Starting phenix.real_space_refine on Mon Feb 19 20:49:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnn_12230/02_2024/7bnn_12230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnn_12230/02_2024/7bnn_12230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnn_12230/02_2024/7bnn_12230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnn_12230/02_2024/7bnn_12230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnn_12230/02_2024/7bnn_12230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnn_12230/02_2024/7bnn_12230.pdb" } resolution = 3.5 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= 0.004 sd= 0.060 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 16402 2.51 5 N 4236 2.21 5 O 5023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25775 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8340 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 8375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8375 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 54, 'TRANS': 1016} Chain breaks: 6 Chain: "C" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8364 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" 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 Time building chain proxies: 13.31, per 1000 atoms: 0.52 Number of scatterers: 25775 At special positions: 0 Unit cell: (160.65, 150.45, 196.35, 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 5023 8.00 N 4236 7.00 C 16402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.04 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 743 " - pdb=" SG CYS A 749 " 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.03 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 10.38 Conformation dependent library (CDL) restraints added in 5.2 seconds 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 57 sheets defined 21.1% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.677A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.523A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.267A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.049A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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: 3.577A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.589A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.698A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.860A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.678A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.023A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.502A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 956 removed outlier: 4.062A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.992A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B1012 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.985A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.753A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.300A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.756A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.931A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1006 removed outlier: 5.947A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1033 removed outlier: 3.565A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.748A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.753A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.706A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.429A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.540A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 142 through 143 removed outlier: 6.479A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 310 through 318 removed outlier: 4.502A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.693A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.693A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 664 through 667 removed outlier: 3.587A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.635A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.620A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.673A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.711A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.663A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC4, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.931A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AC8, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.029A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.149A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.515A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.768A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.720A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.255A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.997A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.621A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1080 through 1082 removed outlier: 6.552A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE7, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.647A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 47 through 49 removed outlier: 4.165A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.824A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.128A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.743A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.641A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.945A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.145A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.646A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 725 through 728 removed outlier: 4.023A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 765 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.56 Time building geometry restraints manager: 11.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8220 1.35 - 1.47: 6659 1.47 - 1.59: 11333 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 26356 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 9.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 26351 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.49: 717 106.49 - 113.37: 14442 113.37 - 120.24: 8906 120.24 - 127.12: 11563 127.12 - 133.99: 234 Bond angle restraints: 35862 Sorted by residual: angle pdb=" N LEU B1012 " pdb=" CA LEU B1012 " pdb=" C LEU B1012 " ideal model delta sigma weight residual 113.18 107.15 6.03 1.33e+00 5.65e-01 2.06e+01 angle pdb=" N GLU C 619 " pdb=" CA GLU C 619 " pdb=" C GLU C 619 " ideal model delta sigma weight residual 113.43 108.83 4.60 1.26e+00 6.30e-01 1.33e+01 angle pdb=" C ASN C 616 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C ILE A 233 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " ideal model delta sigma weight residual 120.82 125.25 -4.43 1.47e+00 4.63e-01 9.06e+00 ... (remaining 35857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 15392 23.40 - 46.80: 800 46.80 - 70.19: 102 70.19 - 93.59: 32 93.59 - 116.99: 24 Dihedral angle restraints: 16350 sinusoidal: 7023 harmonic: 9327 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -148.77 62.77 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -26.06 -59.94 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -137.46 51.46 1 1.00e+01 1.00e-02 3.62e+01 ... (remaining 16347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4005 0.100 - 0.201: 189 0.201 - 0.301: 2 0.301 - 0.401: 5 0.401 - 0.502: 2 Chirality restraints: 4203 Sorted by residual: chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 4200 not shown) Planarity restraints: 4625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 617 " 0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C CYS A 617 " -0.064 2.00e-02 2.50e+03 pdb=" O CYS A 617 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 618 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 209 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 330 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.032 5.00e-02 4.00e+02 ... (remaining 4622 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 698 2.68 - 3.24: 24670 3.24 - 3.79: 37564 3.79 - 4.35: 48309 4.35 - 4.90: 81361 Nonbonded interactions: 192602 Sorted by model distance: nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.129 2.520 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.168 2.440 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.197 2.520 nonbonded pdb=" OD2 ASP B 578 " pdb=" OG1 THR B 581 " model vdw 2.205 2.440 nonbonded pdb=" OG SER B 591 " pdb=" OE1 GLU B 619 " model vdw 2.218 2.440 ... (remaining 192597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 616 or (resid 617 and (name N or name CA or nam \ e C or name CB or name SG )) or resid 618 through 956 or resid 958 through 1006 \ or resid 1008 through 1146 or resid 1301 through 1309)) selection = (chain 'B' and (resid 14 through 616 or (resid 617 and (name N or name CA or nam \ e C or name CB or name SG )) or resid 618 through 620 or resid 641 through 827 o \ r resid 855 through 1006 or resid 1008 through 1146 or resid 1301 through 1309)) \ selection = (chain 'C' and (resid 14 through 620 or resid 641 through 827 or resid 855 throu \ gh 956 or resid 958 through 1146 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.010 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 70.450 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 0.059 26356 Z= 0.242 Angle : 0.604 9.082 35862 Z= 0.312 Chirality : 0.047 0.502 4203 Planarity : 0.004 0.064 4584 Dihedral : 14.573 116.988 10227 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 3167 helix: 1.63 (0.23), residues: 606 sheet: -2.24 (0.19), residues: 673 loop : -2.62 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 886 HIS 0.004 0.001 HIS C 245 PHE 0.015 0.001 PHE B 906 TYR 0.012 0.001 TYR A 508 ARG 0.007 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.929 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7839 (t70) cc_final: 0.7610 (t70) REVERT: A 490 PHE cc_start: 0.8755 (t80) cc_final: 0.8231 (t80) REVERT: B 33 THR cc_start: 0.8157 (p) cc_final: 0.7923 (p) REVERT: B 396 TYR cc_start: 0.7831 (m-80) cc_final: 0.7323 (m-80) REVERT: C 140 PHE cc_start: 0.8527 (p90) cc_final: 0.8086 (p90) REVERT: C 505 TYR cc_start: 0.6653 (t80) cc_final: 0.6356 (t80) REVERT: C 740 MET cc_start: 0.7535 (ttt) cc_final: 0.7200 (ttt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3271 time to fit residues: 116.2735 Evaluate side-chains 148 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 chunk 250 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 152 optimal weight: 40.0000 chunk 186 optimal weight: 1.9990 chunk 290 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 146 HIS C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26356 Z= 0.212 Angle : 0.583 9.651 35862 Z= 0.297 Chirality : 0.046 0.453 4203 Planarity : 0.004 0.048 4584 Dihedral : 9.485 102.562 4481 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.61 % Allowed : 6.10 % Favored : 93.29 % 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: -2.21 (0.15), residues: 3167 helix: 1.75 (0.23), residues: 620 sheet: -1.86 (0.20), residues: 650 loop : -2.59 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 353 HIS 0.004 0.001 HIS C 146 PHE 0.016 0.001 PHE B 342 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 2.750 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6318 (pmm) cc_final: 0.6007 (pmm) REVERT: A 189 LEU cc_start: 0.8379 (tp) cc_final: 0.8075 (mp) REVERT: A 380 TYR cc_start: 0.7247 (m-80) cc_final: 0.6986 (m-10) REVERT: A 392 PHE cc_start: 0.8100 (m-80) cc_final: 0.7763 (m-80) REVERT: A 490 PHE cc_start: 0.8643 (t80) cc_final: 0.8195 (t80) REVERT: A 697 MET cc_start: 0.8335 (mmm) cc_final: 0.7825 (mmm) REVERT: B 396 TYR cc_start: 0.7894 (m-80) cc_final: 0.7421 (m-80) REVERT: C 140 PHE cc_start: 0.8522 (p90) cc_final: 0.7835 (p90) REVERT: C 473 TYR cc_start: 0.8490 (t80) cc_final: 0.8177 (t80) REVERT: C 505 TYR cc_start: 0.6732 (t80) cc_final: 0.6402 (t80) outliers start: 17 outliers final: 10 residues processed: 175 average time/residue: 0.3157 time to fit residues: 94.9146 Evaluate side-chains 159 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 4.9990 chunk 90 optimal weight: 0.0060 chunk 241 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 314 optimal weight: 0.9980 chunk 259 optimal weight: 30.0000 chunk 288 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26356 Z= 0.240 Angle : 0.575 11.764 35862 Z= 0.291 Chirality : 0.046 0.441 4203 Planarity : 0.003 0.046 4584 Dihedral : 8.608 93.163 4481 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.68 % Allowed : 9.17 % Favored : 90.15 % 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: -2.15 (0.15), residues: 3167 helix: 1.72 (0.22), residues: 621 sheet: -1.78 (0.20), residues: 660 loop : -2.54 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.009 0.001 HIS A 66 PHE 0.024 0.001 PHE A 79 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 2.941 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6246 (pmm) cc_final: 0.6019 (pmm) REVERT: A 274 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8440 (t) REVERT: A 380 TYR cc_start: 0.7324 (m-80) cc_final: 0.7084 (m-80) REVERT: A 392 PHE cc_start: 0.8155 (m-80) cc_final: 0.7877 (m-80) REVERT: A 490 PHE cc_start: 0.8626 (t80) cc_final: 0.8188 (t80) REVERT: B 374 PHE cc_start: 0.8516 (m-80) cc_final: 0.8247 (m-80) REVERT: B 396 TYR cc_start: 0.7898 (m-80) cc_final: 0.7408 (m-80) REVERT: C 354 ASN cc_start: 0.8447 (t0) cc_final: 0.8225 (t0) REVERT: C 394 ASN cc_start: 0.8588 (m110) cc_final: 0.8261 (m110) REVERT: C 473 TYR cc_start: 0.8537 (t80) cc_final: 0.8219 (t80) REVERT: C 505 TYR cc_start: 0.6823 (t80) cc_final: 0.6473 (t80) outliers start: 19 outliers final: 11 residues processed: 175 average time/residue: 0.3539 time to fit residues: 107.3097 Evaluate side-chains 160 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 151 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 0.0030 chunk 195 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26356 Z= 0.262 Angle : 0.573 10.618 35862 Z= 0.289 Chirality : 0.046 0.442 4203 Planarity : 0.003 0.048 4584 Dihedral : 8.000 91.584 4481 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.32 % Allowed : 10.45 % Favored : 88.23 % 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: -2.11 (0.15), residues: 3167 helix: 1.64 (0.22), residues: 625 sheet: -1.67 (0.20), residues: 658 loop : -2.50 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.010 0.001 HIS A 66 PHE 0.017 0.001 PHE A 347 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 2.811 Fit side-chains REVERT: A 189 LEU cc_start: 0.8382 (tp) cc_final: 0.8017 (mt) REVERT: A 274 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8476 (t) REVERT: A 380 TYR cc_start: 0.7363 (m-80) cc_final: 0.7096 (m-80) REVERT: A 392 PHE cc_start: 0.8195 (m-80) cc_final: 0.7994 (m-80) REVERT: A 394 ASN cc_start: 0.5587 (t0) cc_final: 0.5146 (t0) REVERT: A 490 PHE cc_start: 0.8673 (t80) cc_final: 0.8186 (t80) REVERT: B 117 LEU cc_start: 0.9118 (tp) cc_final: 0.8861 (tt) REVERT: B 374 PHE cc_start: 0.8555 (m-80) cc_final: 0.8310 (m-80) REVERT: B 396 TYR cc_start: 0.7825 (m-80) cc_final: 0.7232 (m-80) REVERT: C 140 PHE cc_start: 0.8349 (p90) cc_final: 0.7916 (p90) REVERT: C 354 ASN cc_start: 0.8473 (t0) cc_final: 0.8187 (t0) REVERT: C 394 ASN cc_start: 0.8565 (m110) cc_final: 0.8220 (m110) REVERT: C 473 TYR cc_start: 0.8560 (t80) cc_final: 0.8264 (t80) REVERT: C 505 TYR cc_start: 0.6805 (t80) cc_final: 0.6435 (t80) REVERT: C 658 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7918 (p0) outliers start: 37 outliers final: 16 residues processed: 181 average time/residue: 0.3096 time to fit residues: 96.8759 Evaluate side-chains 161 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 157 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 207 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26356 Z= 0.253 Angle : 0.567 10.641 35862 Z= 0.286 Chirality : 0.046 0.439 4203 Planarity : 0.003 0.049 4584 Dihedral : 7.712 92.539 4481 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.28 % Allowed : 12.49 % Favored : 86.23 % 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: -2.08 (0.15), residues: 3167 helix: 1.64 (0.22), residues: 625 sheet: -1.70 (0.20), residues: 677 loop : -2.46 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 886 HIS 0.009 0.001 HIS A 66 PHE 0.014 0.001 PHE C 347 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6342 (pmm) cc_final: 0.5920 (pmm) REVERT: A 189 LEU cc_start: 0.8404 (tp) cc_final: 0.8019 (mt) REVERT: A 274 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8477 (t) REVERT: A 380 TYR cc_start: 0.7388 (m-80) cc_final: 0.7110 (m-80) REVERT: A 392 PHE cc_start: 0.8222 (m-80) cc_final: 0.7941 (m-80) REVERT: A 394 ASN cc_start: 0.5592 (t0) cc_final: 0.5187 (t0) REVERT: A 490 PHE cc_start: 0.8677 (t80) cc_final: 0.8161 (t80) REVERT: B 117 LEU cc_start: 0.9111 (tp) cc_final: 0.8862 (tt) REVERT: B 374 PHE cc_start: 0.8589 (m-80) cc_final: 0.8303 (m-80) REVERT: B 396 TYR cc_start: 0.7796 (m-80) cc_final: 0.7224 (m-80) REVERT: C 140 PHE cc_start: 0.8339 (p90) cc_final: 0.7925 (p90) REVERT: C 258 TRP cc_start: 0.7470 (p-90) cc_final: 0.7045 (p-90) REVERT: C 354 ASN cc_start: 0.8460 (t0) cc_final: 0.8110 (t0) REVERT: C 394 ASN cc_start: 0.8539 (m110) cc_final: 0.8179 (m110) REVERT: C 473 TYR cc_start: 0.8557 (t80) cc_final: 0.8272 (t80) REVERT: C 505 TYR cc_start: 0.6865 (t80) cc_final: 0.6479 (t80) outliers start: 36 outliers final: 21 residues processed: 173 average time/residue: 0.3123 time to fit residues: 93.0134 Evaluate side-chains 168 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26356 Z= 0.219 Angle : 0.551 11.098 35862 Z= 0.276 Chirality : 0.045 0.430 4203 Planarity : 0.003 0.049 4584 Dihedral : 7.226 89.686 4481 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.39 % Allowed : 13.66 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.15), residues: 3167 helix: 1.71 (0.22), residues: 626 sheet: -1.53 (0.20), residues: 658 loop : -2.41 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 886 HIS 0.006 0.001 HIS A 66 PHE 0.019 0.001 PHE C 347 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 2.780 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6376 (pmm) cc_final: 0.6013 (pmm) REVERT: A 189 LEU cc_start: 0.8485 (tp) cc_final: 0.8108 (mt) REVERT: A 274 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8422 (t) REVERT: A 394 ASN cc_start: 0.5360 (t0) cc_final: 0.5007 (t0) REVERT: A 453 TYR cc_start: 0.5983 (p90) cc_final: 0.5747 (p90) REVERT: A 490 PHE cc_start: 0.8667 (t80) cc_final: 0.8136 (t80) REVERT: B 374 PHE cc_start: 0.8615 (m-80) cc_final: 0.8316 (m-80) REVERT: B 396 TYR cc_start: 0.7773 (m-80) cc_final: 0.7219 (m-80) REVERT: C 140 PHE cc_start: 0.8279 (p90) cc_final: 0.7907 (p90) REVERT: C 258 TRP cc_start: 0.7578 (p-90) cc_final: 0.7150 (p-90) REVERT: C 354 ASN cc_start: 0.8483 (t0) cc_final: 0.8119 (t0) REVERT: C 394 ASN cc_start: 0.8514 (m110) cc_final: 0.8145 (m110) REVERT: C 473 TYR cc_start: 0.8579 (t80) cc_final: 0.8309 (t80) REVERT: C 505 TYR cc_start: 0.6901 (t80) cc_final: 0.6529 (t80) outliers start: 39 outliers final: 26 residues processed: 187 average time/residue: 0.3196 time to fit residues: 104.0739 Evaluate side-chains 178 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 chunk 175 optimal weight: 0.4980 chunk 260 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 193 optimal weight: 0.4980 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26356 Z= 0.205 Angle : 0.554 11.380 35862 Z= 0.276 Chirality : 0.045 0.426 4203 Planarity : 0.003 0.049 4584 Dihedral : 6.939 88.188 4481 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.36 % Allowed : 14.52 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 3167 helix: 1.73 (0.22), residues: 626 sheet: -1.42 (0.20), residues: 655 loop : -2.40 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.012 0.001 HIS C 207 PHE 0.037 0.001 PHE A 157 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6333 (pmm) cc_final: 0.5988 (pmm) REVERT: A 189 LEU cc_start: 0.8512 (tp) cc_final: 0.8154 (mt) REVERT: A 274 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8510 (t) REVERT: A 394 ASN cc_start: 0.5390 (t0) cc_final: 0.5052 (t0) REVERT: A 490 PHE cc_start: 0.8685 (t80) cc_final: 0.8109 (t80) REVERT: B 374 PHE cc_start: 0.8603 (m-80) cc_final: 0.8326 (m-80) REVERT: B 396 TYR cc_start: 0.7726 (m-80) cc_final: 0.7200 (m-80) REVERT: C 140 PHE cc_start: 0.8283 (p90) cc_final: 0.7926 (p90) REVERT: C 258 TRP cc_start: 0.7639 (p-90) cc_final: 0.7236 (p-90) REVERT: C 354 ASN cc_start: 0.8489 (t0) cc_final: 0.8114 (t0) REVERT: C 394 ASN cc_start: 0.8525 (m110) cc_final: 0.8152 (m110) REVERT: C 473 TYR cc_start: 0.8592 (t80) cc_final: 0.8345 (t80) REVERT: C 505 TYR cc_start: 0.6935 (t80) cc_final: 0.6582 (t80) REVERT: C 658 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7831 (p0) outliers start: 38 outliers final: 27 residues processed: 186 average time/residue: 0.3099 time to fit residues: 98.6095 Evaluate side-chains 182 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 210 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26356 Z= 0.201 Angle : 0.553 11.590 35862 Z= 0.275 Chirality : 0.045 0.420 4203 Planarity : 0.003 0.049 4584 Dihedral : 6.630 86.446 4481 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.61 % Allowed : 14.73 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 3167 helix: 1.77 (0.22), residues: 625 sheet: -1.36 (0.20), residues: 655 loop : -2.37 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 PHE 0.035 0.001 PHE A 157 TYR 0.030 0.001 TYR A 453 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6343 (pmm) cc_final: 0.6007 (pmm) REVERT: A 189 LEU cc_start: 0.8570 (tp) cc_final: 0.8205 (mt) REVERT: A 274 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8505 (t) REVERT: A 394 ASN cc_start: 0.5246 (t0) cc_final: 0.4961 (t0) REVERT: A 490 PHE cc_start: 0.8685 (t80) cc_final: 0.8163 (t80) REVERT: B 117 LEU cc_start: 0.9029 (tp) cc_final: 0.8782 (tt) REVERT: B 374 PHE cc_start: 0.8608 (m-80) cc_final: 0.8323 (m-80) REVERT: B 396 TYR cc_start: 0.7731 (m-80) cc_final: 0.7225 (m-80) REVERT: C 140 PHE cc_start: 0.8294 (p90) cc_final: 0.7941 (p90) REVERT: C 258 TRP cc_start: 0.7662 (p-90) cc_final: 0.7268 (p-90) REVERT: C 354 ASN cc_start: 0.8525 (t0) cc_final: 0.8154 (t0) REVERT: C 394 ASN cc_start: 0.8522 (m110) cc_final: 0.8153 (m110) REVERT: C 473 TYR cc_start: 0.8592 (t80) cc_final: 0.8355 (t80) REVERT: C 505 TYR cc_start: 0.6948 (t80) cc_final: 0.6591 (t80) REVERT: C 658 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7664 (p0) outliers start: 45 outliers final: 35 residues processed: 191 average time/residue: 0.3421 time to fit residues: 111.1906 Evaluate side-chains 191 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 1.9990 chunk 295 optimal weight: 0.3980 chunk 269 optimal weight: 0.0070 chunk 287 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 225 optimal weight: 0.0570 chunk 88 optimal weight: 0.7980 chunk 259 optimal weight: 30.0000 chunk 271 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26356 Z= 0.148 Angle : 0.539 11.607 35862 Z= 0.267 Chirality : 0.044 0.407 4203 Planarity : 0.003 0.049 4584 Dihedral : 6.246 84.711 4481 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.39 % Allowed : 15.20 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 3167 helix: 1.92 (0.23), residues: 626 sheet: -1.23 (0.21), residues: 654 loop : -2.30 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 258 HIS 0.007 0.001 HIS C 245 PHE 0.034 0.001 PHE A 157 TYR 0.031 0.001 TYR A 453 ARG 0.007 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8541 (tp) cc_final: 0.8172 (mt) REVERT: A 274 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 394 ASN cc_start: 0.5229 (t0) cc_final: 0.4978 (t0) REVERT: A 490 PHE cc_start: 0.8706 (t80) cc_final: 0.8137 (t80) REVERT: A 697 MET cc_start: 0.8071 (mmm) cc_final: 0.7687 (mmt) REVERT: B 117 LEU cc_start: 0.8953 (tp) cc_final: 0.8713 (tt) REVERT: B 374 PHE cc_start: 0.8594 (m-80) cc_final: 0.8320 (m-80) REVERT: B 396 TYR cc_start: 0.7688 (m-80) cc_final: 0.7177 (m-80) REVERT: C 140 PHE cc_start: 0.8270 (p90) cc_final: 0.7939 (p90) REVERT: C 354 ASN cc_start: 0.8485 (t0) cc_final: 0.8101 (t0) REVERT: C 394 ASN cc_start: 0.8534 (m110) cc_final: 0.8167 (m110) REVERT: C 473 TYR cc_start: 0.8593 (t80) cc_final: 0.8360 (t80) REVERT: C 505 TYR cc_start: 0.6927 (t80) cc_final: 0.6579 (t80) outliers start: 39 outliers final: 31 residues processed: 191 average time/residue: 0.3416 time to fit residues: 111.9814 Evaluate side-chains 185 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 0.7980 chunk 303 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 196 optimal weight: 0.2980 chunk 155 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 658 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26356 Z= 0.204 Angle : 0.542 11.523 35862 Z= 0.271 Chirality : 0.044 0.407 4203 Planarity : 0.003 0.049 4584 Dihedral : 6.074 82.704 4481 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.39 % Allowed : 15.31 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 3167 helix: 1.87 (0.22), residues: 625 sheet: -1.26 (0.20), residues: 678 loop : -2.31 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 258 HIS 0.003 0.001 HIS A 66 PHE 0.033 0.001 PHE A 157 TYR 0.031 0.001 TYR A 453 ARG 0.007 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6334 Ramachandran restraints generated. 3167 Oldfield, 0 Emsley, 3167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8564 (tp) cc_final: 0.8166 (mt) REVERT: A 274 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8516 (t) REVERT: A 394 ASN cc_start: 0.5187 (t0) cc_final: 0.4959 (t0) REVERT: A 490 PHE cc_start: 0.8716 (t80) cc_final: 0.8117 (t80) REVERT: A 697 MET cc_start: 0.8083 (mmm) cc_final: 0.7759 (mmt) REVERT: B 117 LEU cc_start: 0.8935 (tp) cc_final: 0.8715 (tt) REVERT: B 374 PHE cc_start: 0.8580 (m-80) cc_final: 0.8308 (m-80) REVERT: B 396 TYR cc_start: 0.7687 (m-80) cc_final: 0.7151 (m-80) REVERT: C 140 PHE cc_start: 0.8314 (p90) cc_final: 0.7974 (p90) REVERT: C 258 TRP cc_start: 0.7792 (p-90) cc_final: 0.7343 (p-90) REVERT: C 343 ASN cc_start: 0.6477 (OUTLIER) cc_final: 0.5544 (m110) REVERT: C 354 ASN cc_start: 0.8509 (t0) cc_final: 0.8128 (t0) REVERT: C 394 ASN cc_start: 0.8578 (m110) cc_final: 0.8221 (m110) REVERT: C 473 TYR cc_start: 0.8596 (t80) cc_final: 0.8371 (t80) REVERT: C 505 TYR cc_start: 0.6948 (t80) cc_final: 0.6613 (t80) outliers start: 39 outliers final: 33 residues processed: 187 average time/residue: 0.3228 time to fit residues: 103.3201 Evaluate side-chains 187 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.139999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091912 restraints weight = 49001.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093955 restraints weight = 32479.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094138 restraints weight = 24054.591| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26356 Z= 0.264 Angle : 0.566 11.350 35862 Z= 0.285 Chirality : 0.045 0.408 4203 Planarity : 0.003 0.051 4584 Dihedral : 6.140 83.062 4481 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.28 % Allowed : 15.59 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 3167 helix: 1.75 (0.22), residues: 625 sheet: -1.28 (0.20), residues: 678 loop : -2.34 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 258 HIS 0.005 0.001 HIS C 245 PHE 0.032 0.001 PHE A 157 TYR 0.029 0.001 TYR A 453 ARG 0.007 0.000 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.59 seconds wall clock time: 82 minutes 46.83 seconds (4966.83 seconds total)