Starting phenix.real_space_refine on Wed Jul 24 06:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0q_42866/07_2024/8v0q_42866.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0q_42866/07_2024/8v0q_42866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0q_42866/07_2024/8v0q_42866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0q_42866/07_2024/8v0q_42866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0q_42866/07_2024/8v0q_42866.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0q_42866/07_2024/8v0q_42866.cif" } resolution = 3.9 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= 0.020 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 15813 2.51 5 N 4068 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" 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: 24795 Number of models: 1 Model: "" Number of chains: 12 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: "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: 14.16, per 1000 atoms: 0.57 Number of scatterers: 24795 At special positions: 0 Unit cell: (137.16, 130.68, 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 4800 8.00 N 4068 7.00 C 15813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.05 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=2.03 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 165 " " 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 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.26 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: 59 helices and 49 sheets defined 24.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.556A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.723A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.568A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.565A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.003A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.654A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.979A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.717A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.672A 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: 3.645A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (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 removed outlier: 3.672A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.399A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.786A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.588A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.538A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.578A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.806A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.515A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.033A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.006A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.633A 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 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.749A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 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 removed outlier: 3.604A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.149A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.807A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.571A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' 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: 3.595A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.052A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.582A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.864A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.561A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.877A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' 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 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.190A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.626A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.691A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.708A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.674A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.617A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.563A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.358A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.343A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.111A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.735A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.735A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.354A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.556A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.693A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.596A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.818A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.669A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.989A 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: 7.045A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.541A 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: 3.712A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.819A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.788A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.568A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.391A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.532A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.582A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.173A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.893A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.965A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.554A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.575A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (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: 3.611A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.273A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.635A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.856A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 909 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.60 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7859 1.34 - 1.47: 6366 1.47 - 1.60: 10978 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25344 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 25339 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.92: 561 105.92 - 113.02: 13555 113.02 - 120.12: 8871 120.12 - 127.22: 11278 127.22 - 134.32: 205 Bond angle restraints: 34470 Sorted by residual: angle pdb=" C LEU C 945 " pdb=" N GLY C 946 " pdb=" CA GLY C 946 " ideal model delta sigma weight residual 119.98 126.18 -6.20 1.11e+00 8.12e-01 3.11e+01 angle pdb=" C LEU A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" C LEU A 518 " pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " ideal model delta sigma weight residual 115.79 110.44 5.35 1.19e+00 7.06e-01 2.02e+01 angle pdb=" C SER A 116 " pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 120.82 127.39 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" CB MET C1050 " pdb=" CG MET C1050 " pdb=" SD MET C1050 " ideal model delta sigma weight residual 112.70 126.07 -13.37 3.00e+00 1.11e-01 1.98e+01 ... (remaining 34465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 14455 21.92 - 43.84: 1037 43.84 - 65.77: 127 65.77 - 87.69: 36 87.69 - 109.61: 5 Dihedral angle restraints: 15660 sinusoidal: 6627 harmonic: 9033 Sorted by residual: dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta harmonic sigma weight residual -180.00 -132.40 -47.60 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA LYS B 462 " pdb=" C LYS B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual -180.00 -136.95 -43.05 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -18.25 -67.75 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 15657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3945 0.124 - 0.248: 90 0.248 - 0.373: 9 0.373 - 0.497: 2 0.497 - 0.621: 1 Chirality restraints: 4047 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C2 NAG C1301 " pdb=" C1 NAG C1301 " pdb=" C3 NAG C1301 " pdb=" N2 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 4044 not shown) Planarity restraints: 4434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 91 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C TYR B 91 " -0.064 2.00e-02 2.50e+03 pdb=" O TYR B 91 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE B 92 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO C 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 118 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C LEU C 118 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU C 118 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 119 " 0.014 2.00e-02 2.50e+03 ... (remaining 4431 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6318 2.80 - 3.33: 20145 3.33 - 3.85: 39830 3.85 - 4.38: 42999 4.38 - 4.90: 77033 Nonbonded interactions: 186325 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.279 2.440 nonbonded pdb=" O ASP B 294 " pdb=" OG SER B 297 " model vdw 2.287 2.440 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.300 2.440 nonbonded pdb=" O VAL A 308 " pdb=" OG1 THR A 602 " model vdw 2.303 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.304 2.440 ... (remaining 186320 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 66.470 Find NCS groups from input model: 2.300 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 0.100 25344 Z= 0.289 Angle : 0.821 14.963 34470 Z= 0.418 Chirality : 0.055 0.621 4047 Planarity : 0.006 0.068 4398 Dihedral : 14.492 109.610 9726 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: -1.79 (0.14), residues: 3057 helix: -0.68 (0.17), residues: 665 sheet: -0.08 (0.21), residues: 539 loop : -1.80 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 64 HIS 0.006 0.001 HIS B 519 PHE 0.036 0.002 PHE A 201 TYR 0.018 0.001 TYR A 453 ARG 0.017 0.001 ARG C1107 *********************** 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 262 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8511 (m-30) cc_final: 0.8299 (m-30) REVERT: A 353 TRP cc_start: 0.8791 (p-90) cc_final: 0.7161 (p-90) REVERT: B 740 MET cc_start: 0.7769 (mmt) cc_final: 0.7442 (mmt) REVERT: B 1019 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7321 (ttp80) REVERT: C 549 THR cc_start: 0.8336 (m) cc_final: 0.8022 (p) REVERT: C 979 ASP cc_start: 0.8681 (m-30) cc_final: 0.8459 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3411 time to fit residues: 145.4620 Evaluate side-chains 183 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.880 ------------------------------------------------------------------------------- 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: 4.9990 chunk 234 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 564 GLN A 926 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 658 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 115 GLN C 448 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 25344 Z= 0.424 Angle : 0.714 12.242 34470 Z= 0.367 Chirality : 0.049 0.469 4047 Planarity : 0.005 0.045 4398 Dihedral : 8.511 98.313 4200 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 1.34 % Allowed : 9.84 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.10 % 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: 0.68 (0.20), residues: 663 sheet: -0.45 (0.20), residues: 582 loop : -1.67 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.006 0.001 HIS A 207 PHE 0.028 0.002 PHE B1089 TYR 0.021 0.002 TYR A1067 ARG 0.004 0.001 ARG C1107 *********************** 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: 36 poor density : 188 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8515 (m-30) cc_final: 0.8300 (m-30) REVERT: B 87 ASN cc_start: 0.7277 (t0) cc_final: 0.7059 (t0) REVERT: B 392 PHE cc_start: 0.7710 (m-10) cc_final: 0.7467 (m-10) REVERT: B 740 MET cc_start: 0.8104 (mmt) cc_final: 0.7501 (mmt) REVERT: C 313 TYR cc_start: 0.8229 (m-80) cc_final: 0.8003 (m-80) REVERT: C 453 TYR cc_start: 0.7623 (p90) cc_final: 0.7088 (p90) REVERT: C 979 ASP cc_start: 0.8676 (m-30) cc_final: 0.8142 (m-30) outliers start: 36 outliers final: 24 residues processed: 214 average time/residue: 0.3496 time to fit residues: 120.9700 Evaluate side-chains 196 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 7.9990 chunk 250 optimal weight: 0.4980 chunk 278 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 422 ASN A 926 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25344 Z= 0.170 Angle : 0.554 12.650 34470 Z= 0.277 Chirality : 0.045 0.483 4047 Planarity : 0.004 0.044 4398 Dihedral : 7.862 96.450 4200 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 0.89 % Allowed : 12.18 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.88 (0.15), residues: 3057 helix: 1.50 (0.20), residues: 658 sheet: -0.37 (0.20), residues: 599 loop : -1.53 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.004 0.001 HIS B 66 PHE 0.021 0.001 PHE B 888 TYR 0.021 0.001 TYR B 91 ARG 0.002 0.000 ARG B 567 *********************** 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 211 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8404 (m-30) cc_final: 0.8172 (m-30) REVERT: B 38 TYR cc_start: 0.8193 (m-10) cc_final: 0.7993 (m-10) REVERT: B 87 ASN cc_start: 0.7257 (t0) cc_final: 0.6910 (t0) REVERT: B 91 TYR cc_start: 0.7883 (t80) cc_final: 0.7546 (t80) REVERT: C 453 TYR cc_start: 0.7660 (p90) cc_final: 0.7107 (p90) REVERT: C 900 MET cc_start: 0.8692 (mtm) cc_final: 0.8464 (mtm) REVERT: C 979 ASP cc_start: 0.8741 (m-30) cc_final: 0.8241 (m-30) outliers start: 24 outliers final: 16 residues processed: 205 average time/residue: 0.3519 time to fit residues: 118.7285 Evaluate side-chains 191 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 938 LEU 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: 2.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 267 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 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 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25344 Z= 0.206 Angle : 0.550 12.309 34470 Z= 0.275 Chirality : 0.045 0.470 4047 Planarity : 0.004 0.043 4398 Dihedral : 7.459 92.221 4200 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 1.63 % Allowed : 13.88 % Favored : 84.48 % 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: -0.70 (0.15), residues: 3057 helix: 1.83 (0.21), residues: 646 sheet: -0.40 (0.20), residues: 624 loop : -1.42 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B 66 PHE 0.021 0.001 PHE B 888 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG B1107 *********************** 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 228 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8528 (m-30) cc_final: 0.8245 (m-30) REVERT: A 421 TYR cc_start: 0.6862 (m-10) cc_final: 0.6660 (m-10) REVERT: A 697 MET cc_start: 0.7270 (tpt) cc_final: 0.6811 (mmm) REVERT: B 38 TYR cc_start: 0.8197 (m-10) cc_final: 0.7950 (m-10) REVERT: B 87 ASN cc_start: 0.7413 (t0) cc_final: 0.7014 (t0) REVERT: B 392 PHE cc_start: 0.7880 (m-10) cc_final: 0.7582 (m-10) REVERT: B 740 MET cc_start: 0.8064 (mmt) cc_final: 0.7519 (mmt) REVERT: C 104 TRP cc_start: 0.7552 (m-90) cc_final: 0.7298 (m-90) REVERT: C 453 TYR cc_start: 0.7675 (p90) cc_final: 0.7115 (p90) REVERT: C 900 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8465 (mtm) REVERT: C 979 ASP cc_start: 0.8749 (m-30) cc_final: 0.8202 (m-30) REVERT: C 1033 VAL cc_start: 0.8593 (t) cc_final: 0.8354 (p) outliers start: 44 outliers final: 32 residues processed: 219 average time/residue: 0.3225 time to fit residues: 116.7848 Evaluate side-chains 210 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 254 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 563 GLN B 658 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25344 Z= 0.354 Angle : 0.644 11.810 34470 Z= 0.327 Chirality : 0.047 0.451 4047 Planarity : 0.004 0.045 4398 Dihedral : 7.552 86.523 4200 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 2.78 % Allowed : 15.00 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: -0.90 (0.15), residues: 3057 helix: 1.39 (0.20), residues: 660 sheet: -0.61 (0.20), residues: 617 loop : -1.42 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 PHE 0.024 0.002 PHE B1089 TYR 0.022 0.002 TYR A 904 ARG 0.008 0.001 ARG C1107 *********************** 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 265 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 190 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7040 (m-10) cc_final: 0.6798 (m-10) REVERT: B 87 ASN cc_start: 0.7627 (t0) cc_final: 0.7233 (t0) REVERT: C 453 TYR cc_start: 0.7840 (p90) cc_final: 0.7283 (p90) REVERT: C 979 ASP cc_start: 0.8643 (m-30) cc_final: 0.8049 (m-30) outliers start: 75 outliers final: 59 residues processed: 250 average time/residue: 0.3225 time to fit residues: 134.2861 Evaluate side-chains 239 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 180 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 658 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25344 Z= 0.191 Angle : 0.560 15.984 34470 Z= 0.279 Chirality : 0.045 0.460 4047 Planarity : 0.003 0.043 4398 Dihedral : 7.158 78.344 4200 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 2.26 % Allowed : 16.41 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: -0.65 (0.15), residues: 3057 helix: 1.76 (0.20), residues: 666 sheet: -0.49 (0.20), residues: 614 loop : -1.32 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE B 888 TYR 0.038 0.001 TYR B 91 ARG 0.002 0.000 ARG C1107 *********************** 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 244 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7017 (m-10) cc_final: 0.6734 (m-10) REVERT: A 697 MET cc_start: 0.7202 (tpt) cc_final: 0.6588 (mmm) REVERT: B 87 ASN cc_start: 0.7721 (t0) cc_final: 0.7280 (t0) REVERT: B 740 MET cc_start: 0.7969 (mmt) cc_final: 0.7404 (mmt) REVERT: B 900 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: C 453 TYR cc_start: 0.7786 (p90) cc_final: 0.7249 (p90) REVERT: C 979 ASP cc_start: 0.8614 (m-30) cc_final: 0.8010 (m-30) REVERT: C 1033 VAL cc_start: 0.8641 (t) cc_final: 0.8391 (p) outliers start: 61 outliers final: 44 residues processed: 229 average time/residue: 0.3151 time to fit residues: 121.1653 Evaluate side-chains 221 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 218 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 251 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 186 optimal weight: 0.1980 chunk 181 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25344 Z= 0.177 Angle : 0.548 15.269 34470 Z= 0.272 Chirality : 0.045 0.456 4047 Planarity : 0.003 0.043 4398 Dihedral : 6.811 58.852 4200 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 2.30 % Allowed : 17.63 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.54 (0.15), residues: 3057 helix: 1.93 (0.21), residues: 669 sheet: -0.40 (0.20), residues: 614 loop : -1.29 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 PHE 0.037 0.001 PHE A 106 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG C 102 *********************** 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 250 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 188 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8103 (m-10) REVERT: A 177 MET cc_start: 0.4462 (mmm) cc_final: 0.4162 (mmm) REVERT: A 420 ASP cc_start: 0.8699 (m-30) cc_final: 0.8290 (m-30) REVERT: A 421 TYR cc_start: 0.7096 (m-10) cc_final: 0.6870 (m-10) REVERT: A 697 MET cc_start: 0.7371 (tpt) cc_final: 0.6722 (mmm) REVERT: B 87 ASN cc_start: 0.7737 (t0) cc_final: 0.7300 (t0) REVERT: B 740 MET cc_start: 0.7948 (mmt) cc_final: 0.7388 (mmt) REVERT: C 453 TYR cc_start: 0.7816 (p90) cc_final: 0.7248 (p90) REVERT: C 900 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: C 979 ASP cc_start: 0.8642 (m-30) cc_final: 0.7987 (m-30) REVERT: C 1033 VAL cc_start: 0.8583 (t) cc_final: 0.8336 (p) outliers start: 62 outliers final: 49 residues processed: 236 average time/residue: 0.3310 time to fit residues: 130.4065 Evaluate side-chains 227 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 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 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25344 Z= 0.158 Angle : 0.548 16.012 34470 Z= 0.268 Chirality : 0.044 0.446 4047 Planarity : 0.003 0.045 4398 Dihedral : 6.585 58.640 4200 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.41 % Allowed : 17.56 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: -0.42 (0.15), residues: 3057 helix: 2.08 (0.21), residues: 669 sheet: -0.32 (0.21), residues: 603 loop : -1.25 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.003 0.000 HIS B 66 PHE 0.034 0.001 PHE A 106 TYR 0.037 0.001 TYR B 91 ARG 0.002 0.000 ARG B 567 *********************** 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 251 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 186 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8266 (m-10) REVERT: A 420 ASP cc_start: 0.8746 (m-30) cc_final: 0.8295 (m-30) REVERT: A 421 TYR cc_start: 0.7068 (m-10) cc_final: 0.6752 (m-10) REVERT: A 697 MET cc_start: 0.7337 (tpt) cc_final: 0.6727 (mmm) REVERT: B 87 ASN cc_start: 0.7737 (t0) cc_final: 0.7290 (t0) REVERT: B 900 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (mtp) REVERT: C 453 TYR cc_start: 0.7821 (p90) cc_final: 0.7256 (p90) REVERT: C 900 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7998 (mtm) REVERT: C 979 ASP cc_start: 0.8645 (m-30) cc_final: 0.7991 (m-30) outliers start: 65 outliers final: 50 residues processed: 237 average time/residue: 0.3195 time to fit residues: 126.3822 Evaluate side-chains 229 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 176 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.3980 chunk 285 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 417 ASN B 563 GLN B 613 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25344 Z= 0.149 Angle : 0.552 16.159 34470 Z= 0.268 Chirality : 0.044 0.441 4047 Planarity : 0.003 0.045 4398 Dihedral : 6.458 58.633 4200 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 2.23 % Allowed : 18.23 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.35 (0.15), residues: 3057 helix: 2.16 (0.21), residues: 669 sheet: -0.26 (0.20), residues: 618 loop : -1.22 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.002 0.000 HIS B 66 PHE 0.036 0.001 PHE A 106 TYR 0.029 0.001 TYR B 91 ARG 0.001 0.000 ARG C1107 *********************** 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 245 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 185 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: A 177 MET cc_start: 0.4795 (mmm) cc_final: 0.4557 (mmm) REVERT: A 226 LEU cc_start: 0.5841 (tp) cc_final: 0.5606 (tp) REVERT: A 421 TYR cc_start: 0.7096 (m-10) cc_final: 0.6778 (m-10) REVERT: A 697 MET cc_start: 0.7322 (tpt) cc_final: 0.6692 (mmm) REVERT: A 731 MET cc_start: 0.8652 (ptp) cc_final: 0.8117 (ptp) REVERT: B 87 ASN cc_start: 0.7744 (t0) cc_final: 0.7292 (t0) REVERT: B 424 LYS cc_start: 0.8459 (tppt) cc_final: 0.7962 (mmtm) REVERT: B 1081 ILE cc_start: 0.9183 (tp) cc_final: 0.8892 (tp) REVERT: C 453 TYR cc_start: 0.7807 (p90) cc_final: 0.7215 (p90) REVERT: C 900 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: C 979 ASP cc_start: 0.8610 (m-30) cc_final: 0.7942 (m-30) outliers start: 60 outliers final: 54 residues processed: 228 average time/residue: 0.3260 time to fit residues: 124.6945 Evaluate side-chains 233 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25344 Z= 0.213 Angle : 0.578 16.441 34470 Z= 0.284 Chirality : 0.046 0.558 4047 Planarity : 0.003 0.045 4398 Dihedral : 6.392 59.276 4200 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 2.19 % Allowed : 18.23 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 1.94 (0.20), residues: 681 sheet: -0.31 (0.20), residues: 612 loop : -1.22 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 PHE 0.038 0.001 PHE A 106 TYR 0.026 0.001 TYR B 91 ARG 0.002 0.000 ARG C 905 ********************** 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 235 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 176 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8258 (m-10) REVERT: A 177 MET cc_start: 0.4818 (mmm) cc_final: 0.4573 (mmm) REVERT: A 226 LEU cc_start: 0.5903 (tp) cc_final: 0.5668 (tp) REVERT: A 697 MET cc_start: 0.7398 (tpt) cc_final: 0.6795 (mmm) REVERT: B 87 ASN cc_start: 0.7771 (t0) cc_final: 0.7345 (t0) REVERT: C 453 TYR cc_start: 0.7794 (p90) cc_final: 0.7204 (p90) REVERT: C 900 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8047 (mtm) REVERT: C 979 ASP cc_start: 0.8617 (m-30) cc_final: 0.7956 (m-30) outliers start: 59 outliers final: 54 residues processed: 220 average time/residue: 0.3165 time to fit residues: 116.2736 Evaluate side-chains 225 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 68 optimal weight: 0.0470 chunk 245 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 563 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093535 restraints weight = 58640.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094022 restraints weight = 34200.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094758 restraints weight = 32729.807| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25344 Z= 0.306 Angle : 0.631 16.218 34470 Z= 0.315 Chirality : 0.047 0.677 4047 Planarity : 0.004 0.043 4398 Dihedral : 6.681 59.855 4200 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 2.30 % Allowed : 18.45 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.63 (0.15), residues: 3057 helix: 1.64 (0.20), residues: 677 sheet: -0.47 (0.20), residues: 613 loop : -1.26 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.005 0.001 HIS C1048 PHE 0.023 0.002 PHE B 392 TYR 0.024 0.001 TYR B 91 ARG 0.004 0.000 ARG C 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3948.87 seconds wall clock time: 72 minutes 50.43 seconds (4370.43 seconds total)