Starting phenix.real_space_refine on Wed Jul 24 05:59:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uir_42302/07_2024/8uir_42302.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uir_42302/07_2024/8uir_42302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uir_42302/07_2024/8uir_42302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uir_42302/07_2024/8uir_42302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uir_42302/07_2024/8uir_42302.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uir_42302/07_2024/8uir_42302.cif" } resolution = 3.2 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= -0.001 sd= 0.050 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 114 5.16 5 C 15861 2.51 5 N 4074 2.21 5 O 4830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24879 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8069 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} 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: "L" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 12.96, per 1000 atoms: 0.52 Number of scatterers: 24879 At special positions: 0 Unit cell: (139.32, 132.84, 174.96, 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 114 16.00 O 4830 8.00 N 4074 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=2, 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 L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN C 234 " " NAG C1301 " - " ASN A 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.33 Conformation dependent library (CDL) restraints added in 4.3 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 51 sheets defined 24.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.048A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.815A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.050A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.389A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.619A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.951A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.850A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.789A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.576A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.920A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.049A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.584A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.662A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.588A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.049A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.788A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.853A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.684A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.668A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.073A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.667A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.531A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.741A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.634A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 947 through 965 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 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.674A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.054A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.769A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.082A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.727A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.547A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.709A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 removed outlier: 3.730A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.535A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.080A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.594A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.578A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.993A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.218A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.640A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.512A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.881A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.674A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.668A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.639A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.447A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.028A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.523A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.679A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.923A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.459A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.545A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.820A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.177A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.498A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.633A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.435A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.607A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.197A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.898A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.662A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.202A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.586A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.603A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.535A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.190A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.142A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.428A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 928 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.00 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7875 1.35 - 1.47: 6567 1.47 - 1.60: 10845 1.60 - 1.73: 0 1.73 - 1.86: 141 Bond restraints: 25428 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 25423 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.05: 571 106.05 - 113.04: 13739 113.04 - 120.04: 8599 120.04 - 127.03: 11440 127.03 - 134.03: 235 Bond angle restraints: 34584 Sorted by residual: angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 122.46 130.56 -8.10 1.41e+00 5.03e-01 3.30e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ASN C 87 " pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta sigma weight residual 122.46 129.30 -6.84 1.41e+00 5.03e-01 2.35e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 117.02 -4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" N GLY C 648 " pdb=" CA GLY C 648 " pdb=" C GLY C 648 " ideal model delta sigma weight residual 112.04 108.11 3.93 1.02e+00 9.61e-01 1.49e+01 ... (remaining 34579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14178 17.92 - 35.83: 1294 35.83 - 53.75: 235 53.75 - 71.67: 70 71.67 - 89.59: 15 Dihedral angle restraints: 15792 sinusoidal: 6759 harmonic: 9033 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -147.84 61.84 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 145.02 34.98 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -27.01 -58.99 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3552 0.083 - 0.167: 504 0.167 - 0.250: 12 0.250 - 0.334: 4 0.334 - 0.417: 5 Chirality restraints: 4077 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C2 NAG B1310 " pdb=" C1 NAG B1310 " pdb=" C3 NAG B1310 " pdb=" N2 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 4074 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.006 2.00e-02 2.50e+03 4.00e-02 2.00e+01 pdb=" CG ASN A 343 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 561 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A1143 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.040 5.00e-02 4.00e+02 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7299 2.83 - 3.34: 19517 3.34 - 3.86: 39699 3.86 - 4.38: 44163 4.38 - 4.90: 80310 Nonbonded interactions: 190988 Sorted by model distance: nonbonded pdb=" O ALA B 879 " pdb=" OG1 THR B 883 " model vdw 2.307 2.440 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.315 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.332 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.342 2.440 nonbonded pdb=" NH2 ARG B 995 " pdb=" OD2 ASP C 994 " model vdw 2.344 2.520 ... (remaining 190983 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' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 24 through 1147 or resid 1301 through 1309)) } 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' selection = chain 'L' } 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 individual isotropic 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: 2.160 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: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 65.700 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.062 25428 Z= 0.280 Angle : 0.705 12.566 34584 Z= 0.364 Chirality : 0.053 0.417 4077 Planarity : 0.006 0.084 4404 Dihedral : 14.126 89.586 9852 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.14), residues: 3057 helix: -0.48 (0.17), residues: 672 sheet: 0.50 (0.22), residues: 561 loop : -1.51 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.007 0.001 HIS C 66 PHE 0.033 0.001 PHE C 592 TYR 0.028 0.001 TYR A 837 ARG 0.011 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7016 (t80) cc_final: 0.6532 (t80) REVERT: A 200 TYR cc_start: 0.5658 (t80) cc_final: 0.5251 (t80) REVERT: A 641 ASN cc_start: 0.7284 (m110) cc_final: 0.6924 (m110) REVERT: B 339 HIS cc_start: 0.7030 (t-90) cc_final: 0.6667 (t70) REVERT: B 568 ASP cc_start: 0.7477 (t0) cc_final: 0.7037 (t0) REVERT: C 177 MET cc_start: 0.6190 (pmm) cc_final: 0.5967 (pmm) REVERT: C 493 GLN cc_start: 0.8067 (tt0) cc_final: 0.7807 (tt0) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3451 time to fit residues: 125.2503 Evaluate side-chains 188 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 157 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN A 919 ASN A 935 GLN B 207 HIS B 339 HIS B1106 GLN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25428 Z= 0.177 Angle : 0.511 9.942 34584 Z= 0.261 Chirality : 0.045 0.386 4077 Planarity : 0.004 0.056 4404 Dihedral : 7.222 59.518 4326 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.52 % Allowed : 4.97 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.43 (0.15), residues: 3057 helix: 1.23 (0.20), residues: 675 sheet: 0.67 (0.21), residues: 639 loop : -1.34 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS A 207 PHE 0.017 0.001 PHE A 906 TYR 0.011 0.001 TYR A1067 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7187 (t80) cc_final: 0.6622 (t80) REVERT: A 200 TYR cc_start: 0.5477 (t80) cc_final: 0.5222 (t80) REVERT: A 641 ASN cc_start: 0.7323 (m110) cc_final: 0.6964 (m110) REVERT: A 869 MET cc_start: 0.8843 (mtp) cc_final: 0.8639 (mtm) REVERT: B 339 HIS cc_start: 0.7071 (t70) cc_final: 0.6755 (t70) REVERT: C 388 ASN cc_start: 0.8811 (m-40) cc_final: 0.8611 (m-40) REVERT: C 448 ASN cc_start: 0.7594 (t0) cc_final: 0.7243 (t0) REVERT: C 493 GLN cc_start: 0.7374 (tt0) cc_final: 0.7130 (tt0) outliers start: 14 outliers final: 10 residues processed: 216 average time/residue: 0.3427 time to fit residues: 120.1950 Evaluate side-chains 193 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 281 optimal weight: 0.0670 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25428 Z= 0.160 Angle : 0.485 9.586 34584 Z= 0.246 Chirality : 0.044 0.362 4077 Planarity : 0.003 0.051 4404 Dihedral : 6.784 59.620 4326 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.63 % Allowed : 7.39 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.16 (0.15), residues: 3057 helix: 1.75 (0.21), residues: 663 sheet: 0.67 (0.21), residues: 633 loop : -1.19 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A 207 PHE 0.018 0.001 PHE B 168 TYR 0.012 0.001 TYR A 837 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7236 (t80) cc_final: 0.6630 (t80) REVERT: A 200 TYR cc_start: 0.5457 (t80) cc_final: 0.5228 (t80) REVERT: A 641 ASN cc_start: 0.7294 (m110) cc_final: 0.6915 (m110) REVERT: A 751 ASN cc_start: 0.8405 (m-40) cc_final: 0.8119 (m-40) REVERT: B 339 HIS cc_start: 0.7083 (t70) cc_final: 0.6706 (t70) REVERT: C 448 ASN cc_start: 0.7605 (t0) cc_final: 0.7284 (t0) REVERT: C 1092 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7355 (mt-10) outliers start: 17 outliers final: 12 residues processed: 211 average time/residue: 0.3240 time to fit residues: 112.3171 Evaluate side-chains 201 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 804 GLN A 935 GLN A1005 GLN C 339 HIS C 901 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25428 Z= 0.225 Angle : 0.517 9.789 34584 Z= 0.262 Chirality : 0.046 0.366 4077 Planarity : 0.004 0.051 4404 Dihedral : 6.587 59.306 4326 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.08 % Allowed : 9.35 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.13 (0.15), residues: 3057 helix: 2.04 (0.21), residues: 645 sheet: 0.61 (0.21), residues: 612 loop : -1.20 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.021 0.001 PHE A 906 TYR 0.013 0.001 TYR C1067 ARG 0.003 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7407 (t80) cc_final: 0.6679 (t80) REVERT: A 498 ARG cc_start: 0.6081 (mmt-90) cc_final: 0.5687 (mpt90) REVERT: A 641 ASN cc_start: 0.7295 (m110) cc_final: 0.6929 (m110) REVERT: A 751 ASN cc_start: 0.8441 (m-40) cc_final: 0.8166 (m-40) REVERT: A 1029 MET cc_start: 0.8703 (tpp) cc_final: 0.8410 (tpp) REVERT: B 339 HIS cc_start: 0.7034 (t70) cc_final: 0.6724 (t-90) REVERT: C 339 HIS cc_start: 0.7074 (t70) cc_final: 0.6850 (t-90) REVERT: C 448 ASN cc_start: 0.7762 (t0) cc_final: 0.7409 (t0) REVERT: C 1092 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7402 (mt-10) outliers start: 29 outliers final: 20 residues processed: 232 average time/residue: 0.3385 time to fit residues: 127.2487 Evaluate side-chains 224 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 4.9990 chunk 169 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 222 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 254 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN A 935 GLN C 901 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25428 Z= 0.191 Angle : 0.501 11.864 34584 Z= 0.252 Chirality : 0.045 0.365 4077 Planarity : 0.003 0.051 4404 Dihedral : 6.531 58.389 4326 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.97 % Allowed : 10.58 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.15), residues: 3057 helix: 2.15 (0.21), residues: 645 sheet: 0.60 (0.21), residues: 612 loop : -1.16 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.012 0.001 PHE B 377 TYR 0.014 0.001 TYR A1067 ARG 0.002 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7417 (t80) cc_final: 0.6671 (t80) REVERT: A 498 ARG cc_start: 0.6060 (mmt-90) cc_final: 0.5625 (mpt90) REVERT: A 641 ASN cc_start: 0.7279 (m110) cc_final: 0.6915 (m110) REVERT: A 751 ASN cc_start: 0.8424 (m-40) cc_final: 0.8156 (m-40) REVERT: A 1029 MET cc_start: 0.8700 (tpp) cc_final: 0.8404 (tpp) REVERT: B 339 HIS cc_start: 0.7047 (t70) cc_final: 0.6703 (t-90) REVERT: B 740 MET cc_start: 0.8358 (mmm) cc_final: 0.8150 (mmm) REVERT: C 339 HIS cc_start: 0.7049 (t70) cc_final: 0.6844 (t-90) REVERT: C 448 ASN cc_start: 0.7768 (t0) cc_final: 0.7429 (t0) REVERT: C 1092 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7411 (mt-10) outliers start: 26 outliers final: 22 residues processed: 221 average time/residue: 0.3405 time to fit residues: 121.8069 Evaluate side-chains 223 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN B 607 GLN B1010 GLN B1106 GLN C 314 GLN C 405 ASN C 450 ASN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25428 Z= 0.304 Angle : 0.554 9.961 34584 Z= 0.280 Chirality : 0.047 0.369 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.642 59.860 4326 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.56 % Allowed : 10.47 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.27 (0.15), residues: 3057 helix: 1.81 (0.21), residues: 666 sheet: 0.52 (0.21), residues: 606 loop : -1.28 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 PHE 0.023 0.002 PHE B 906 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7262 (tpp-160) cc_final: 0.6774 (tpp-160) REVERT: A 170 TYR cc_start: 0.7417 (t80) cc_final: 0.6611 (t80) REVERT: A 498 ARG cc_start: 0.5896 (mmt-90) cc_final: 0.5494 (mpt90) REVERT: A 641 ASN cc_start: 0.7225 (m110) cc_final: 0.6892 (m110) REVERT: A 1029 MET cc_start: 0.8720 (tpp) cc_final: 0.8495 (tpp) REVERT: B 339 HIS cc_start: 0.7089 (t70) cc_final: 0.6717 (t-90) REVERT: B 529 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7475 (ttpp) REVERT: C 66 HIS cc_start: 0.6949 (m-70) cc_final: 0.6667 (m-70) REVERT: C 448 ASN cc_start: 0.7817 (t0) cc_final: 0.7421 (t0) REVERT: C 450 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8206 (t0) REVERT: C 1092 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7591 (mt-10) outliers start: 42 outliers final: 31 residues processed: 239 average time/residue: 0.3389 time to fit residues: 130.5828 Evaluate side-chains 236 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN C 339 HIS C 450 ASN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25428 Z= 0.222 Angle : 0.520 9.751 34584 Z= 0.263 Chirality : 0.045 0.367 4077 Planarity : 0.003 0.052 4404 Dihedral : 6.585 59.545 4326 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.52 % Allowed : 11.06 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3057 helix: 1.77 (0.21), residues: 681 sheet: 0.55 (0.21), residues: 600 loop : -1.21 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.016 0.001 PHE C 592 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 212 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7227 (tpp-160) cc_final: 0.6721 (tpp-160) REVERT: A 170 TYR cc_start: 0.7431 (t80) cc_final: 0.6605 (t80) REVERT: A 392 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: A 498 ARG cc_start: 0.5922 (mmt-90) cc_final: 0.5503 (mpt90) REVERT: A 641 ASN cc_start: 0.7205 (m110) cc_final: 0.6871 (m110) REVERT: A 1029 MET cc_start: 0.8716 (tpp) cc_final: 0.8486 (tpp) REVERT: B 339 HIS cc_start: 0.7119 (t70) cc_final: 0.6779 (t-90) REVERT: B 529 LYS cc_start: 0.7794 (mtpp) cc_final: 0.7460 (ttpp) REVERT: B 574 ASP cc_start: 0.8220 (t0) cc_final: 0.7909 (t0) REVERT: C 66 HIS cc_start: 0.6910 (m-70) cc_final: 0.6621 (m-70) REVERT: C 448 ASN cc_start: 0.7741 (t0) cc_final: 0.7344 (t0) REVERT: C 450 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7521 (t0) REVERT: C 1092 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7587 (mt-10) outliers start: 41 outliers final: 33 residues processed: 237 average time/residue: 0.3364 time to fit residues: 129.9807 Evaluate side-chains 240 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 394 ASN C 314 GLN C 339 HIS C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25428 Z= 0.268 Angle : 0.540 11.840 34584 Z= 0.273 Chirality : 0.046 0.366 4077 Planarity : 0.004 0.052 4404 Dihedral : 6.634 59.803 4326 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.74 % Allowed : 11.17 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.26 (0.15), residues: 3057 helix: 1.73 (0.21), residues: 681 sheet: 0.49 (0.21), residues: 600 loop : -1.24 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 PHE 0.023 0.001 PHE B 168 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 202 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7445 (t80) cc_final: 0.6584 (t80) REVERT: A 392 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: A 498 ARG cc_start: 0.6249 (mmt-90) cc_final: 0.5793 (mpt90) REVERT: A 641 ASN cc_start: 0.7219 (m110) cc_final: 0.6888 (m110) REVERT: A 1029 MET cc_start: 0.8720 (tpp) cc_final: 0.8499 (tpp) REVERT: B 339 HIS cc_start: 0.7060 (t70) cc_final: 0.6793 (t70) REVERT: B 529 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7450 (ttpp) REVERT: B 574 ASP cc_start: 0.8229 (t0) cc_final: 0.7923 (t0) REVERT: C 66 HIS cc_start: 0.6899 (m-70) cc_final: 0.6597 (m-70) REVERT: C 448 ASN cc_start: 0.7864 (t0) cc_final: 0.7380 (t0) REVERT: C 450 ASN cc_start: 0.8055 (t0) cc_final: 0.7287 (t0) REVERT: C 498 ARG cc_start: 0.8574 (mmt90) cc_final: 0.7845 (mmt180) REVERT: C 900 MET cc_start: 0.8428 (mtp) cc_final: 0.8102 (mtp) outliers start: 47 outliers final: 38 residues processed: 234 average time/residue: 0.3378 time to fit residues: 128.5649 Evaluate side-chains 241 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 250 optimal weight: 0.0170 chunk 262 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 394 ASN C 314 GLN C 339 HIS C 405 ASN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25428 Z= 0.156 Angle : 0.507 11.488 34584 Z= 0.253 Chirality : 0.046 0.648 4077 Planarity : 0.003 0.051 4404 Dihedral : 6.549 59.401 4326 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 11.62 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.00 (0.15), residues: 3057 helix: 2.12 (0.21), residues: 660 sheet: 0.58 (0.21), residues: 600 loop : -1.08 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.012 0.001 PHE B1121 TYR 0.016 0.001 TYR A 495 ARG 0.004 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7438 (t80) cc_final: 0.6543 (t80) REVERT: A 392 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: A 498 ARG cc_start: 0.6129 (mmt-90) cc_final: 0.5686 (mpt90) REVERT: A 641 ASN cc_start: 0.7310 (m110) cc_final: 0.6963 (m110) REVERT: A 1029 MET cc_start: 0.8713 (tpp) cc_final: 0.8453 (tpp) REVERT: B 377 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6244 (t80) REVERT: B 529 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7419 (ttpp) REVERT: B 574 ASP cc_start: 0.8121 (t0) cc_final: 0.7643 (t0) REVERT: C 66 HIS cc_start: 0.6814 (m-70) cc_final: 0.6494 (m-70) REVERT: C 448 ASN cc_start: 0.7981 (t0) cc_final: 0.7448 (t0) REVERT: C 450 ASN cc_start: 0.8228 (t0) cc_final: 0.7414 (t0) REVERT: C 724 THR cc_start: 0.9382 (m) cc_final: 0.9110 (p) REVERT: C 900 MET cc_start: 0.8357 (mtp) cc_final: 0.8032 (mtp) REVERT: C 1107 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7434 (mtt90) outliers start: 38 outliers final: 28 residues processed: 233 average time/residue: 0.3330 time to fit residues: 126.5141 Evaluate side-chains 232 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 204 optimal weight: 0.0060 chunk 307 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 189 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 26 GLN B 394 ASN C 314 GLN C 339 HIS C 405 ASN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25428 Z= 0.152 Angle : 0.495 11.486 34584 Z= 0.248 Chirality : 0.045 0.372 4077 Planarity : 0.003 0.050 4404 Dihedral : 6.451 59.838 4326 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.22 % Allowed : 12.14 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.08 (0.15), residues: 3057 helix: 2.21 (0.21), residues: 660 sheet: 0.61 (0.21), residues: 603 loop : -1.03 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.025 0.001 PHE B 168 TYR 0.021 0.001 TYR C 313 ARG 0.005 0.000 ARG B 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7446 (t80) cc_final: 0.6550 (t80) REVERT: A 392 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: A 641 ASN cc_start: 0.7352 (m110) cc_final: 0.7013 (m110) REVERT: A 904 TYR cc_start: 0.7067 (m-10) cc_final: 0.6052 (m-80) REVERT: A 1029 MET cc_start: 0.8701 (tpp) cc_final: 0.8407 (tpp) REVERT: B 377 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6213 (t80) REVERT: B 529 LYS cc_start: 0.7787 (mtpp) cc_final: 0.7432 (ttpp) REVERT: B 568 ASP cc_start: 0.7359 (t0) cc_final: 0.6976 (t0) REVERT: B 574 ASP cc_start: 0.8131 (t0) cc_final: 0.7678 (t0) REVERT: C 66 HIS cc_start: 0.6811 (m-70) cc_final: 0.6490 (m-70) REVERT: C 314 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7895 (mm-40) REVERT: C 448 ASN cc_start: 0.8031 (t0) cc_final: 0.7500 (t0) REVERT: C 450 ASN cc_start: 0.8283 (t0) cc_final: 0.7412 (t0) REVERT: C 498 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8048 (mmt180) REVERT: C 724 THR cc_start: 0.9392 (m) cc_final: 0.9146 (p) outliers start: 33 outliers final: 27 residues processed: 230 average time/residue: 0.3370 time to fit residues: 126.5331 Evaluate side-chains 234 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 26 GLN ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 314 GLN C 339 HIS C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126384 restraints weight = 28204.327| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.77 r_work: 0.2939 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25428 Z= 0.368 Angle : 0.599 11.174 34584 Z= 0.303 Chirality : 0.049 0.366 4077 Planarity : 0.004 0.050 4404 Dihedral : 6.739 59.811 4326 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.41 % Allowed : 11.92 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3057 helix: 2.05 (0.21), residues: 642 sheet: 0.39 (0.21), residues: 603 loop : -1.20 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 886 HIS 0.007 0.001 HIS C1048 PHE 0.022 0.002 PHE C 377 TYR 0.032 0.002 TYR C 313 ARG 0.009 0.001 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.27 seconds wall clock time: 79 minutes 27.88 seconds (4767.88 seconds total)