 2178 helix: -0.75 (0.20), residues: 627 sheet: -1.53 (0.32), residues: 243 loop : -3.83 (0.15), residues: 1308 *********************** 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 221 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.953 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 outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2852 time to fit residues: 94.5504 Evaluate side-chains 168 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4603 ------------------------------------------------------------------------------- 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: 0.0770 chunk 98 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 ASN C 435 ASN C 437 ASN ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16608 Z= 0.217 Angle : 0.944 15.022 22605 Z= 0.487 Chirality : 0.050 0.235 2646 Planarity : 0.004 0.044 2958 Dihedral : 7.115 47.802 2343 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.24 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 3.58 % Twisted Proline : 5.05 % 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: -3.37 (0.17), residues: 2178 helix: -0.13 (0.22), residues: 597 sheet: -1.40 (0.32), residues: 249 loop : -3.68 (0.15), residues: 1332 ********************** 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 246 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.106 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 outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2682 time to fit residues: 99.5643 Evaluate side-chains 181 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5546 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.3980 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 ASN ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.109061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081821 restraints weight = 62556.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.083485 restraints weight = 42374.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084522 restraints weight = 31944.619| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6315 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= 0.235 Angle : 0.930 14.218 22605 Z= 0.482 Chirality : 0.049 0.280 2646 Planarity : 0.004 0.035 2958 Dihedral : 6.999 47.315 2343 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 17.95 % Favored : 81.91 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -3.25 (0.17), residues: 2178 helix: -0.01 (0.22), residues: 588 sheet: -1.13 (0.34), residues: 237 loop : -3.62 (0.15), residues: 1353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.36 seconds wall clock time: 60 minutes 39.49 seconds (3639.49 seconds total)