Starting phenix.real_space_refine on Sun Feb 18 21:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgy_32492/02_2024/7wgy_32492_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgy_32492/02_2024/7wgy_32492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgy_32492/02_2024/7wgy_32492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgy_32492/02_2024/7wgy_32492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgy_32492/02_2024/7wgy_32492_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgy_32492/02_2024/7wgy_32492_neut.pdb" } resolution = 4.0 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= 0.003 sd= 0.072 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 101 5.16 5 C 14608 2.51 5 N 3763 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22914 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8078 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 49, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6393 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 37, 'TRANS': 783} Chain breaks: 8 Chain: "C" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8009 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 49, 'TRANS': 975} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.49, per 1000 atoms: 0.50 Number of scatterers: 22914 At special positions: 0 Unit cell: (141.75, 125.55, 179.55, 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 101 16.00 O 4442 8.00 N 3763 7.00 C 14608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG B1301 " - " ASN B 709 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1305 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.42 Conformation dependent library (CDL) restraints added in 4.1 seconds 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 43 sheets defined 27.0% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.609A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.203A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.219A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.808A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.922A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.612A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.948A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.638A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.901A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.885A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.540A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.552A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.938A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.594A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.670A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.537A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.474A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.583A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.880A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.590A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.500A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.373A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 4.124A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.168A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.287A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.705A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.562A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.956A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.323A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 987 through 1033 removed outlier: 4.256A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.018A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.061A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.892A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.533A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 162 removed outlier: 8.944A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.247A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.502A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.890A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.788A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.534A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.781A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.642A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.371A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 55 removed outlier: 4.289A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.295A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.250A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.947A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.544A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.182A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.858A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.858A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 9.230A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.653A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.242A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.044A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.550A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.707A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.554A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.329A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 714 Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.195A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.570A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.597A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 960 hydrogen bonds defined for protein. 2637 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: 10.18 Time building geometry restraints manager: 10.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3749 1.31 - 1.44: 6357 1.44 - 1.57: 13176 1.57 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 23408 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.21e+01 ... (remaining 23403 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.35: 429 105.35 - 112.52: 12246 112.52 - 119.68: 7471 119.68 - 126.85: 11487 126.85 - 134.01: 207 Bond angle restraints: 31840 Sorted by residual: angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 120.33 124.15 -3.82 8.00e-01 1.56e+00 2.28e+01 angle pdb=" N PRO B 621 " pdb=" CA PRO B 621 " pdb=" C PRO B 621 " ideal model delta sigma weight residual 112.47 120.45 -7.98 2.06e+00 2.36e-01 1.50e+01 angle pdb=" CA PRO B 621 " pdb=" N PRO B 621 " pdb=" CD PRO B 621 " ideal model delta sigma weight residual 112.00 106.94 5.06 1.40e+00 5.10e-01 1.31e+01 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N VAL A 90 " ideal model delta sigma weight residual 114.73 119.05 -4.32 1.30e+00 5.92e-01 1.10e+01 angle pdb=" C HIS C 207 " pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 122.74 114.78 7.96 2.44e+00 1.68e-01 1.06e+01 ... (remaining 31835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 13518 24.13 - 48.26: 591 48.26 - 72.39: 83 72.39 - 96.52: 38 96.52 - 120.65: 35 Dihedral angle restraints: 14265 sinusoidal: 5883 harmonic: 8382 Sorted by residual: dihedral pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " pdb=" CA PRO C 621 " ideal model delta harmonic sigma weight residual 180.00 -149.58 -30.42 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 14262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2835 0.053 - 0.106: 725 0.106 - 0.159: 158 0.159 - 0.212: 12 0.212 - 0.265: 2 Chirality restraints: 3732 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.90e+00 chirality pdb=" CA PRO B 621 " pdb=" N PRO B 621 " pdb=" C PRO B 621 " pdb=" CB PRO B 621 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3729 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.084 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO B 621 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 620 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 621 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 621 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 621 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " -0.066 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO A 621 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.053 5.00e-02 4.00e+02 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 424 2.66 - 3.22: 22164 3.22 - 3.78: 33589 3.78 - 4.34: 45031 4.34 - 4.90: 74335 Nonbonded interactions: 175543 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.104 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.144 2.440 nonbonded pdb=" O PRO B1053 " pdb=" NE2 GLN B1054 " model vdw 2.163 2.520 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.213 2.440 nonbonded pdb=" O GLY A 889 " pdb=" NZ LYS C1045 " model vdw 2.214 2.520 ... (remaining 175538 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' and (resid 26 through 67 or resid 79 through 143 or resid 156 through \ 828 or resid 848 through 1147 or resid 1301 through 1305)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 0.880 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: 4.830 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 63.270 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.180 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.008 0.116 23408 Z= 0.563 Angle : 0.769 9.638 31840 Z= 0.388 Chirality : 0.049 0.265 3732 Planarity : 0.005 0.126 4079 Dihedral : 15.642 120.655 8855 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 2829 helix: 0.19 (0.20), residues: 635 sheet: 0.38 (0.19), residues: 630 loop : -1.24 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.007 0.001 HIS B1058 PHE 0.030 0.002 PHE C 906 TYR 0.023 0.002 TYR A 904 ARG 0.004 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.7153 (tpp) cc_final: 0.6777 (tpp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3419 time to fit residues: 60.3503 Evaluate side-chains 54 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 chunk 74 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 224 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 856 ASN B 613 GLN C 901 GLN C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23408 Z= 0.235 Angle : 0.589 9.915 31840 Z= 0.307 Chirality : 0.044 0.271 3732 Planarity : 0.005 0.122 4079 Dihedral : 11.027 117.329 3716 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.52 % Favored : 95.16 % Rotamer: Outliers : 0.52 % Allowed : 5.88 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 2829 helix: 1.26 (0.20), residues: 645 sheet: 0.36 (0.19), residues: 650 loop : -1.21 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.001 PHE A 782 TYR 0.017 0.001 TYR B 265 ARG 0.004 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 PHE cc_start: 0.6877 (m-80) cc_final: 0.6198 (m-80) REVERT: B 697 MET cc_start: 0.7437 (mmm) cc_final: 0.7100 (tpt) REVERT: C 867 ASP cc_start: 0.6312 (p0) cc_final: 0.6082 (p0) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.3260 time to fit residues: 43.6882 Evaluate side-chains 60 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 734 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 232 optimal weight: 20.0000 chunk 258 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 chunk 209 optimal weight: 0.3980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 388 ASN C 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 23408 Z= 0.150 Angle : 0.520 9.398 31840 Z= 0.269 Chirality : 0.043 0.275 3732 Planarity : 0.005 0.121 4079 Dihedral : 9.694 117.267 3716 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.07 % Favored : 95.62 % Rotamer: Outliers : 0.71 % Allowed : 8.18 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2829 helix: 1.92 (0.21), residues: 640 sheet: 0.52 (0.20), residues: 630 loop : -1.09 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A1048 PHE 0.008 0.001 PHE A 817 TYR 0.014 0.001 TYR B1067 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 214 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.4589 (tpm170) outliers start: 18 outliers final: 7 residues processed: 79 average time/residue: 0.3232 time to fit residues: 44.5772 Evaluate side-chains 65 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 0.0770 chunk 196 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 175 optimal weight: 0.0170 chunk 262 optimal weight: 0.3980 chunk 277 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 23408 Z= 0.135 Angle : 0.499 8.338 31840 Z= 0.255 Chirality : 0.043 0.270 3732 Planarity : 0.004 0.121 4079 Dihedral : 8.247 117.072 3716 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.03 % Favored : 95.65 % Rotamer: Outliers : 1.03 % Allowed : 8.46 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2829 helix: 2.25 (0.21), residues: 627 sheet: 0.59 (0.20), residues: 642 loop : -0.98 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS A1048 PHE 0.008 0.001 PHE A 400 TYR 0.014 0.001 TYR A 265 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.7634 (tpt) cc_final: 0.7115 (tpt) REVERT: C 214 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.4901 (tpm170) outliers start: 26 outliers final: 10 residues processed: 94 average time/residue: 0.3241 time to fit residues: 52.6760 Evaluate side-chains 67 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 206 optimal weight: 20.0000 chunk 114 optimal weight: 0.0870 chunk 236 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 70 optimal weight: 0.0470 overall best weight: 2.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 23408 Z= 0.220 Angle : 0.538 8.413 31840 Z= 0.276 Chirality : 0.043 0.261 3732 Planarity : 0.004 0.123 4079 Dihedral : 7.474 118.507 3716 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.56 % Favored : 95.12 % Rotamer: Outliers : 1.23 % Allowed : 10.32 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2829 helix: 2.20 (0.21), residues: 629 sheet: 0.51 (0.20), residues: 652 loop : -1.02 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.010 0.001 PHE A 192 TYR 0.016 0.001 TYR C 904 ARG 0.004 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 58 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7737 (mmt) cc_final: 0.7487 (mmp) REVERT: B 697 MET cc_start: 0.7772 (tpt) cc_final: 0.7157 (tpt) REVERT: C 214 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.4856 (tpm170) outliers start: 31 outliers final: 17 residues processed: 87 average time/residue: 0.3124 time to fit residues: 47.1805 Evaluate side-chains 72 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 277 optimal weight: 8.9990 chunk 230 optimal weight: 0.0470 chunk 128 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 overall best weight: 2.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23408 Z= 0.211 Angle : 0.539 11.514 31840 Z= 0.274 Chirality : 0.042 0.265 3732 Planarity : 0.004 0.123 4079 Dihedral : 6.865 118.153 3716 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.24 % Favored : 95.44 % Rotamer: Outliers : 1.07 % Allowed : 11.27 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2829 helix: 2.13 (0.21), residues: 645 sheet: 0.51 (0.20), residues: 642 loop : -1.05 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.011 0.001 PHE A 92 TYR 0.018 0.001 TYR B 265 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7729 (mmt) cc_final: 0.7482 (mmp) REVERT: B 697 MET cc_start: 0.7845 (tpt) cc_final: 0.7308 (tpt) REVERT: B 900 MET cc_start: 0.7358 (mtt) cc_final: 0.6973 (mtt) REVERT: C 214 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.4955 (tpm170) outliers start: 27 outliers final: 21 residues processed: 85 average time/residue: 0.3070 time to fit residues: 46.2491 Evaluate side-chains 77 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 10.0000 chunk 31 optimal weight: 0.2980 chunk 158 optimal weight: 0.0170 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 173 optimal weight: 0.0670 chunk 168 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 949 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 23408 Z= 0.152 Angle : 0.502 9.650 31840 Z= 0.256 Chirality : 0.042 0.269 3732 Planarity : 0.004 0.123 4079 Dihedral : 6.307 116.494 3716 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.21 % Favored : 95.48 % Rotamer: Outliers : 1.23 % Allowed : 11.51 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2829 helix: 2.28 (0.21), residues: 638 sheet: 0.58 (0.20), residues: 660 loop : -0.99 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 PHE 0.018 0.001 PHE B 65 TYR 0.013 0.001 TYR A 265 ARG 0.002 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6225 (tpt) cc_final: 0.5927 (tpt) REVERT: A 900 MET cc_start: 0.7680 (mmt) cc_final: 0.7420 (mmp) REVERT: B 697 MET cc_start: 0.7833 (tpt) cc_final: 0.7200 (tpt) REVERT: C 214 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5161 (tpm170) outliers start: 31 outliers final: 18 residues processed: 96 average time/residue: 0.3067 time to fit residues: 51.0916 Evaluate side-chains 74 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 23408 Z= 0.193 Angle : 0.524 9.258 31840 Z= 0.267 Chirality : 0.042 0.262 3732 Planarity : 0.004 0.124 4079 Dihedral : 6.209 116.711 3716 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.21 % Favored : 95.48 % Rotamer: Outliers : 1.15 % Allowed : 11.99 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2829 helix: 2.13 (0.21), residues: 652 sheet: 0.52 (0.20), residues: 656 loop : -1.00 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.010 0.001 PHE A 92 TYR 0.015 0.001 TYR C 904 ARG 0.016 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 56 time to evaluate : 2.822 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.7709 (mmt) cc_final: 0.7459 (mmp) REVERT: B 697 MET cc_start: 0.7756 (tpt) cc_final: 0.7217 (tpt) REVERT: C 214 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.4887 (tpm170) outliers start: 29 outliers final: 24 residues processed: 82 average time/residue: 0.2962 time to fit residues: 42.7351 Evaluate side-chains 79 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 54 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 0.0050 chunk 241 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 532 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23408 Z= 0.222 Angle : 0.546 10.896 31840 Z= 0.278 Chirality : 0.042 0.261 3732 Planarity : 0.004 0.124 4079 Dihedral : 6.292 116.768 3716 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.67 % Favored : 95.02 % Rotamer: Outliers : 1.19 % Allowed : 12.23 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2829 helix: 2.14 (0.21), residues: 650 sheet: 0.47 (0.20), residues: 648 loop : -1.05 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS B 49 PHE 0.014 0.001 PHE B 65 TYR 0.017 0.001 TYR C 904 ARG 0.003 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 2.751 Fit side-chains REVERT: A 900 MET cc_start: 0.7806 (mmt) cc_final: 0.7537 (mmp) REVERT: B 697 MET cc_start: 0.7760 (tpt) cc_final: 0.7182 (tpt) REVERT: C 214 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5087 (tpm170) outliers start: 30 outliers final: 25 residues processed: 82 average time/residue: 0.3031 time to fit residues: 43.9679 Evaluate side-chains 77 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 51 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 189 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 227 optimal weight: 0.0870 chunk 23 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 23408 Z= 0.138 Angle : 0.509 9.293 31840 Z= 0.259 Chirality : 0.043 0.272 3732 Planarity : 0.004 0.123 4079 Dihedral : 5.918 114.713 3716 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.82 % Favored : 95.86 % Rotamer: Outliers : 0.87 % Allowed : 12.70 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2829 helix: 2.27 (0.21), residues: 648 sheet: 0.71 (0.20), residues: 642 loop : -0.95 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1102 HIS 0.003 0.000 HIS B 207 PHE 0.017 0.001 PHE B 65 TYR 0.013 0.001 TYR B 265 ARG 0.002 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7579 (mmt) cc_final: 0.7320 (mmp) outliers start: 22 outliers final: 19 residues processed: 78 average time/residue: 0.3152 time to fit residues: 42.8573 Evaluate side-chains 74 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.0060 chunk 180 optimal weight: 8.9990 chunk 242 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 209 optimal weight: 0.0980 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 234 optimal weight: 0.3980 chunk 28 optimal weight: 9.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.039277 restraints weight = 146099.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040642 restraints weight = 79416.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041531 restraints weight = 52622.863| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 23408 Z= 0.144 Angle : 0.507 8.970 31840 Z= 0.257 Chirality : 0.042 0.266 3732 Planarity : 0.004 0.123 4079 Dihedral : 5.773 113.905 3716 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.85 % Favored : 95.83 % Rotamer: Outliers : 0.71 % Allowed : 12.74 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2829 helix: 2.27 (0.21), residues: 648 sheet: 0.74 (0.20), residues: 642 loop : -0.92 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.000 HIS B 207 PHE 0.025 0.001 PHE A 92 TYR 0.013 0.001 TYR C 904 ARG 0.001 0.000 ARG C 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.89 seconds wall clock time: 58 minutes 30.54 seconds (3510.54 seconds total)